Starting phenix.real_space_refine
on Sat Sep 12 08:51:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pew_13359/09_2026/7pew_13359.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pew_13359/09_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_13359/09_2026/7pew_13359.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pew_13359/09_2026/7pew_13359.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pew_13359/09_2026/7pew_13359.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pew_13359/09_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-2.2.1-6174/lib/python3.11/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: 2.60, per 1000 atoms: 0.20
  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: 1.10
  Conformation dependent library (CDL) restraints added in 379.9 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: 2.15
  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: 3.55

  Time building geometry restraints manager: 1.49 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=" C3'  DC I  12 "
       pdb=" O3'  DC I  12 "
    ideal  model  delta    sigma   weight residual
    1.435  1.486 -0.051 1.30e-02 5.92e+03 1.56e+01
  bond pdb=" C3'  DT J 671 "
       pdb=" C2'  DT J 671 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 8.00e-03 1.56e+04 1.47e+01
  bond pdb=" C5'  DC I 168 "
       pdb=" C4'  DC I 168 "
    ideal  model  delta    sigma   weight residual
    1.512  1.538 -0.026 7.00e-03 2.04e+04 1.43e+01
  bond pdb=" C3'  DG I 140 "
       pdb=" O3'  DG I 140 "
    ideal  model  delta    sigma   weight residual
    1.435  1.482 -0.047 1.30e-02 5.92e+03 1.31e+01
  bond pdb=" C3'  DC I 123 "
       pdb=" O3'  DC I 123 "
    ideal  model  delta    sigma   weight residual
    1.435  1.392  0.043 1.30e-02 5.92e+03 1.10e+01
  ... (remaining 14257 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 19662
        2.20 -     4.41: 1008
        4.41 -     6.61: 76
        6.61 -     8.81: 22
        8.81 -    11.01: 6
  Bond angle restraints: 20774
  Sorted by residual:
  angle pdb=" O4'  DG I 112 "
        pdb=" C4'  DG I 112 "
        pdb=" C3'  DG I 112 "
      ideal   model   delta    sigma   weight residual
     106.00  102.06    3.94 6.00e-01 2.78e+00 4.32e+01
  angle pdb=" O4'  DC I  92 "
        pdb=" C4'  DC I  92 "
        pdb=" C3'  DC I  92 "
      ideal   model   delta    sigma   weight residual
     106.00  102.24    3.76 6.00e-01 2.78e+00 3.94e+01
  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=" O4'  DA I 153 "
        pdb=" C4'  DA I 153 "
        pdb=" C3'  DA I 153 "
      ideal   model   delta    sigma   weight residual
     106.00  103.05    2.95 6.00e-01 2.78e+00 2.41e+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: 1642
       0.050 -    0.100: 559
       0.100 -    0.150: 129
       0.150 -    0.200: 24
       0.200 -    0.251: 6
  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=" C3'  DG I 140 "
            pdb=" C4'  DG I 140 "
            pdb=" O3'  DG I 140 "
            pdb=" C2'  DG I 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.51   -0.22 2.00e-01 2.50e+01 1.22e+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:             1.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     15.340
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
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      :  0.007   0.058  14262  Z= 0.625
  Angle     :  1.049  11.014  20774  Z= 0.822
  Chirality :  0.054   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/Z
  covalent geometry    : bond        0.00715 /  0.62 (14262)
  covalent geometry    : angle       1.04925 /  0.82 (20774)
  hydrogen bonds       : bond        0.11094 /  7.44 (  855)
  hydrogen bonds       : angle       4.80549 /  3.46 ( 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  : 0.335 
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: 0.9144 (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: 0.1190
  time to fit residues: 29.5551
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  : 0.322 
-------------------------------------------------------------------------------
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:   30.0000
   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:   20.0000
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    3.4788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
C 104 GLN
D 109 HIS
E  55 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  49 HIS
H  95 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.028359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2489 r_free = 0.2489 target = 0.020979 restraints weight = 173123.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2534 r_free = 0.2534 target = 0.021746 restraints weight = 85132.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.022265 restraints weight = 51634.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.022637 restraints weight = 35643.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2594 r_free = 0.2594 target = 0.022846 restraints weight = 26776.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.2575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.1188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  14262  Z= 0.202
