Starting phenix.real_space_refine
on Fri Sep 27 03:27:12 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/09_2024/7pew_13359.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/09_2024/7pew_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/09_2024/7pew_13359.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/09_2024/7pew_13359.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/09_2024/7pew_13359.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/09_2024/7pew_13359.cif"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 7.55, per 1000 atoms: 0.57
  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: 3.43
  Conformation dependent library (CDL) restraints added in 897.4 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: 6.95
  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: 6.02

  Time building geometry restraints manager: 3.98 seconds

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

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

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

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

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

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

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

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.100
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.560
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     37.000
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  14262  Z= 0.335
  Angle     :  0.912  11.014  20774  Z= 0.518
  Chirality :  0.048   0.251   2360
  Planarity :  0.007   0.075   1408
  Dihedral  : 30.189 179.839   6204
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 HIS   0.009   0.002   HIS H 109 
 PHE   0.024   0.003   PHE G  25 
 TYR   0.035   0.003   TYR D  37 
 ARG   0.009   0.001   ARG F  92 

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.876 
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: 0.8280 (mmmm) cc_final: 0.7645 (tmmt)
REVERT: E   50 GLU cc_start: 0.9493 (mp0) cc_final: 0.8860 (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: 0.9092 (mp0) cc_final: 0.8764 (pm20)
REVERT: E   90 MET cc_start: 0.9429 (mmp) cc_final: 0.9138 (mmp)
REVERT: E   93 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8047 (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: 0.9333 (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: 0.9014 (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: G  102 ILE cc_start: 0.8328 (mm) cc_final: 0.8102 (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: 0.8309 (tm-30)
REVERT: H  109 HIS cc_start: 0.9391 (m90) cc_final: 0.8441 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.2547
  time to fit residues: 61.8386
Evaluate side-chains
  120 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:   20.0000
   chunk 80 optimal weight:    7.9990
   chunk 44 optimal weight:    7.9990
   chunk 27 optimal weight:   10.0000
   chunk 54 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   chunk 61 optimal weight:    4.9990
   chunk 96 optimal weight:    6.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 HIS
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045  14262  Z= 0.368
  Angle     :  0.708  12.076  20774  Z= 0.416
  Chirality :  0.038   0.140   2360
  Planarity :  0.006   0.053   1408
  Dihedral  : 33.137 178.115   4680
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 20.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  5.82 %
    Favored  : 93.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.28), residues: 752
  helix:  1.23 (0.21), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.14 (0.37), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS D  49 
 PHE   0.021   0.003   PHE E  67 
 TYR   0.016   0.002   TYR D  40 
 ARG   0.008   0.001   ARG C  42 

