Starting phenix.real_space_refine
on Thu Feb 13 00:09:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8eu2_28602/02_2025/8eu2_28602_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8eu2_28602/02_2025/8eu2_28602.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8eu2_28602/02_2025/8eu2_28602.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8eu2_28602/02_2025/8eu2_28602.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8eu2_28602/02_2025/8eu2_28602_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8eu2_28602/02_2025/8eu2_28602_neut.cif"
  }
  resolution = 2.93
  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=   0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     218      5.49       5
     S       8      5.16       5
     C    4769      2.51       5
     N    1634      2.21       5
     O    2053      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8682
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "I"
      Number of atoms: 2240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 2240
          Classifications: {'DNA': 110}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 109}
    Chain: "J"
      Number of atoms: 2264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 2264
          Classifications: {'DNA': 110}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 109}
    Chain: "K"
      Number of atoms: 610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 610
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
    Chain: "L"
      Number of atoms: 576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 576
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 1, 'TRANS': 70}
    Chain: "M"
      Number of atoms: 813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 813
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "N"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "O"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "P"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
  Time building chain proxies: 6.78, per 1000 atoms: 0.78
  Number of scatterers: 8682
  At special positions: 0
  Unit cell: (121.91, 102.705, 106.045, 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       8     16.00
     P     218     15.00
     O    2053      8.00
     N    1634      7.00
     C    4769      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: 2.31
  Conformation dependent library (CDL) restraints added in 561.4 milliseconds
  

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  986

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 7 sheets defined
      75.4% alpha, 2.7% beta
      109 base pairs and 193 stacking pairs defined.
    Time for finding SS restraints: 4.55
  Creating SS restraints...
    Processing helix  chain 'K' and resid 63 through 76
      removed outlier: 3.527A  pdb=" N   PHE K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 85 through 114
    Processing helix  chain 'K' and resid 120 through 132
      removed outlier: 3.579A  pdb=" N   ILE K 124 " --> pdb=" O   MET K 120 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 24 through 29
      removed outlier: 3.825A  pdb=" N   GLN L  27 " --> pdb=" O   ASP L  24 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 30 through 41
      removed outlier: 3.586A  pdb=" N   GLY L  41 " --> pdb=" O   LEU L  37 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 49 through 76
      removed outlier: 3.888A  pdb=" N   GLU L  53 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLY L  56 " --> pdb=" O   GLU L  52 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   ASP L  68 " --> pdb=" O   ASN L  64 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ALA L  76 " --> pdb=" O   TYR L  72 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 82 through 94
    Processing helix  chain 'M' and resid 16 through 22
    Processing helix  chain 'M' and resid 27 through 37
    Processing helix  chain 'M' and resid 46 through 73
    Processing helix  chain 'M' and resid 79 through 90
      removed outlier: 3.586A  pdb=" N   ASN M  89 " --> pdb=" O   LEU M  85 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ASP M  90 " --> pdb=" O   ALA M  86 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 90 through 97
    Processing helix  chain 'M' and resid 112 through 116
    Processing helix  chain 'N' and resid 34 through 46
    Processing helix  chain 'N' and resid 52 through 81
      removed outlier: 3.577A  pdb=" N   ASN N  81 " --> pdb=" O   LEU N  77 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 99
    Processing helix  chain 'N' and resid 100 through 121
      removed outlier: 3.656A  pdb=" N   ALA N 104 " --> pdb=" O   PRO N 100 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS N 105 " --> pdb=" O   GLY N 101 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 44 through 57
    Processing helix  chain 'O' and resid 63 through 79
      removed outlier: 3.688A  pdb=" N   PHE O  67 " --> pdb=" O   ARG O  63 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ASP O  77 " --> pdb=" O   GLU O  73 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   PHE O  78 " --> pdb=" O   ILE O  74 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LYS O  79 " --> pdb=" O   ALA O  75 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 85 through 114
      removed outlier: 3.506A  pdb=" N   VAL O  89 " --> pdb=" O   GLN O  85 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA O 114 " --> pdb=" O   ALA O 110 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 120 through 131
      removed outlier: 3.571A  pdb=" N   ILE O 124 " --> pdb=" O   MET O 120 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 25 through 29
    Processing helix  chain 'P' and resid 30 through 41
    Processing helix  chain 'P' and resid 49 through 76
      removed outlier: 4.166A  pdb=" N   GLU P  53 " --> pdb=" O   LEU P  49 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 82 through 93
      removed outlier: 3.552A  pdb=" N   VAL P  86 " --> pdb=" O   THR P  82 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLN P  93 " --> pdb=" O   ALA P  89 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84
      removed outlier: 7.486A  pdb=" N   ARG K  83 " --> pdb=" O   VAL L  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'K' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'M' and resid 42 through 43
      removed outlier: 7.328A  pdb=" N   ARG M  42 " --> pdb=" O   ILE N  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'M' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'M' and resid 101 through 102
      removed outlier: 6.727A  pdb=" N   THR M 101 " --> pdb=" O   TYR P  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'O' and resid 83 through 84
      removed outlier: 6.577A  pdb=" N   ARG O  83 " --> pdb=" O   VAL P  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'O' and resid 118 through 119