  Angle     :  0.762   9.713  20774  Z= 0.434
  Chirality :  0.050   0.280   2360
  Planarity :  0.005   0.051   1408
  Dihedral  : 33.442 179.399   4680
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  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:  0.99 (0.29), residues: 752
  helix:  1.08 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.22 (0.37), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  42 
 TYR   0.017   0.002   TYR B  88 
 PHE   0.018   0.002   PHE E  67 
 HIS   0.014   0.002   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.20 (14262)
  covalent geometry    : angle       0.76175 /  0.43 (20774)
  hydrogen bonds       : bond        0.06681 /  4.54 (  855)
  hydrogen bonds       : angle       3.74392 /  2.67 ( 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
  149 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.254 
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   90 MET cc_start: 0.9354 (mpp) cc_final: 0.8873 (mpp)
REVERT: A  104 PHE cc_start: 0.9397 (m-80) cc_final: 0.8951 (m-80)
REVERT: A  120 MET cc_start: 0.8492 (mtt) cc_final: 0.7889 (mpp)
REVERT: B   59 LYS cc_start: 0.9641 (tmtt) cc_final: 0.9404 (tptt)
REVERT: D   34 LYS cc_start: 0.8115 (mmmm) cc_final: 0.7783 (tmmt)
REVERT: D   59 MET cc_start: 0.9196 (tpp) cc_final: 0.8875 (tpt)
REVERT: D  109 HIS cc_start: 0.9389 (m90) cc_final: 0.8892 (m90)
REVERT: E   50 GLU cc_start: 0.9479 (mp0) cc_final: 0.9212 (mp0)
REVERT: E   59 GLU cc_start: 0.9084 (mp0) cc_final: 0.8775 (pm20)
REVERT: E   90 MET cc_start: 0.9469 (mmp) cc_final: 0.9190 (mmp)
REVERT: E   93 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8570 (tm-30)
REVERT: E  104 PHE cc_start: 0.9630 (m-10) cc_final: 0.9367 (m-10)
REVERT: E  120 MET cc_start: 0.8759 (mtm) cc_final: 0.8106 (mtt)
REVERT: E  123 ASP cc_start: 0.9495 (m-30) cc_final: 0.8792 (m-30)
REVERT: F   59 LYS cc_start: 0.9649 (tttp) cc_final: 0.9208 (tppp)
REVERT: F   60 VAL cc_start: 0.9656 (t) cc_final: 0.9124 (t)
REVERT: F   62 LEU cc_start: 0.9792 (mt) cc_final: 0.9403 (pp)
REVERT: F   63 GLU cc_start: 0.9701 (mt-10) cc_final: 0.9343 (mt-10)
REVERT: F   74 GLU cc_start: 0.9232 (pp20) cc_final: 0.8967 (pp20)
REVERT: G   61 GLU cc_start: 0.9379 (pp20) cc_final: 0.9062 (pp20)
REVERT: G   64 GLU cc_start: 0.9126 (mp0) cc_final: 0.8906 (mp0)
REVERT: G   68 ASN cc_start: 0.9005 (p0) cc_final: 0.8724 (p0)
REVERT: G  102 ILE cc_start: 0.8425 (mm) cc_final: 0.8222 (mm)
REVERT: H  108 LYS cc_start: 0.9336 (ptpp) cc_final: 0.9106 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1136
  time to fit residues: 24.4291
Evaluate side-chains
  113 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
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:   30.0000
   chunk 86 optimal weight:   30.0000
   chunk 98 optimal weight:   30.0000
   chunk 38 optimal weight:    0.9990
   chunk 79 optimal weight:   20.0000
   chunk 74 optimal weight:   30.0000
   chunk 81 optimal weight:   20.0000
   chunk 23 optimal weight:    0.2980
   chunk 32 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    3.6588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** 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 = 0.2836 r_free = 0.2836 target = 0.027974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2477 r_free = 0.2477 target = 0.020700 restraints weight = 176542.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2522 r_free = 0.2522 target = 0.021468 restraints weight = 86238.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2550 r_free = 0.2550 target = 0.021983 restraints weight = 51923.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2571 r_free = 0.2571 target = 0.022349 restraints weight = 35721.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.022605 restraints weight = 26707.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.2567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  14262  Z= 0.205
  Angle     :  0.709  10.175  20774  Z= 0.411
  Chirality :  0.047   0.292   2360
  Planarity :  0.005   0.055   1408
  Dihedral  : 33.355 178.895   4680
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  3.62 %
    Favored  : 96.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.28 (0.29), residues: 752
  helix:  1.29 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.11 (0.38), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG G  29 
 TYR   0.011   0.002   TYR C  57 
 PHE   0.029   0.002   PHE C  25 
 HIS   0.005   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00355 /  0.20 (14262)
  covalent geometry    : angle       0.70851 /  0.41 (20774)
  hydrogen bonds       : bond        0.06536 /  4.42 (  855)
  hydrogen bonds       : angle       3.60566 /  2.55 ( 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