*********************** 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
  145 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 143
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8869 (pm20) cc_final: 0.8650 (pm20)
REVERT: A   90 MET cc_start: 0.9366 (mpp) cc_final: 0.9123 (mpp)
REVERT: A  104 PHE cc_start: 0.9469 (m-80) cc_final: 0.9165 (m-80)
REVERT: A  106 ASP cc_start: 0.9400 (m-30) cc_final: 0.9188 (m-30)
REVERT: B   59 LYS cc_start: 0.9664 (tmtt) cc_final: 0.9437 (tptt)
REVERT: B   74 GLU cc_start: 0.9773 (tm-30) cc_final: 0.9516 (tm-30)
REVERT: D  109 HIS cc_start: 0.9409 (m90) cc_final: 0.8974 (m-70)
REVERT: E   59 GLU cc_start: 0.9206 (mp0) cc_final: 0.8783 (pm20)
REVERT: E   90 MET cc_start: 0.9481 (mmp) cc_final: 0.9191 (mmp)
REVERT: E   93 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8568 (tm-30)
REVERT: E  104 PHE cc_start: 0.9585 (m-10) cc_final: 0.9287 (m-10)
REVERT: E  120 MET cc_start: 0.8582 (mtm) cc_final: 0.7876 (mtt)
REVERT: E  123 ASP cc_start: 0.9407 (m-30) cc_final: 0.8626 (m-30)
REVERT: F   60 VAL cc_start: 0.9682 (t) cc_final: 0.9230 (t)
REVERT: F   63 GLU cc_start: 0.9709 (mt-10) cc_final: 0.9503 (mt-10)
REVERT: F   74 GLU cc_start: 0.9354 (pp20) cc_final: 0.9145 (pp20)
REVERT: G   61 GLU cc_start: 0.9266 (pp20) cc_final: 0.9034 (pp20)
REVERT: G   64 GLU cc_start: 0.9126 (mp0) cc_final: 0.8835 (mp0)
REVERT: G  102 ILE cc_start: 0.8460 (mm) cc_final: 0.8192 (mm)
REVERT: H   95 GLN cc_start: 0.9412 (pt0) cc_final: 0.9156 (pt0)
REVERT: H  120 LYS cc_start: 0.9644 (mppt) cc_final: 0.9269 (mttp)
  outliers start: 2
  outliers final: 1
  residues processed: 145
  average time/residue: 0.2558
  time to fit residues: 52.8831
Evaluate side-chains
  106 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 80 optimal weight:    7.9990
   chunk 65 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   chunk 104 optimal weight:    6.9990
   chunk 85 optimal weight:    7.9990
   chunk 95 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 77 optimal weight:    6.9990
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.3206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049  14262  Z= 0.396
  Angle     :  0.715  11.462  20774  Z= 0.420
  Chirality :  0.039   0.173   2360
  Planarity :  0.005   0.045   1408
  Dihedral  : 33.224 178.968   4680
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 19.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.28), residues: 752
  helix:  1.29 (0.21), residues: 522
  sheet:  None (None), residues: 0
  loop : -0.34 (0.36), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS H 109 
 PHE   0.018   0.002   PHE D  65 
 TYR   0.018   0.002   TYR D  40 
 ARG   0.008   0.001   ARG C  42 

*********************** 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
  137 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.992 
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: 0.9392 (mpp) cc_final: 0.9037 (mmm)
REVERT: A  104 PHE cc_start: 0.9517 (m-80) cc_final: 0.9306 (m-80)
REVERT: B   59 LYS cc_start: 0.9695 (tmtt) cc_final: 0.9471 (tptt)
REVERT: B   74 GLU cc_start: 0.9791 (tm-30) cc_final: 0.9533 (tm-30)
REVERT: B   85 ASP cc_start: 0.8545 (m-30) cc_final: 0.8335 (m-30)
REVERT: C  104 GLN cc_start: 0.8738 (tp-100) cc_final: 0.8530 (tp-100)
REVERT: D  109 HIS cc_start: 0.9437 (m90) cc_final: 0.9212 (m170)
REVERT: E   59 GLU cc_start: 0.9117 (mp0) cc_final: 0.8734 (pm20)
REVERT: E   90 MET cc_start: 0.9491 (mmp) cc_final: 0.9171 (mmm)
REVERT: E  104 PHE cc_start: 0.9526 (m-10) cc_final: 0.9284 (m-10)
REVERT: E  120 MET cc_start: 0.8640 (mtm) cc_final: 0.7909 (mtt)
REVERT: F   63 GLU cc_start: 0.9683 (mt-10) cc_final: 0.9462 (mt-10)
REVERT: F   79 LYS cc_start: 0.9604 (tptp) cc_final: 0.9323 (tttt)
REVERT: G   72 ASP cc_start: 0.9375 (m-30) cc_final: 0.9146 (m-30)
REVERT: H   95 GLN cc_start: 0.9377 (pt0) cc_final: 0.9114 (pt0)
REVERT: H  108 LYS cc_start: 0.9305 (ptpp) cc_final: 0.9057 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.2522
  time to fit residues: 49.8565
Evaluate side-chains
  97 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 96 optimal weight:    5.9990
   chunk 102 optimal weight:    5.9990
   chunk 91 optimal weight:    7.9990
   chunk 27 optimal weight:    9.9990
   chunk 85 optimal weight:    7.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  89 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.3476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038  14262  Z= 0.311
  Angle     :  0.663   9.928  20774  Z= 0.392
  Chirality :  0.037   0.149   2360
  Planarity :  0.005   0.055   1408
  Dihedral  : 33.046 179.271   4680
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 16.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.67 %
    Favored  : 97.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.29), residues: 752
  helix:  1.45 (0.22), residues: 524
  sheet:  None (None), residues: 0
  loop : -0.36 (0.37), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.012   0.002   PHE E  67 
 TYR   0.014   0.002   TYR D 121 
 ARG   0.007   0.001   ARG C  42 