    278 hydrogen bonds defined for protein.
    816 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      283 hydrogen bonds
      566 hydrogen bond angles
      0 basepair planarities
      109 basepair parallelities
      193 stacking parallelities
  Total time for adding SS restraints: 3.49

  Time building geometry restraints manager: 2.71 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: 1562
        1.33 -     1.45: 3155
        1.45 -     1.57: 4112
        1.57 -     1.69: 437
        1.69 -     1.81: 16
  Bond restraints: 9282
  Sorted by residual:
  bond pdb=" N   ASP L  24 "
       pdb=" CA  ASP L  24 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.027 1.29e-02 6.01e+03 4.46e+00
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.484 -0.062 3.00e-02 1.11e+03 4.28e+00
  bond pdb=" CB  PRO O  43 "
       pdb=" CG  PRO O  43 "
    ideal  model  delta    sigma   weight residual
    1.492  1.592 -0.100 5.00e-02 4.00e+02 4.02e+00
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.477 -0.055 3.00e-02 1.11e+03 3.35e+00
  bond pdb=" CG  PRO O  43 "
       pdb=" CD  PRO O  43 "
    ideal  model  delta    sigma   weight residual
    1.503  1.564 -0.061 3.40e-02 8.65e+02 3.17e+00
  ... (remaining 9277 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 12875
        1.83 -     3.67: 531
        3.67 -     5.50: 49
        5.50 -     7.33: 13
        7.33 -     9.17: 9
  Bond angle restraints: 13477
  Sorted by residual:
  angle pdb=" CA  PRO O  43 "
        pdb=" N   PRO O  43 "
        pdb=" CD  PRO O  43 "
      ideal   model   delta    sigma   weight residual
     112.00  103.66    8.34 1.40e+00 5.10e-01 3.55e+01
  angle pdb=" N   GLU M  61 "
        pdb=" CA  GLU M  61 "
        pdb=" CB  GLU M  61 "
      ideal   model   delta    sigma   weight residual
     110.16  117.49   -7.33 1.48e+00 4.57e-01 2.45e+01
  angle pdb=" C   ARG L  23 "
        pdb=" N   ASP L  24 "
        pdb=" CA  ASP L  24 "
      ideal   model   delta    sigma   weight residual
     121.54  129.30   -7.76 1.91e+00 2.74e-01 1.65e+01
  angle pdb=" CG  ARG N  96 "
        pdb=" CD  ARG N  96 "
        pdb=" NE  ARG N  96 "
      ideal   model   delta    sigma   weight residual
     112.00  119.73   -7.73 2.20e+00 2.07e-01 1.24e+01
  angle pdb=" C3'  DG J  20 "
        pdb=" O3'  DG J  20 "
        pdb=" P    DG J  21 "
      ideal   model   delta    sigma   weight residual
     120.20  124.98   -4.78 1.50e+00 4.44e-01 1.02e+01
  ... (remaining 13472 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.93: 3934
       34.93 -    69.86: 1057
       69.86 -   104.79: 10
      104.79 -   139.72: 0
      139.72 -   174.65: 2
  Dihedral angle restraints: 5003
    sinusoidal: 3480
      harmonic: 1523
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   34.65 -174.65     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   69.06  150.94     1      3.50e+01 8.16e-04 1.47e+01
  dihedral pdb=" CA  ILE P  29 "
           pdb=" C   ILE P  29 "
           pdb=" N   THR P  30 "
           pdb=" CA  THR P  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.88  -19.12     0      5.00e+00 4.00e-02 1.46e+01
  ... (remaining 5000 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1234
       0.053 -    0.105: 243
       0.105 -    0.158: 48
       0.158 -    0.211: 7
       0.211 -    0.263: 4
  Chirality restraints: 1536
  Sorted by residual:
  chirality pdb=" CA  GLU M  61 "
            pdb=" N   GLU M  61 "
            pdb=" C   GLU M  61 "
            pdb=" CB  GLU M  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CG  LEU M 115 "
            pdb=" CB  LEU M 115 "
            pdb=" CD1 LEU M 115 "
            pdb=" CD2 LEU M 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CA  ILE M  79 "
            pdb=" N   ILE M  79 "
            pdb=" C   ILE M  79 "
            pdb=" CB  ILE M  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1533 not shown)