  149 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 147
  time to evaluate  : 0.328 
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: 0.9368 (mpp) cc_final: 0.9133 (mpp)
REVERT: A  104 PHE cc_start: 0.9464 (m-80) cc_final: 0.9088 (m-80)
REVERT: A  120 MET cc_start: 0.8368 (mtt) cc_final: 0.7172 (mpp)
REVERT: D   34 LYS cc_start: 0.8440 (mmmm) cc_final: 0.7786 (tmmt)
REVERT: D  109 HIS cc_start: 0.9308 (m90) cc_final: 0.8906 (m90)
REVERT: E   50 GLU cc_start: 0.9550 (mp0) cc_final: 0.9284 (mp0)
REVERT: E   51 ILE cc_start: 0.9749 (mt) cc_final: 0.9524 (mt)
REVERT: E   59 GLU cc_start: 0.9076 (mp0) cc_final: 0.8694 (pm20)
REVERT: E   90 MET cc_start: 0.9498 (mmp) cc_final: 0.9216 (mmp)
REVERT: E   93 GLN cc_start: 0.9197 (tm-30) cc_final: 0.8513 (tm-30)
REVERT: E  105 GLU cc_start: 0.9242 (pp20) cc_final: 0.8981 (pp20)
REVERT: E  106 ASP cc_start: 0.8780 (m-30) cc_final: 0.8263 (m-30)
REVERT: E  120 MET cc_start: 0.8677 (mtm) cc_final: 0.7850 (mtt)
REVERT: E  123 ASP cc_start: 0.9245 (m-30) cc_final: 0.8574 (m-30)
REVERT: F   59 LYS cc_start: 0.9650 (tttp) cc_final: 0.9436 (tppp)
REVERT: F   60 VAL cc_start: 0.9668 (t) cc_final: 0.9198 (t)
REVERT: F   63 GLU cc_start: 0.9731 (mt-10) cc_final: 0.9486 (mt-10)
REVERT: F   74 GLU cc_start: 0.9247 (pp20) cc_final: 0.8967 (pp20)
REVERT: G   72 ASP cc_start: 0.9336 (m-30) cc_final: 0.9096 (m-30)
REVERT: G  102 ILE cc_start: 0.8462 (mm) cc_final: 0.8235 (mm)
REVERT: H  120 LYS cc_start: 0.9637 (mppt) cc_final: 0.9251 (mtmm)
  outliers start: 2
  outliers final: 2
  residues processed: 147
  average time/residue: 0.1234
  time to fit residues: 26.2469
Evaluate side-chains
  115 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 94 optimal weight:   30.0000
   chunk 83 optimal weight:   30.0000
   chunk 56 optimal weight:   10.0000
   chunk 52 optimal weight:    7.9990
   chunk 26 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 101 optimal weight:   20.0000
   chunk 85 optimal weight:   30.0000
   overall best weight:    5.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  47 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.027165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2443 r_free = 0.2443 target = 0.019961 restraints weight = 180399.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2487 r_free = 0.2487 target = 0.020702 restraints weight = 88326.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2515 r_free = 0.2515 target = 0.021200 restraints weight = 53260.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2536 r_free = 0.2536 target = 0.021546 restraints weight = 36777.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2549 r_free = 0.2549 target = 0.021779 restraints weight = 27783.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.2528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  14262  Z= 0.254
  Angle     :  0.755  10.671  20774  Z= 0.429
  Chirality :  0.047   0.293   2360
  Planarity :  0.005   0.058   1408
  Dihedral  : 33.334 179.549   4680
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 16.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  4.40 %
    Favored  : 95.44 %
  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:  1.21 (0.29), residues: 752
  helix:  1.24 (0.21), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.13 (0.39), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  42 
 TYR   0.017   0.002   TYR C  57 
 PHE   0.018   0.002   PHE E  67 
 HIS   0.006   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00456 /  0.25 (14262)
  covalent geometry    : angle       0.75486 /  0.43 (20774)
  hydrogen bonds       : bond        0.07997 /  5.35 (  855)
  hydrogen bonds       : angle       3.84879 /  2.74 ( 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
  137 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9380 (mpp) cc_final: 0.9023 (mmm)
REVERT: A  104 PHE cc_start: 0.9542 (m-80) cc_final: 0.9201 (m-80)
REVERT: A  106 ASP cc_start: 0.9491 (m-30) cc_final: 0.9270 (m-30)
REVERT: A  120 MET cc_start: 0.8251 (mtt) cc_final: 0.8000 (mtt)
REVERT: B   74 GLU cc_start: 0.9692 (tm-30) cc_final: 0.9422 (tm-30)
REVERT: C   50 TYR cc_start: 0.9107 (t80) cc_final: 0.8831 (t80)
REVERT: D  109 HIS cc_start: 0.9287 (m90) cc_final: 0.8876 (m90)
REVERT: E   50 GLU cc_start: 0.9545 (mp0) cc_final: 0.9314 (mp0)
REVERT: E   59 GLU cc_start: 0.9068 (mp0) cc_final: 0.8614 (pm20)
REVERT: E   90 MET cc_start: 0.9502 (mmp) cc_final: 0.9223 (mmp)
REVERT: E   93 GLN cc_start: 0.9251 (tm-30) cc_final: 0.8389 (tm-30)
REVERT: E   94 GLU cc_start: 0.9117 (tp30) cc_final: 0.8277 (tp30)
REVERT: E   97 GLU cc_start: 0.9085 (pt0) cc_final: 0.8489 (pp20)
REVERT: E  104 PHE cc_start: 0.9439 (m-10) cc_final: 0.9173 (m-80)
REVERT: E  120 MET cc_start: 0.8538 (mtm) cc_final: 0.7720 (mtt)
REVERT: E  123 ASP cc_start: 0.9310 (m-30) cc_final: 0.8741 (m-30)
REVERT: F   60 VAL cc_start: 0.9673 (t) cc_final: 0.9195 (t)
REVERT: F   63 GLU cc_start: 0.9736 (mt-10) cc_final: 0.9495 (mt-10)