*********************** 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
  136 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 135
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9354 (mpp) cc_final: 0.8969 (mpp)
REVERT: A  104 PHE cc_start: 0.9563 (m-80) cc_final: 0.9315 (m-80)
REVERT: A  105 GLU cc_start: 0.9435 (OUTLIER) cc_final: 0.9152 (pp20)
REVERT: A  106 ASP cc_start: 0.9471 (m-30) cc_final: 0.8768 (m-30)
REVERT: B   63 GLU cc_start: 0.9445 (tt0) cc_final: 0.8851 (tm-30)
REVERT: B   74 GLU cc_start: 0.9801 (tm-30) cc_final: 0.9512 (tm-30)
REVERT: B   85 ASP cc_start: 0.8579 (m-30) cc_final: 0.8314 (m-30)
REVERT: D  109 HIS cc_start: 0.9436 (m90) cc_final: 0.8823 (m90)
REVERT: E   50 GLU cc_start: 0.9499 (mp0) cc_final: 0.9245 (mp0)
REVERT: E   59 GLU cc_start: 0.9104 (mp0) cc_final: 0.8726 (pm20)
REVERT: E   82 LEU cc_start: 0.8190 (mm) cc_final: 0.7900 (mm)
REVERT: E   90 MET cc_start: 0.9467 (mmp) cc_final: 0.9140 (mmp)
REVERT: E  104 PHE cc_start: 0.9572 (m-10) cc_final: 0.9298 (m-10)
REVERT: E  120 MET cc_start: 0.8576 (mtm) cc_final: 0.7867 (mtt)
REVERT: F   63 GLU cc_start: 0.9668 (mt-10) cc_final: 0.9456 (mt-10)
REVERT: F   79 LYS cc_start: 0.9596 (tptp) cc_final: 0.9310 (tttt)
REVERT: G   36 LYS cc_start: 0.9357 (mmtt) cc_final: 0.8862 (mmtm)
REVERT: G   64 GLU cc_start: 0.9190 (mp0) cc_final: 0.8919 (mp0)
REVERT: H   95 GLN cc_start: 0.9324 (pt0) cc_final: 0.9082 (pt0)
  outliers start: 1
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2558
  time to fit residues: 49.6121
Evaluate side-chains
  103 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 58 optimal weight:    8.9990
   chunk 1 optimal weight:    7.9990
   chunk 76 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 87 optimal weight:   10.0000
   chunk 70 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    2.5784

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
C 104 GLN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  55 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14262  Z= 0.240
  Angle     :  0.630   8.745  20774  Z= 0.373
  Chirality :  0.035   0.137   2360
  Planarity :  0.004   0.054   1408
  Dihedral  : 32.822 179.972   4680
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.46 %
    Favored  : 96.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.30), residues: 752
  helix:  1.51 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.23 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.011   0.002   PHE E  67 
 TYR   0.010   0.001   TYR D 121 
 ARG   0.005   0.000   ARG D  31 