  Planarity restraints: 944
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG O  42 "    0.073 5.00e-02 4.00e+02   1.05e-01 1.77e+01
        pdb=" N   PRO O  43 "   -0.182 5.00e-02 4.00e+02
        pdb=" CA  PRO O  43 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO O  43 "    0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE M  79 "    0.056 5.00e-02 4.00e+02   8.40e-02 1.13e+01
        pdb=" N   PRO M  80 "   -0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO M  80 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO M  80 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE M  62 "    0.011 2.00e-02 2.50e+03   2.19e-02 4.80e+00
        pdb=" C   ILE M  62 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   ILE M  62 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LEU M  63 "    0.013 2.00e-02 2.50e+03
  ... (remaining 941 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 2644
        2.88 -     3.39: 7338
        3.39 -     3.89: 17030
        3.89 -     4.40: 18879
        4.40 -     4.90: 26074
  Nonbonded interactions: 71965
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN O 108 "
            pdb=" O   GLY P  42 "
     model   vdw
     2.381 3.120
  nonbonded pdb=" OE1 GLU O  50 "
            pdb=" NH1 ARG P  39 "
     model   vdw
     2.413 3.120
  nonbonded pdb=" OE1 GLU O  73 "
            pdb=" ND2 ASN P  25 "
     model   vdw
     2.415 3.120
  nonbonded pdb=" OP1  DC I -23 "
            pdb=" NH1 ARG K  72 "
     model   vdw
     2.417 3.120
  nonbonded pdb=" OP1  DG J  48 "
            pdb=" OH  TYR N  37 "
     model   vdw
     2.428 3.040
  ... (remaining 71960 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 'L' and resid 24 through 94)
  selection = (chain 'P' and resid 24 through 94)
}

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 individual isotropic
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:             11.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     27.780
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  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:12.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
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      :  0.005   0.100   9282  Z= 0.279
  Angle     :  0.823   9.165  13477  Z= 0.475
  Chirality :  0.046   0.263   1536
  Planarity :  0.009   0.105    944
  Dihedral  : 28.134 174.646   4017
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.81 (0.33), residues: 512
  helix: -0.24 (0.24), residues: 379
  sheet:  None (None), residues: 0
  loop : -1.01 (0.50), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS M  31 
 PHE   0.027   0.003   PHE K  78 
 TYR   0.014   0.002   TYR P  72 
 ARG   0.014   0.001   ARG K 128 

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   45 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7603 (mtp-110)
REVERT: M   77 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.7316 (ttp-170)
REVERT: N   64 ASN cc_start: 0.8346 (m-40) cc_final: 0.8027 (m-40)
REVERT: N   73 GLU cc_start: 0.7708 (tp30) cc_final: 0.7333 (tp30)
REVERT: N  112 THR cc_start: 0.8772 (p) cc_final: 0.8506 (t)
REVERT: O   70 LEU cc_start: 0.8505 (tp) cc_final: 0.8189 (tm)
REVERT: O  116 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7860 (ttp80)
REVERT: O  120 MET cc_start: 0.6907 (mtt) cc_final: 0.6515 (mtt)
REVERT: O  128 ARG cc_start: 0.8595 (mtp-110) cc_final: 0.8293 (mtp180)
REVERT: O  130 ILE cc_start: 0.8824 (mm) cc_final: 0.8553 (mt)
  outliers start: 0
  outliers final: 1
  residues processed: 193
  average time/residue: 1.4653
  time to fit residues: 297.5849
Evaluate side-chains
  191 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 190
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   56 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 53 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0470
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
L  27 GLN
M  68 ASN
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  89 ASN
M  94 ASN
** N  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  55 GLN
** O  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.129779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.103769 restraints weight = 15655.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 1.55
r_work: 0.3385 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.1313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   9282  Z= 0.294
  Angle     :  0.629   8.283  13477  Z= 0.376
  Chirality :  0.037   0.152   1536
  Planarity :  0.005   0.066    944
  Dihedral  : 30.655 172.591   2971
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 18.99 %
    Favored  : 78.03 %
  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:  1.41 (0.37), residues: 512
  helix:  1.45 (0.27), residues: 387
  sheet:  None (None), residues: 0
  loop : -0.57 (0.52), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS M  31 
 PHE   0.011   0.001   PHE K 104 
 TYR   0.016   0.001   TYR M  57 
 ARG   0.005   0.001   ARG O  63 