REVERT: F   74 GLU cc_start: 0.9302 (pp20) cc_final: 0.9055 (pp20)
REVERT: G   64 GLU cc_start: 0.9194 (mp0) cc_final: 0.8979 (mp0)
REVERT: G   68 ASN cc_start: 0.8969 (p0) cc_final: 0.8755 (p0)
REVERT: G  102 ILE cc_start: 0.8512 (mm) cc_final: 0.8238 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1186
  time to fit residues: 23.7715
Evaluate side-chains
  103 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
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:   30.0000
   chunk 12 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 102 optimal weight:   20.0000
   chunk 31 optimal weight:    0.8980
   chunk 105 optimal weight:   40.0000
   chunk 39 optimal weight:    1.9990
   chunk 103 optimal weight:   30.0000
   chunk 34 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 99 optimal weight:   30.0000
   overall best weight:    2.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  93 GLN
E  55 GLN
** 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 = 0.2830 r_free = 0.2830 target = 0.027831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2475 r_free = 0.2475 target = 0.020627 restraints weight = 176856.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2520 r_free = 0.2520 target = 0.021404 restraints weight = 84368.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2551 r_free = 0.2551 target = 0.021939 restraints weight = 49958.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2570 r_free = 0.2570 target = 0.022278 restraints weight = 33721.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.022535 restraints weight = 25212.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.2567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  14262  Z= 0.165
  Angle     :  0.688   7.803  20774  Z= 0.399
  Chirality :  0.046   0.313   2360
  Planarity :  0.004   0.057   1408
  Dihedral  : 33.219 179.186   4680
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  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:  1.41 (0.29), residues: 752
  helix:  1.43 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.18 (0.38), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  83 
 TYR   0.015   0.001   TYR C  57 
 PHE   0.014   0.002   PHE E  67 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.16 (14262)
  covalent geometry    : angle       0.68831 /  0.40 (20774)
  hydrogen bonds       : bond        0.05154 /  3.45 (  855)
  hydrogen bonds       : angle       3.54100 /  2.51 ( 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
  154 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.348 
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   90 MET cc_start: 0.9375 (mpp) cc_final: 0.8974 (mpp)
REVERT: A   93 GLN cc_start: 0.9390 (OUTLIER) cc_final: 0.8989 (tp40)
REVERT: A  104 PHE cc_start: 0.9531 (m-80) cc_final: 0.9168 (m-80)
REVERT: A  120 MET cc_start: 0.8189 (mtt) cc_final: 0.7912 (mtt)
REVERT: B   74 GLU cc_start: 0.9688 (tm-30) cc_final: 0.9412 (tm-30)
REVERT: C   50 TYR cc_start: 0.9083 (t80) cc_final: 0.8664 (t80)
REVERT: E   50 GLU cc_start: 0.9519 (mp0) cc_final: 0.9280 (pt0)
REVERT: E   59 GLU cc_start: 0.9034 (mp0) cc_final: 0.8630 (pm20)
REVERT: E   90 MET cc_start: 0.9468 (mmp) cc_final: 0.9183 (mmm)
REVERT: E   93 GLN cc_start: 0.9274 (tm-30) cc_final: 0.7611 (tm-30)
REVERT: E  104 PHE cc_start: 0.9444 (m-10) cc_final: 0.9190 (m-80)
REVERT: E  105 GLU cc_start: 0.9229 (pp20) cc_final: 0.8934 (pp20)
REVERT: E  106 ASP cc_start: 0.8750 (m-30) cc_final: 0.8292 (m-30)
REVERT: E  120 MET cc_start: 0.8493 (mtm) cc_final: 0.7765 (mtt)
REVERT: E  123 ASP cc_start: 0.9268 (m-30) cc_final: 0.8760 (m-30)
REVERT: F   60 VAL cc_start: 0.9654 (t) cc_final: 0.9130 (t)
REVERT: F   62 LEU cc_start: 0.9807 (mt) cc_final: 0.9438 (pp)
REVERT: F   63 GLU cc_start: 0.9697 (mt-10) cc_final: 0.9325 (mt-10)
REVERT: F   74 GLU cc_start: 0.9260 (pp20) cc_final: 0.8986 (pp20)
REVERT: F   79 LYS cc_start: 0.9508 (tptp) cc_final: 0.9187 (tttt)
REVERT: G   61 GLU cc_start: 0.9195 (pp20) cc_final: 0.8768 (pp20)
REVERT: G  102 ILE cc_start: 0.8491 (mm) cc_final: 0.8218 (mm)
REVERT: H  120 LYS cc_start: 0.9625 (mppt) cc_final: 0.9255 (mtmm)
  outliers start: 1
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1145
  time to fit residues: 25.9488
Evaluate side-chains
  108 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 20 optimal weight:   10.0000
   chunk 1 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    8.9990
   chunk 72 optimal weight:   50.0000
   chunk 45 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  93 GLN
C 104 GLN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 HIS