*********************** 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
  138 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8946 (pm20) cc_final: 0.8734 (pm20)
REVERT: A   93 GLN cc_start: 0.9185 (tp-100) cc_final: 0.8803 (tp40)
REVERT: A   94 GLU cc_start: 0.9433 (mp0) cc_final: 0.9103 (mp0)
REVERT: A  104 PHE cc_start: 0.9402 (m-80) cc_final: 0.9078 (m-80)
REVERT: A  106 ASP cc_start: 0.9476 (m-30) cc_final: 0.9250 (m-30)
REVERT: A  120 MET cc_start: 0.8273 (mtt) cc_final: 0.7347 (mtt)
REVERT: B   63 GLU cc_start: 0.9390 (tt0) cc_final: 0.8824 (tm-30)
REVERT: B   74 GLU cc_start: 0.9804 (tm-30) cc_final: 0.9506 (tm-30)
REVERT: B   85 ASP cc_start: 0.8562 (m-30) cc_final: 0.8289 (m-30)
REVERT: C   90 ASP cc_start: 0.7672 (t0) cc_final: 0.7339 (t70)
REVERT: E   59 GLU cc_start: 0.9080 (mp0) cc_final: 0.8663 (pm20)
REVERT: E   82 LEU cc_start: 0.8183 (mm) cc_final: 0.7920 (mm)
REVERT: E   90 MET cc_start: 0.9430 (mmp) cc_final: 0.9117 (mmp)
REVERT: E  104 PHE cc_start: 0.9621 (m-10) cc_final: 0.9303 (m-80)
REVERT: E  120 MET cc_start: 0.8566 (mtm) cc_final: 0.7818 (mtt)
REVERT: E  123 ASP cc_start: 0.9352 (m-30) cc_final: 0.8640 (m-30)
REVERT: F   60 VAL cc_start: 0.9640 (t) cc_final: 0.9204 (t)
REVERT: F   63 GLU cc_start: 0.9647 (mt-10) cc_final: 0.9437 (mt-10)
REVERT: F   74 GLU cc_start: 0.9340 (pp20) cc_final: 0.9120 (pp20)
REVERT: F   79 LYS cc_start: 0.9608 (tptp) cc_final: 0.9301 (tttt)
REVERT: G   90 ASP cc_start: 0.8627 (t70) cc_final: 0.8323 (t0)
REVERT: H   95 GLN cc_start: 0.9311 (pt0) cc_final: 0.9055 (pt0)
  outliers start: 1
  outliers final: 0
  residues processed: 137
  average time/residue: 0.2557
  time to fit residues: 50.5211
Evaluate side-chains
  106 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 92 optimal weight:    7.9990
   chunk 20 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 102 optimal weight:    7.9990
   chunk 85 optimal weight:    7.9990
   chunk 47 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 53 optimal weight:   20.0000
   chunk 98 optimal weight:    4.9990
   overall best weight:    1.5386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.3729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14262  Z= 0.200
  Angle     :  0.606   7.317  20774  Z= 0.359
  Chirality :  0.034   0.161   2360
  Planarity :  0.004   0.054   1408
  Dihedral  : 32.535 179.954   4680
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  2.04 %
    Favored  : 97.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.30), residues: 752
  helix:  1.65 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.21 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.019   0.001   PHE G  25 
 TYR   0.011   0.001   TYR F  98 
 ARG   0.006   0.000   ARG D  31 