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 199
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  131 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8493 (mtt-85)
REVERT: M   61 GLU cc_start: 0.7938 (mp0) cc_final: 0.7676 (mp0)
REVERT: M   64 GLU cc_start: 0.8230 (tp30) cc_final: 0.7759 (tp30)
REVERT: M   68 ASN cc_start: 0.8494 (m-40) cc_final: 0.7018 (m-40)
REVERT: N   64 ASN cc_start: 0.8810 (m-40) cc_final: 0.8546 (m-40)
REVERT: N   73 GLU cc_start: 0.8482 (tp30) cc_final: 0.8236 (tp30)
REVERT: O   69 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.7720 (mtm-85)
REVERT: O  120 MET cc_start: 0.7938 (mtt) cc_final: 0.7600 (mtm)
REVERT: P   84 MET cc_start: 0.7905 (tpt) cc_final: 0.7689 (tpt)
  outliers start: 13
  outliers final: 8
  residues processed: 201
  average time/residue: 1.4951
  time to fit residues: 315.8059
Evaluate side-chains
  205 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 196
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  109 LEU
Chi-restraints excluded: chain K residue  131 ARG
Chi-restraints excluded: chain L residue   86 VAL
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain N residue   33 SER
Chi-restraints excluded: chain N residue   75 SER
Chi-restraints excluded: chain N residue   76 ARG
Chi-restraints excluded: chain N residue  119 THR
Chi-restraints excluded: chain P residue   86 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 60 optimal weight:    0.1980
   chunk 31 optimal weight:    0.0970
   chunk 50 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 70 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
K 108 ASN
M  94 ASN
O  68 GLN
** O  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.130434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.104734 restraints weight = 15829.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 1.52
r_work: 0.3406 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9282  Z= 0.232
  Angle     :  0.594   7.524  13477  Z= 0.355
  Chirality :  0.035   0.144   1536
  Planarity :  0.004   0.062    944
  Dihedral  : 30.552 172.958   2968
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 23.11 %
    Favored  : 72.77 %
  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:  2.21 (0.37), residues: 512
  helix:  2.11 (0.27), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.55 (0.51), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS N  79 
 PHE   0.012   0.001   PHE K  78 
 TYR   0.013   0.001   TYR M  57 
 ARG   0.008   0.001   ARG M  71 