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.028146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2490 r_free = 0.2490 target = 0.020862 restraints weight = 174152.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2535 r_free = 0.2535 target = 0.021653 restraints weight = 83258.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2564 r_free = 0.2564 target = 0.022181 restraints weight = 49558.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.022535 restraints weight = 33797.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2593 r_free = 0.2593 target = 0.022702 restraints weight = 25157.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.2575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14262  Z= 0.151
  Angle     :  0.681   7.203  20774  Z= 0.392
  Chirality :  0.045   0.310   2360
  Planarity :  0.004   0.065   1408
  Dihedral  : 33.046 178.694   4680
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  1.57 %
    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:  1.50 (0.30), residues: 752
  helix:  1.51 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.17 (0.39), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  42 
 TYR   0.014   0.001   TYR A  99 
 PHE   0.020   0.002   PHE E  67 
 HIS   0.010   0.001   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.15 (14262)
  covalent geometry    : angle       0.68097 /  0.39 (20774)
  hydrogen bonds       : bond        0.04829 /  3.24 (  855)
  hydrogen bonds       : angle       3.47462 /  2.49 ( 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
  151 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 148
  time to evaluate  : 0.347 
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: A   90 MET cc_start: 0.9359 (mpp) cc_final: 0.9136 (mpp)
REVERT: A  104 PHE cc_start: 0.9513 (m-80) cc_final: 0.9139 (m-80)
REVERT: A  120 MET cc_start: 0.8150 (mtt) cc_final: 0.7431 (mtt)
REVERT: B   74 GLU cc_start: 0.9689 (tm-30) cc_final: 0.9396 (tm-30)
REVERT: C   50 TYR cc_start: 0.9054 (t80) cc_final: 0.8764 (t80)
REVERT: D  109 HIS cc_start: 0.9370 (m90) cc_final: 0.9116 (m170)
REVERT: E   50 GLU cc_start: 0.9521 (mp0) cc_final: 0.9314 (pm20)
REVERT: E   59 GLU cc_start: 0.9023 (mp0) cc_final: 0.8517 (pm20)
REVERT: E   90 MET cc_start: 0.9464 (mmp) cc_final: 0.9214 (mmp)
REVERT: E   93 GLN cc_start: 0.9421 (tm-30) cc_final: 0.8780 (tm-30)
REVERT: E  104 PHE cc_start: 0.9493 (m-10) cc_final: 0.9202 (m-80)
REVERT: E  120 MET cc_start: 0.8411 (mtm) cc_final: 0.7714 (mtt)
REVERT: E  123 ASP cc_start: 0.9237 (m-30) cc_final: 0.8718 (m-30)
REVERT: F   60 VAL cc_start: 0.9648 (t) cc_final: 0.9152 (t)
REVERT: F   63 GLU cc_start: 0.9698 (mt-10) cc_final: 0.9440 (mt-10)
REVERT: F   74 GLU cc_start: 0.9250 (pp20) cc_final: 0.8959 (pp20)
REVERT: F   79 LYS cc_start: 0.9493 (tptp) cc_final: 0.9163 (tttt)
REVERT: G   36 LYS cc_start: 0.9428 (mmtm) cc_final: 0.8957 (mmtm)
REVERT: G   61 GLU cc_start: 0.9095 (pp20) cc_final: 0.8841 (pp20)
REVERT: G   90 ASP cc_start: 0.8717 (t0) cc_final: 0.8308 (t0)
REVERT: G  102 ILE cc_start: 0.8379 (mm) cc_final: 0.8147 (mm)
REVERT: H  108 LYS cc_start: 0.9317 (ptpp) cc_final: 0.9010 (ptpp)
  outliers start: 3
  outliers final: 2
  residues processed: 150
  average time/residue: 0.1146
  time to fit residues: 25.4054
Evaluate side-chains
  113 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 111
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
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:   50.0000
   chunk 32 optimal weight:    0.7980
   chunk 92 optimal weight:   30.0000
   chunk 49 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 73 optimal weight:   40.0000
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  93 GLN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.028652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2514 r_free = 0.2514 target = 0.021357 restraints weight = 171044.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2559 r_free = 0.2559 target = 0.022150 restraints weight = 82794.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.022690 restraints weight = 49469.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2608 r_free = 0.2608 target = 0.023048 restraints weight = 33651.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.023290 restraints weight = 25284.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.2606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  14262  Z= 0.142
  Angle     :  0.677   7.289  20774  Z= 0.391
  Chirality :  0.045   0.311   2360
  Planarity :  0.004   0.067   1408
  Dihedral  : 32.870 178.799   4680
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.42 %
    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:  1.38 (0.29), residues: 752
  helix:  1.44 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.30 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  49 
 TYR   0.012   0.001   TYR C  57 
 PHE   0.012   0.002   PHE D  65 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.14 (14262)
  covalent geometry    : angle       0.67736 /  0.39 (20774)
  hydrogen bonds       : bond        0.04252 /  2.86 (  855)
  hydrogen bonds       : angle       3.42219 /  2.44 ( 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
  150 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 149
  time to evaluate  : 0.346 