*********************** 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
  148 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 146
  time to evaluate  : 0.986 
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: A   59 GLU cc_start: 0.8886 (pm20) cc_final: 0.8663 (pm20)
REVERT: A  104 PHE cc_start: 0.9346 (m-80) cc_final: 0.8984 (m-80)
REVERT: A  120 MET cc_start: 0.8265 (mtt) cc_final: 0.7245 (mtt)
REVERT: B   74 GLU cc_start: 0.9802 (tm-30) cc_final: 0.9516 (tm-30)
REVERT: B   85 ASP cc_start: 0.8560 (m-30) cc_final: 0.8293 (m-30)
REVERT: D   68 ASP cc_start: 0.9345 (t0) cc_final: 0.9042 (t0)
REVERT: E   50 GLU cc_start: 0.9463 (mp0) cc_final: 0.9161 (mp0)
REVERT: E   59 GLU cc_start: 0.9016 (mp0) cc_final: 0.8599 (pm20)
REVERT: E   82 LEU cc_start: 0.8203 (mm) cc_final: 0.7901 (mm)
REVERT: E   90 MET cc_start: 0.9412 (mmp) cc_final: 0.9128 (mmp)
REVERT: E  104 PHE cc_start: 0.9669 (m-10) cc_final: 0.9401 (m-80)
REVERT: E  120 MET cc_start: 0.8571 (mtm) cc_final: 0.7812 (mtt)
REVERT: E  123 ASP cc_start: 0.9323 (m-30) cc_final: 0.8593 (m-30)
REVERT: F   60 VAL cc_start: 0.9619 (t) cc_final: 0.9166 (t)
REVERT: F   74 GLU cc_start: 0.9272 (pp20) cc_final: 0.9020 (pp20)
REVERT: F   79 LYS cc_start: 0.9487 (tppt) cc_final: 0.9108 (tttt)
REVERT: G   36 LYS cc_start: 0.9562 (mmmt) cc_final: 0.9024 (mmtm)
REVERT: G   64 GLU cc_start: 0.9160 (mp0) cc_final: 0.8906 (mp0)
  outliers start: 2
  outliers final: 1
  residues processed: 147
  average time/residue: 0.2513
  time to fit residues: 53.2387
Evaluate side-chains
  107 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 58 optimal weight:    4.9990
   chunk 74 optimal weight:    7.9990
   chunk 86 optimal weight:   10.0000
   chunk 57 optimal weight:    0.6980
   chunk 102 optimal weight:    7.9990
   chunk 63 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0970
   chunk 47 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    2.5582

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
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: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.3914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  14262  Z= 0.238
  Angle     :  0.623   8.148  20774  Z= 0.367
  Chirality :  0.035   0.169   2360
  Planarity :  0.004   0.054   1408
  Dihedral  : 32.517 178.733   4680
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.30), residues: 752
  helix:  1.65 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.21 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS D 109 
 PHE   0.013   0.001   PHE G  25 
 TYR   0.011   0.002   TYR E  99 
 ARG   0.008   0.000   ARG D  31 

*********************** 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
  135 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8895 (pm20) cc_final: 0.8655 (pm20)
REVERT: A   90 MET cc_start: 0.9314 (mpp) cc_final: 0.9075 (mpp)
REVERT: A  104 PHE cc_start: 0.9396 (m-80) cc_final: 0.9043 (m-80)
REVERT: B   74 GLU cc_start: 0.9809 (tm-30) cc_final: 0.9483 (tm-30)
REVERT: B   85 ASP cc_start: 0.8585 (m-30) cc_final: 0.8286 (m-30)
REVERT: B   91 LYS cc_start: 0.9358 (tmmt) cc_final: 0.9150 (tmmt)
REVERT: D  109 HIS cc_start: 0.9452 (m90) cc_final: 0.9248 (m170)
REVERT: E   59 GLU cc_start: 0.9026 (mp0) cc_final: 0.8563 (pm20)
REVERT: E   82 LEU cc_start: 0.8197 (mm) cc_final: 0.7903 (mm)
REVERT: E   90 MET cc_start: 0.9463 (mmp) cc_final: 0.9156 (mmp)
REVERT: E   94 GLU cc_start: 0.9395 (tp30) cc_final: 0.9062 (tt0)
REVERT: E  104 PHE cc_start: 0.9689 (m-10) cc_final: 0.9396 (m-80)
REVERT: E  120 MET cc_start: 0.8615 (mtm) cc_final: 0.7680 (mtt)
REVERT: E  123 ASP cc_start: 0.9562 (m-30) cc_final: 0.8717 (m-30)
REVERT: F   60 VAL cc_start: 0.9636 (t) cc_final: 0.9167 (t)
REVERT: F   74 GLU cc_start: 0.9297 (pp20) cc_final: 0.9069 (pp20)
REVERT: F   79 LYS cc_start: 0.9552 (tppt) cc_final: 0.9164 (tttt)
REVERT: G   36 LYS cc_start: 0.9571 (mmmt) cc_final: 0.9050 (mmtm)
REVERT: G   64 GLU cc_start: 0.9180 (mp0) cc_final: 0.8907 (mp0)
REVERT: G   92 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8441 (pm20)
REVERT: H   95 GLN cc_start: 0.9290 (pt0) cc_final: 0.9027 (pt0)
REVERT: H  108 LYS cc_start: 0.9296 (ptpp) cc_final: 0.9056 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2408
  time to fit residues: 47.7077
Evaluate side-chains
  103 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 20 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9980
   chunk 64 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 80 optimal weight:    8.9990
   chunk 92 optimal weight:    7.9990
   chunk 97 optimal weight:    6.9990
   chunk 89 optimal weight:   20.0000
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.4051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  14262  Z= 0.240
  Angle     :  0.620   7.924  20774  Z= 0.367
  Chirality :  0.035   0.211   2360
  Planarity :  0.004   0.056   1408
  Dihedral  : 32.519 178.315   4680
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.30), residues: 752
  helix:  1.67 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.19 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.013   0.002   PHE G  25 
 TYR   0.011   0.002   TYR D  40 
 ARG   0.006   0.000   ARG D  31 