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 203
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  109 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8511 (tm)
REVERT: K  125 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7876 (mp10)
REVERT: K  131 ARG cc_start: 0.8679 (ttt180) cc_final: 0.8365 (mtt-85)
REVERT: L   92 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8074 (mmm-85)
REVERT: M   61 GLU cc_start: 0.7922 (mp0) cc_final: 0.7564 (mp0)
REVERT: M   64 GLU cc_start: 0.8163 (tp30) cc_final: 0.7754 (tp30)
REVERT: M   68 ASN cc_start: 0.8388 (m-40) cc_final: 0.7164 (m-40)
REVERT: N   39 TYR cc_start: 0.8562 (t80) cc_final: 0.8168 (t80)
REVERT: N   43 LYS cc_start: 0.9082 (mmtp) cc_final: 0.8744 (tppp)
REVERT: N   64 ASN cc_start: 0.8805 (m-40) cc_final: 0.8535 (m-40)
REVERT: N   73 GLU cc_start: 0.8477 (tp30) cc_final: 0.8159 (tp30)
REVERT: O   70 LEU cc_start: 0.8845 (tp) cc_final: 0.8502 (tm)
REVERT: O  116 ARG cc_start: 0.8636 (ttp80) cc_final: 0.8372 (ttp80)
REVERT: O  120 MET cc_start: 0.7938 (mtt) cc_final: 0.7637 (mtm)
REVERT: O  129 ARG cc_start: 0.8573 (mmm-85) cc_final: 0.8227 (tmm-80)
REVERT: P   84 MET cc_start: 0.7890 (tpt) cc_final: 0.7636 (tpt)
REVERT: P   91 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8559 (ttmt)
  outliers start: 18
  outliers final: 9
  residues processed: 204
  average time/residue: 1.4904
  time to fit residues: 319.9836
Evaluate side-chains
  212 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 200
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  109 LEU
Chi-restraints excluded: chain K residue  124 ILE
Chi-restraints excluded: chain K residue  125 GLN
Chi-restraints excluded: chain L residue   92 ARG
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue   68 GLU
Chi-restraints excluded: chain N residue   75 SER
Chi-restraints excluded: chain O residue   57 SER
Chi-restraints excluded: chain O residue   65 LEU
Chi-restraints excluded: chain O residue  126 LEU
Chi-restraints excluded: chain P residue   86 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 10 optimal weight:    8.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
K 108 ASN
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 104 GLN
** N  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  55 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.126634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.101019 restraints weight = 15803.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 1.54
r_work: 0.3337 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   9282  Z= 0.372
  Angle     :  0.663   8.997  13477  Z= 0.392
  Chirality :  0.040   0.148   1536
  Planarity :  0.005   0.058    944
  Dihedral  : 30.592 166.217   2968
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 24.94 %
    Favored  : 70.02 %
  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:  2.27 (0.37), residues: 512
  helix:  2.20 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop : -0.58 (0.51), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS K 113 
 PHE   0.017   0.002   PHE K  78 
 TYR   0.011   0.001   TYR N 118 
 ARG   0.009   0.001   ARG M  20 

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 208
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
REVERT: K  125 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7890 (mp10)
REVERT: K  131 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8464 (mtt-85)
REVERT: L   45 ARG cc_start: 0.8346 (mmm-85) cc_final: 0.7876 (mtp-110)
REVERT: L   57 VAL cc_start: 0.9255 (m) cc_final: 0.9052 (t)
REVERT: L   92 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8035 (ttm-80)
REVERT: M   64 GLU cc_start: 0.8180 (tp30) cc_final: 0.7714 (tp30)
REVERT: M   68 ASN cc_start: 0.8438 (m-40) cc_final: 0.7547 (m-40)
REVERT: N   39 TYR cc_start: 0.8678 (t80) cc_final: 0.8323 (t80)
REVERT: N   43 LYS cc_start: 0.9130 (mmtp) cc_final: 0.8871 (mmtp)
REVERT: N   64 ASN cc_start: 0.8856 (m-40) cc_final: 0.8605 (m-40)
REVERT: O   70 LEU cc_start: 0.8926 (tp) cc_final: 0.8560 (tm)
REVERT: O   97 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8140 (mm-30)
REVERT: O  116 ARG cc_start: 0.8713 (ttp80) cc_final: 0.8313 (ttp80)
REVERT: O  120 MET cc_start: 0.8009 (mtt) cc_final: 0.7553 (mtp)
  outliers start: 22
  outliers final: 15
  residues processed: 210
  average time/residue: 1.4767
  time to fit residues: 325.7018
Evaluate side-chains
  223 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 205
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  124 ILE
Chi-restraints excluded: chain K residue  125 GLN
Chi-restraints excluded: chain K residue  130 ILE
Chi-restraints excluded: chain K residue  131 ARG
Chi-restraints excluded: chain L residue   86 VAL
Chi-restraints excluded: chain L residue   92 ARG
Chi-restraints excluded: chain M residue   59 THR
Chi-restraints excluded: chain M residue  101 THR
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain N residue   42 LEU
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue   68 GLU
Chi-restraints excluded: chain N residue   75 SER
Chi-restraints excluded: chain N residue  119 THR
Chi-restraints excluded: chain O residue   57 SER
Chi-restraints excluded: chain O residue  100 LEU
Chi-restraints excluded: chain O residue  126 LEU
Chi-restraints excluded: chain P residue   86 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 67 optimal weight:    0.5980
   chunk 35 optimal weight:    0.3980
   chunk 42 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 38 optimal weight:    0.1980
   chunk 39 optimal weight:    0.0970
   chunk 22 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.3778