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   65 LEU cc_start: 0.9416 (tp) cc_final: 0.9193 (tp)
REVERT: A   90 MET cc_start: 0.9356 (mpp) cc_final: 0.9075 (mpp)
REVERT: A   93 GLN cc_start: 0.9478 (OUTLIER) cc_final: 0.9001 (tp40)
REVERT: A   97 GLU cc_start: 0.9318 (pm20) cc_final: 0.9065 (pm20)
REVERT: A  104 PHE cc_start: 0.9488 (m-80) cc_final: 0.9073 (m-80)
REVERT: A  120 MET cc_start: 0.8120 (mtt) cc_final: 0.7423 (mtt)
REVERT: C   50 TYR cc_start: 0.9123 (t80) cc_final: 0.8825 (t80)
REVERT: D  109 HIS cc_start: 0.9449 (m90) cc_final: 0.9191 (m170)
REVERT: D  121 TYR cc_start: 0.9478 (t80) cc_final: 0.9269 (t80)
REVERT: E   59 GLU cc_start: 0.9004 (mp0) cc_final: 0.8588 (pm20)
REVERT: E   82 LEU cc_start: 0.8282 (mm) cc_final: 0.8011 (mm)
REVERT: E   90 MET cc_start: 0.9458 (mmp) cc_final: 0.9216 (mmp)
REVERT: E   93 GLN cc_start: 0.9367 (tm-30) cc_final: 0.8697 (tm-30)
REVERT: E  104 PHE cc_start: 0.9525 (m-10) cc_final: 0.9251 (m-80)
REVERT: E  105 GLU cc_start: 0.9195 (pp20) cc_final: 0.8905 (pp20)
REVERT: E  106 ASP cc_start: 0.8721 (m-30) cc_final: 0.8185 (m-30)
REVERT: E  120 MET cc_start: 0.8412 (mtm) cc_final: 0.7704 (mtt)
REVERT: E  123 ASP cc_start: 0.9219 (m-30) cc_final: 0.8711 (m-30)
REVERT: F   60 VAL cc_start: 0.9627 (t) cc_final: 0.9125 (t)
REVERT: F   63 GLU cc_start: 0.9688 (mt-10) cc_final: 0.9432 (mt-10)
REVERT: F   74 GLU cc_start: 0.9234 (pp20) cc_final: 0.8953 (pp20)
REVERT: F   79 LYS cc_start: 0.9516 (tptp) cc_final: 0.9203 (tttt)
REVERT: G   90 ASP cc_start: 0.8663 (t0) cc_final: 0.8268 (t0)
REVERT: G  102 ILE cc_start: 0.8374 (mm) cc_final: 0.8147 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1124
  time to fit residues: 24.9737
Evaluate side-chains
  118 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
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:   30.0000
   chunk 72 optimal weight:   50.0000
   chunk 33 optimal weight:    0.8980
   chunk 77 optimal weight:   20.0000
   chunk 58 optimal weight:    0.9990
   chunk 9 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 7 optimal weight:    4.9990
   chunk 99 optimal weight:   30.0000
   overall best weight:    1.4784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  93 GLN
C 104 GLN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.028619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2512 r_free = 0.2512 target = 0.021325 restraints weight = 171450.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2558 r_free = 0.2558 target = 0.022123 restraints weight = 83390.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.022644 restraints weight = 49724.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2608 r_free = 0.2608 target = 0.023007 restraints weight = 34121.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.023247 restraints weight = 25527.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  14262  Z= 0.144
  Angle     :  0.671   7.956  20774  Z= 0.385
  Chirality :  0.044   0.304   2360
  Planarity :  0.004   0.068   1408
  Dihedral  : 32.771 179.044   4680
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  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:  1.49 (0.30), residues: 752
  helix:  1.51 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.21 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  42 
 TYR   0.011   0.001   TYR A  99 
 PHE   0.022   0.002   PHE G  25 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.14 (14262)
  covalent geometry    : angle       0.67115 /  0.39 (20774)
  hydrogen bonds       : bond        0.04474 /  3.02 (  855)
  hydrogen bonds       : angle       3.40688 /  2.42 ( 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
  143 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.306 
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: A   65 LEU cc_start: 0.9332 (tp) cc_final: 0.9125 (tp)
REVERT: A   93 GLN cc_start: 0.9109 (tp40) cc_final: 0.8682 (tp40)
REVERT: A  104 PHE cc_start: 0.9494 (m-80) cc_final: 0.9093 (m-80)
REVERT: A  105 GLU cc_start: 0.9341 (tm-30) cc_final: 0.8954 (tm-30)
REVERT: A  106 ASP cc_start: 0.9397 (m-30) cc_final: 0.8817 (m-30)
REVERT: A  120 MET cc_start: 0.8094 (mtt) cc_final: 0.7411 (mtt)
REVERT: B   74 GLU cc_start: 0.9680 (tm-30) cc_final: 0.9393 (tm-30)
REVERT: B   91 LYS cc_start: 0.9261 (tmmt) cc_final: 0.8869 (pttm)
REVERT: C   50 TYR cc_start: 0.9121 (t80) cc_final: 0.8781 (t80)
REVERT: D  109 HIS cc_start: 0.9467 (m90) cc_final: 0.9224 (m170)
REVERT: D  121 TYR cc_start: 0.9481 (t80) cc_final: 0.9258 (t80)
REVERT: E   59 GLU cc_start: 0.8999 (mp0) cc_final: 0.8526 (pm20)
REVERT: E   82 LEU cc_start: 0.8263 (mm) cc_final: 0.8055 (mm)
REVERT: E   90 MET cc_start: 0.9453 (mmp) cc_final: 0.8777 (mmp)
REVERT: E   93 GLN cc_start: 0.9387 (tm-30) cc_final: 0.8953 (pt0)
REVERT: E  104 PHE cc_start: 0.9557 (m-10) cc_final: 0.9228 (m-80)
REVERT: E  120 MET cc_start: 0.8386 (mtm) cc_final: 0.7796 (mtt)
REVERT: F   60 VAL cc_start: 0.9624 (t) cc_final: 0.9109 (t)