*********************** 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
  139 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8886 (pm20) cc_final: 0.8647 (pm20)
REVERT: A   90 MET cc_start: 0.9357 (mpp) cc_final: 0.9119 (mpp)
REVERT: A   93 GLN cc_start: 0.8763 (tp-100) cc_final: 0.8559 (tp40)
REVERT: A  104 PHE cc_start: 0.9433 (m-80) cc_final: 0.9158 (m-80)
REVERT: A  123 ASP cc_start: 0.9624 (m-30) cc_final: 0.9410 (m-30)
REVERT: B   74 GLU cc_start: 0.9808 (tm-30) cc_final: 0.9480 (tm-30)
REVERT: B   85 ASP cc_start: 0.8638 (m-30) cc_final: 0.8349 (m-30)
REVERT: B   91 LYS cc_start: 0.9323 (tmmt) cc_final: 0.9105 (tmmt)
REVERT: D  109 HIS cc_start: 0.9457 (m90) cc_final: 0.9250 (m170)
REVERT: E   50 GLU cc_start: 0.9445 (mp0) cc_final: 0.9212 (mp0)
REVERT: E   59 GLU cc_start: 0.8998 (mp0) cc_final: 0.8599 (pm20)
REVERT: E   82 LEU cc_start: 0.7947 (mm) cc_final: 0.7644 (mm)
REVERT: E   90 MET cc_start: 0.9448 (mmp) cc_final: 0.9169 (mmp)
REVERT: E   94 GLU cc_start: 0.9379 (tp30) cc_final: 0.9069 (tt0)
REVERT: E  104 PHE cc_start: 0.9695 (m-10) cc_final: 0.9479 (m-10)
REVERT: E  105 GLU cc_start: 0.9164 (pp20) cc_final: 0.8911 (pp20)
REVERT: E  106 ASP cc_start: 0.8635 (m-30) cc_final: 0.8193 (m-30)
REVERT: E  120 MET cc_start: 0.8600 (mtm) cc_final: 0.7665 (mtt)
REVERT: E  123 ASP cc_start: 0.9544 (m-30) cc_final: 0.8672 (m-30)
REVERT: F   74 GLU cc_start: 0.9320 (pp20) cc_final: 0.9064 (pp20)
REVERT: F   79 LYS cc_start: 0.9572 (tppt) cc_final: 0.9254 (tttt)
REVERT: G   64 GLU cc_start: 0.9178 (mp0) cc_final: 0.8922 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.2442
  time to fit residues: 49.9358
Evaluate side-chains
  108 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 97 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 74 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 86 optimal weight:    8.9990
   chunk 90 optimal weight:   10.0000
   chunk 94 optimal weight:    6.9990
   chunk 62 optimal weight:    0.1980
   chunk 100 optimal weight:    7.9990
   overall best weight:    3.0386