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

Flipped N/Q/H residues before XYZ refinement:
L  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.129996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.104412 restraints weight = 15797.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 1.51
r_work: 0.3406 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9282  Z= 0.214
  Angle     :  0.590   7.296  13477  Z= 0.353
  Chirality :  0.035   0.141   1536
  Planarity :  0.005   0.059    944
  Dihedral  : 30.395 173.292   2968
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 27.69 %
    Favored  : 67.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.72 (0.37), residues: 512
  helix:  2.50 (0.27), residues: 385
  sheet:  None (None), residues: 0
  loop : -0.44 (0.51), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS M  31 
 PHE   0.013   0.001   PHE K  78 
 TYR   0.010   0.001   TYR P  51 
 ARG   0.008   0.001   ARG K  72 

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 200
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
REVERT: K   72 ARG cc_start: 0.8955 (mtt-85) cc_final: 0.8610 (mtt180)
REVERT: K  125 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.7853 (mp10)
REVERT: K  131 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8398 (mtt-85)
REVERT: L   45 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7913 (mtp-110)
REVERT: L   92 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7977 (ttm-80)
REVERT: M   61 GLU cc_start: 0.8185 (mp0) cc_final: 0.7667 (mp0)
REVERT: M   64 GLU cc_start: 0.8080 (tp30) cc_final: 0.7712 (tp30)
REVERT: M   68 ASN cc_start: 0.8323 (m-40) cc_final: 0.7544 (m-40)
REVERT: N   39 TYR cc_start: 0.8601 (t80) cc_final: 0.8340 (t80)
REVERT: N   43 LYS cc_start: 0.9100 (mmtp) cc_final: 0.8858 (mmtm)
REVERT: N   64 ASN cc_start: 0.8815 (m-40) cc_final: 0.8570 (m-40)
REVERT: O   97 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8095 (mm-30)
REVERT: O  120 MET cc_start: 0.7897 (mtt) cc_final: 0.7581 (mtm)
  outliers start: 19
  outliers final: 10
  residues processed: 203
  average time/residue: 1.4770
  time to fit residues: 315.2008
Evaluate side-chains
  216 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 202
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  100 LEU
Chi-restraints excluded: chain K residue  124 ILE
Chi-restraints excluded: chain K residue  125 GLN
Chi-restraints excluded: chain K residue  131 ARG
Chi-restraints excluded: chain L residue   45 ARG
Chi-restraints excluded: chain L residue   92 ARG
Chi-restraints excluded: chain M residue   59 THR
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue   68 GLU
Chi-restraints excluded: chain N residue   75 SER
Chi-restraints excluded: chain N residue   98 LEU
Chi-restraints excluded: chain O residue   57 SER
Chi-restraints excluded: chain P residue   86 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 63 optimal weight:    0.1980
   chunk 8 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 61 optimal weight:    0.2980
   chunk 43 optimal weight:    0.9990
   chunk 31 optimal weight:    0.4980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
K 108 ASN
O  55 GLN
P  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.129377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.103786 restraints weight = 15552.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.49
r_work: 0.3397 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   9282  Z= 0.245
  Angle     :  0.614   9.372  13477  Z= 0.361
  Chirality :  0.036   0.192   1536
  Planarity :  0.005   0.061    944
  Dihedral  : 30.405 171.379   2968
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 28.38 %
    Favored  : 66.13 %
  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:  2.68 (0.37), residues: 512
  helix:  2.46 (0.26), residues: 385
  sheet:  None (None), residues: 0
  loop : -0.43 (0.50), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS M  31 
 PHE   0.012   0.001   PHE K  78 
 TYR   0.010   0.001   TYR P  51 
 ARG   0.009   0.001   ARG M  35 