REVERT: F   63 GLU cc_start: 0.9682 (mt-10) cc_final: 0.9434 (mt-10)
REVERT: F   74 GLU cc_start: 0.9241 (pp20) cc_final: 0.8967 (pp20)
REVERT: F   79 LYS cc_start: 0.9515 (tptp) cc_final: 0.9239 (tttt)
REVERT: G   36 LYS cc_start: 0.9542 (mmmt) cc_final: 0.9002 (mmtm)
REVERT: G   90 ASP cc_start: 0.8599 (t0) cc_final: 0.8175 (t0)
REVERT: G  102 ILE cc_start: 0.8380 (mm) cc_final: 0.8155 (mm)
REVERT: H  108 LYS cc_start: 0.9305 (ptpp) cc_final: 0.8947 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1072
  time to fit residues: 22.7634
Evaluate side-chains
  107 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 75 optimal weight:   20.0000
   chunk 48 optimal weight:    3.9990
   chunk 94 optimal weight:   30.0000
   chunk 70 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 53 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 96 optimal weight:   30.0000
   chunk 63 optimal weight:   10.0000
   chunk 68 optimal weight:    2.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** 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 = 0.027751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2478 r_free = 0.2478 target = 0.020593 restraints weight = 178701.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2524 r_free = 0.2524 target = 0.021359 restraints weight = 86606.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2552 r_free = 0.2552 target = 0.021869 restraints weight = 51953.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2573 r_free = 0.2573 target = 0.022218 restraints weight = 35635.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2586 r_free = 0.2586 target = 0.022458 restraints weight = 26717.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.2567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  14262  Z= 0.197
  Angle     :  0.713   9.024  20774  Z= 0.405
  Chirality :  0.044   0.295   2360
  Planarity :  0.005   0.069   1408
  Dihedral  : 32.799 178.731   4680
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  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:  1.43 (0.30), residues: 752
  helix:  1.42 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.10 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  42 
 TYR   0.011   0.002   TYR C  50 
 PHE   0.016   0.002   PHE A  67 
 HIS   0.005   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.20 (14262)
  covalent geometry    : angle       0.71347 /  0.40 (20774)
  hydrogen bonds       : bond        0.06168 /  4.15 (  855)
  hydrogen bonds       : angle       3.62782 /  2.57 ( 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
  135 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.298 
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: A   90 MET cc_start: 0.9561 (mmm) cc_final: 0.9224 (mmm)
REVERT: A   94 GLU cc_start: 0.9449 (mp0) cc_final: 0.9210 (mp0)
REVERT: A  104 PHE cc_start: 0.9517 (m-80) cc_final: 0.9198 (m-80)
REVERT: A  105 GLU cc_start: 0.9340 (tm-30) cc_final: 0.8977 (tm-30)
REVERT: A  106 ASP cc_start: 0.9410 (m-30) cc_final: 0.8843 (m-30)
REVERT: A  120 MET cc_start: 0.8060 (mtt) cc_final: 0.7363 (mtt)
REVERT: B   74 GLU cc_start: 0.9698 (tm-30) cc_final: 0.9423 (tm-30)
REVERT: B   91 LYS cc_start: 0.9335 (tmmt) cc_final: 0.8935 (pttm)
REVERT: D  109 HIS cc_start: 0.9470 (m90) cc_final: 0.9214 (m170)
REVERT: D  121 TYR cc_start: 0.9459 (t80) cc_final: 0.9244 (t80)
REVERT: E   51 ILE cc_start: 0.9673 (mt) cc_final: 0.9464 (mt)
REVERT: E   59 GLU cc_start: 0.9020 (mp0) cc_final: 0.8584 (pm20)
REVERT: E   90 MET cc_start: 0.9398 (mmp) cc_final: 0.8822 (mmp)
REVERT: E  104 PHE cc_start: 0.9562 (m-10) cc_final: 0.9246 (m-80)
REVERT: E  105 GLU cc_start: 0.9166 (pp20) cc_final: 0.8924 (pp20)
REVERT: E  106 ASP cc_start: 0.8755 (m-30) cc_final: 0.8212 (m-30)
REVERT: E  120 MET cc_start: 0.8451 (mtm) cc_final: 0.7818 (mtt)
REVERT: F   60 VAL cc_start: 0.9636 (t) cc_final: 0.9139 (t)
REVERT: F   63 GLU cc_start: 0.9684 (mt-10) cc_final: 0.9443 (mt-10)
REVERT: F   74 GLU cc_start: 0.9284 (pp20) cc_final: 0.9027 (pp20)
REVERT: G   36 LYS cc_start: 0.9543 (mmmt) cc_final: 0.9025 (mmtm)
REVERT: G   90 ASP cc_start: 0.8667 (t0) cc_final: 0.8227 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1078
  time to fit residues: 21.5400
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  : 0.388 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 101 optimal weight:   20.0000
   chunk 41 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 84 optimal weight:   30.0000
   chunk 85 optimal weight:   20.0000
   chunk 50 optimal weight:    9.9990
   chunk 23 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 44 optimal weight:    0.3980
   overall best weight:    1.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