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  95 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.4186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  14262  Z= 0.265
  Angle     :  0.643   8.929  20774  Z= 0.377
  Chirality :  0.035   0.217   2360
  Planarity :  0.004   0.055   1408
  Dihedral  : 32.554 177.915   4680
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 15.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.30), residues: 752
  helix:  1.80 (0.22), residues: 524
  sheet:  None (None), residues: 0
  loop : -0.20 (0.39), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.014   0.002   PHE G  25 
 TYR   0.012   0.002   TYR F  98 
 ARG   0.006   0.000   ARG C  42 

*********************** 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
  136 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8891 (pm20) cc_final: 0.8658 (pm20)
REVERT: A   90 MET cc_start: 0.9348 (mpp) cc_final: 0.8984 (mpp)
REVERT: A  104 PHE cc_start: 0.9522 (m-80) cc_final: 0.9221 (m-80)
REVERT: A  120 MET cc_start: 0.8381 (mtt) cc_final: 0.7417 (mtt)
REVERT: A  123 ASP cc_start: 0.9618 (m-30) cc_final: 0.9118 (m-30)
REVERT: B   74 GLU cc_start: 0.9813 (tm-30) cc_final: 0.9477 (tm-30)
REVERT: B   91 LYS cc_start: 0.9340 (tmmt) cc_final: 0.9117 (tmmt)
REVERT: D  109 HIS cc_start: 0.9472 (m90) cc_final: 0.9258 (m170)
REVERT: E   50 GLU cc_start: 0.9471 (mp0) cc_final: 0.9213 (mp0)
REVERT: E   59 GLU cc_start: 0.9008 (mp0) cc_final: 0.8564 (pm20)
REVERT: E   82 LEU cc_start: 0.7883 (mm) cc_final: 0.7662 (mm)
REVERT: E   90 MET cc_start: 0.9464 (mmp) cc_final: 0.9173 (mmp)
REVERT: E   94 GLU cc_start: 0.9404 (tp30) cc_final: 0.9050 (tt0)
REVERT: E  104 PHE cc_start: 0.9688 (m-10) cc_final: 0.9459 (m-10)
REVERT: E  105 GLU cc_start: 0.9169 (pp20) cc_final: 0.8915 (pp20)
REVERT: E  106 ASP cc_start: 0.8629 (m-30) cc_final: 0.8189 (m-30)
REVERT: E  120 MET cc_start: 0.8627 (mtm) cc_final: 0.7729 (mtt)
REVERT: E  123 ASP cc_start: 0.9562 (m-30) cc_final: 0.8764 (m-30)
REVERT: F   74 GLU cc_start: 0.9314 (pp20) cc_final: 0.9067 (pp20)
REVERT: F   79 LYS cc_start: 0.9590 (tppt) cc_final: 0.9264 (tttt)
REVERT: G   36 LYS cc_start: 0.9532 (mmmt) cc_final: 0.9218 (mmtm)
REVERT: G   64 GLU cc_start: 0.9219 (mp0) cc_final: 0.8946 (mp0)
REVERT: G   90 ASP cc_start: 0.8573 (t70) cc_final: 0.8281 (t70)
REVERT: G   92 GLU cc_start: 0.8773 (mt-10) cc_final: 0.7038 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.2445
  time to fit residues: 48.4307
Evaluate side-chains
  104 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 47 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9990
   chunk 105 optimal weight:   10.0000
   chunk 97 optimal weight:    7.9990
   chunk 84 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 64 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 89 optimal weight:   20.0000
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.4271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  14262  Z= 0.234
  Angle     :  0.631   8.420  20774  Z= 0.373
  Chirality :  0.035   0.179   2360
  Planarity :  0.004   0.056   1408
  Dihedral  : 32.510 178.042   4680
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.30), residues: 752
  helix:  1.61 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.18 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.016   0.002   PHE G  25 
 TYR   0.012   0.002   TYR H  37 
 ARG   0.006   0.000   ARG D  31 

********************** 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
  142 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8856 (pm20) cc_final: 0.8618 (pm20)
REVERT: A   90 MET cc_start: 0.9331 (mpp) cc_final: 0.8908 (mpp)
REVERT: A  104 PHE cc_start: 0.9521 (m-80) cc_final: 0.9199 (m-80)
REVERT: A  120 MET cc_start: 0.8384 (mtt) cc_final: 0.7414 (mtt)
REVERT: A  123 ASP cc_start: 0.9625 (m-30) cc_final: 0.9128 (m-30)
REVERT: B   74 GLU cc_start: 0.9811 (tm-30) cc_final: 0.9463 (tm-30)
REVERT: B   85 ASP cc_start: 0.8645 (m-30) cc_final: 0.8359 (m-30)
REVERT: B   91 LYS cc_start: 0.9291 (tmmt) cc_final: 0.9064 (tmmt)
REVERT: D  109 HIS cc_start: 0.9474 (m90) cc_final: 0.9246 (m170)
REVERT: E   50 GLU cc_start: 0.9441 (mp0) cc_final: 0.9208 (mp0)
REVERT: E   59 GLU cc_start: 0.8980 (mp0) cc_final: 0.8602 (pm20)
REVERT: E   82 LEU cc_start: 0.7920 (mm) cc_final: 0.7632 (mm)
REVERT: E   90 MET cc_start: 0.9457 (mmp) cc_final: 0.9168 (mmp)
REVERT: E   94 GLU cc_start: 0.9286 (tp30) cc_final: 0.8993 (tt0)
REVERT: E  104 PHE cc_start: 0.9702 (m-10) cc_final: 0.9483 (m-10)
REVERT: E  105 GLU cc_start: 0.9152 (pp20) cc_final: 0.8901 (pp20)
REVERT: E  106 ASP cc_start: 0.8620 (m-30) cc_final: 0.8179 (m-30)
REVERT: E  120 MET cc_start: 0.8622 (mtm) cc_final: 0.7730 (mtt)
REVERT: E  123 ASP cc_start: 0.9550 (m-30) cc_final: 0.8708 (m-30)
REVERT: F   74 GLU cc_start: 0.9299 (pp20) cc_final: 0.9041 (pp20)
REVERT: F   79 LYS cc_start: 0.9568 (tppt) cc_final: 0.9265 (tttt)
REVERT: G   64 GLU cc_start: 0.9213 (mp0) cc_final: 0.8925 (mp0)
REVERT: H   95 GLN cc_start: 0.9235 (pt0) cc_final: 0.8964 (pt0)
REVERT: H  102 LEU cc_start: 0.8971 (mt) cc_final: 0.8712 (mp)
REVERT: H  108 LYS cc_start: 0.9245 (ptpp) cc_final: 0.8991 (ptpp)
REVERT: H  120 LYS cc_start: 0.9601 (mppt) cc_final: 0.9335 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.2488
  time to fit residues: 51.9996
Evaluate side-chains
  105 residues out of total 636 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   chunk 12 optimal weight:    0.8980
   chunk 23 optimal weight:    6.9990
   chunk 84 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 86 optimal weight:    8.9990
   chunk 10 optimal weight:   10.0000
   chunk 15 optimal weight:    0.7980
   chunk 73 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   overall best weight:    3.3386

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

Flipped N/Q/H residues before XYZ refinement:
C  84 GLN
C 104 GLN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.029881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2489 r_free = 0.2489 target = 0.023365 restraints weight = 197917.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2538 r_free = 0.2538 target = 0.024140 restraints weight = 91938.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2572 r_free = 0.2572 target = 0.024695 restraints weight = 53962.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.2512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.4474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  14262  Z= 0.284
  Angle     :  0.660   8.913  20774  Z= 0.387
  Chirality :  0.036   0.181   2360
  Planarity :  0.005   0.058   1408
  Dihedral  : 32.645 177.487   4680
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 16.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.30), residues: 752
  helix:  1.69 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.13 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.014   0.002   PHE G  25 
 TYR   0.012   0.002   TYR D  40 
 ARG   0.006   0.001   ARG C  42 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1954.06 seconds
wall clock time: 38 minutes 4.88 seconds (2284.88 seconds total)