** D  63 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 = 0.2846 r_free = 0.2846 target = 0.028168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2497 r_free = 0.2497 target = 0.020988 restraints weight = 173898.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2542 r_free = 0.2542 target = 0.021759 restraints weight = 83562.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2571 r_free = 0.2571 target = 0.022273 restraints weight = 49855.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2590 r_free = 0.2590 target = 0.022619 restraints weight = 34004.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2605 r_free = 0.2605 target = 0.022870 restraints weight = 25430.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.2587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  14262  Z= 0.158
  Angle     :  0.696   8.084  20774  Z= 0.402
  Chirality :  0.044   0.308   2360
  Planarity :  0.005   0.068   1408
  Dihedral  : 32.790 178.556   4680
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  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:  1.28 (0.30), residues: 752
  helix:  1.34 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.24 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 131 
 TYR   0.011   0.001   TYR C  57 
 PHE   0.017   0.002   PHE G  25 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.16 (14262)
  covalent geometry    : angle       0.69632 /  0.40 (20774)
  hydrogen bonds       : bond        0.04762 /  3.21 (  855)
  hydrogen bonds       : angle       3.69502 /  2.62 ( 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
  137 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.342 
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: A   90 MET cc_start: 0.9544 (mmm) cc_final: 0.9191 (mmm)
REVERT: A   94 GLU cc_start: 0.9467 (mp0) cc_final: 0.9215 (mp0)
REVERT: A  104 PHE cc_start: 0.9498 (m-80) cc_final: 0.9169 (m-80)
REVERT: A  120 MET cc_start: 0.8070 (mtt) cc_final: 0.7362 (mtt)
REVERT: B   74 GLU cc_start: 0.9696 (tm-30) cc_final: 0.9411 (tm-30)
REVERT: B   91 LYS cc_start: 0.9291 (tmmt) cc_final: 0.8891 (pttm)
REVERT: D  109 HIS cc_start: 0.9450 (m90) cc_final: 0.9209 (m170)
REVERT: E   59 GLU cc_start: 0.9039 (mp0) cc_final: 0.8586 (pm20)
REVERT: E   82 LEU cc_start: 0.8163 (mm) cc_final: 0.7862 (mm)
REVERT: E   93 GLN cc_start: 0.9421 (pm20) cc_final: 0.8982 (pm20)
REVERT: E  104 PHE cc_start: 0.9566 (m-10) cc_final: 0.9272 (m-80)
REVERT: E  105 GLU cc_start: 0.9148 (pp20) cc_final: 0.8885 (pp20)
REVERT: E  106 ASP cc_start: 0.8732 (m-30) cc_final: 0.8190 (m-30)
REVERT: E  120 MET cc_start: 0.8458 (mtm) cc_final: 0.7805 (mtt)
REVERT: F   60 VAL cc_start: 0.9638 (t) cc_final: 0.9143 (t)
REVERT: F   63 GLU cc_start: 0.9673 (mt-10) cc_final: 0.9439 (mt-10)
REVERT: F   74 GLU cc_start: 0.9271 (pp20) cc_final: 0.8998 (pp20)
REVERT: G   36 LYS cc_start: 0.9554 (mmmt) cc_final: 0.9263 (mmtm)
REVERT: G   90 ASP cc_start: 0.8607 (t0) cc_final: 0.8152 (t0)
REVERT: G  102 ILE cc_start: 0.8423 (mm) cc_final: 0.8184 (mm)
REVERT: H  108 LYS cc_start: 0.9296 (ptpp) cc_final: 0.8933 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1127
  time to fit residues: 22.9132
Evaluate side-chains
  104 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
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:   50.0000
   chunk 22 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 85 optimal weight:   20.0000
   chunk 31 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0970
   chunk 21 optimal weight:    1.9990
   chunk 78 optimal weight:   20.0000
   chunk 76 optimal weight:   30.0000
   chunk 94 optimal weight:   30.0000
   overall best weight:    3.0186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.030873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2531 r_free = 0.2531 target = 0.024255 restraints weight = 192221.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2578 r_free = 0.2578 target = 0.025039 restraints weight = 89803.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.025577 restraints weight = 52680.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.025939 restraints weight = 34927.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.026187 restraints weight = 25460.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.2587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14262  Z= 0.185
  Angle     :  0.710   8.739  20774  Z= 0.406
  Chirality :  0.044   0.299   2360
  Planarity :  0.005   0.069   1408
  Dihedral  : 32.776 178.880   4680
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.31 %
    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:  1.21 (0.30), residues: 752
  helix:  1.29 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.26 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  42 
 TYR   0.011   0.002   TYR D  37 
 PHE   0.016   0.002   PHE G  25 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.19 (14262)
  covalent geometry    : angle       0.71023 /  0.41 (20774)
  hydrogen bonds       : bond        0.05854 /  3.93 (  855)
  hydrogen bonds       : angle       3.74856 /  2.65 ( 2102)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1813.23 seconds
wall clock time: 32 minutes 14.97 seconds (1934.97 seconds total)