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 199
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
REVERT: K  125 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7876 (mp10)
REVERT: K  131 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8410 (mtt-85)
REVERT: L   45 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7915 (mtp-110)
REVERT: L   92 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7948 (ttm-80)
REVERT: M   61 GLU cc_start: 0.8223 (mp0) cc_final: 0.7867 (mp0)
REVERT: M   64 GLU cc_start: 0.8100 (tp30) cc_final: 0.7670 (tp30)
REVERT: M   68 ASN cc_start: 0.8343 (m-40) cc_final: 0.7488 (m-40)
REVERT: N   64 ASN cc_start: 0.8834 (m-40) cc_final: 0.8586 (m-40)
REVERT: O  120 MET cc_start: 0.7937 (mtt) cc_final: 0.7736 (mtp)
REVERT: P   31 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8471 (tptm)
  outliers start: 24
  outliers final: 13
  residues processed: 202
  average time/residue: 1.4509
  time to fit residues: 307.9844
Evaluate side-chains
  215 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 197
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  100 LEU
Chi-restraints excluded: chain K residue  124 ILE
Chi-restraints excluded: chain K residue  125 GLN
Chi-restraints excluded: chain K residue  131 ARG
Chi-restraints excluded: chain L residue   45 ARG
Chi-restraints excluded: chain L residue   92 ARG
Chi-restraints excluded: chain M residue   59 THR
Chi-restraints excluded: chain M residue  101 THR
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain N residue   33 SER
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue   68 GLU
Chi-restraints excluded: chain N residue   75 SER
Chi-restraints excluded: chain O residue   57 SER
Chi-restraints excluded: chain O residue   65 LEU
Chi-restraints excluded: chain P residue   31 LYS
Chi-restraints excluded: chain P residue   86 VAL
Chi-restraints excluded: chain P residue   90 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 60 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 39 optimal weight:    0.4980
   chunk 57 optimal weight:    0.2980
   chunk 30 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
K 108 ASN
** M  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O  55 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.129104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.103526 restraints weight = 15851.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 1.51
r_work: 0.3388 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   9282  Z= 0.260
  Angle     :  0.617   7.478  13477  Z= 0.363
  Chirality :  0.036   0.163   1536
  Planarity :  0.005   0.060    944
  Dihedral  : 30.371 170.311   2968
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 27.46 %
    Favored  : 67.51 %
  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:  2.68 (0.37), residues: 512
  helix:  2.48 (0.26), residues: 385
  sheet:  None (None), residues: 0
  loop : -0.48 (0.50), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS K 113 
 PHE   0.011   0.001   PHE K  78 
 TYR   0.011   0.001   TYR N 118 
 ARG   0.009   0.001   ARG K  72 

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 205
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
REVERT: K   72 ARG cc_start: 0.8980 (mtt-85) cc_final: 0.8627 (mtt180)
REVERT: K  125 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.7872 (mp10)
REVERT: K  131 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8393 (mtt-85)
REVERT: L   92 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7898 (ttm-80)
REVERT: M   61 GLU cc_start: 0.8241 (mp0) cc_final: 0.7890 (mp0)
REVERT: M   64 GLU cc_start: 0.8120 (tp30) cc_final: 0.7763 (tp30)
REVERT: M   68 ASN cc_start: 0.8372 (m-40) cc_final: 0.7723 (m-40)
REVERT: N   64 ASN cc_start: 0.8817 (m-40) cc_final: 0.8569 (m-40)
REVERT: O   70 LEU cc_start: 0.8891 (tp) cc_final: 0.8529 (tm)
REVERT: O  120 MET cc_start: 0.7961 (mtt) cc_final: 0.7720 (mtm)
REVERT: P   31 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8480 (tptm)
  outliers start: 22
  outliers final: 14
  residues processed: 209
  average time/residue: 1.4732
  time to fit residues: 323.5189
Evaluate side-chains
  223 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 205
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  100 LEU
Chi-restraints excluded: chain K residue  124 ILE
Chi-restraints excluded: chain K residue  125 GLN
Chi-restraints excluded: chain K residue  131 ARG
Chi-restraints excluded: chain L residue   47 SER
Chi-restraints excluded: chain L residue   92 ARG
Chi-restraints excluded: chain M residue   59 THR
Chi-restraints excluded: chain M residue  101 THR
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain N residue   33 SER
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue   68 GLU
Chi-restraints excluded: chain N residue   75 SER
Chi-restraints excluded: chain N residue   98 LEU
Chi-restraints excluded: chain O residue   57 SER
Chi-restraints excluded: chain O residue   65 LEU
Chi-restraints excluded: chain P residue   31 LYS
Chi-restraints excluded: chain P residue   86 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 34 optimal weight:    0.0870
   chunk 29 optimal weight:    0.0670
   chunk 20 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 69 optimal weight:    0.1980
   chunk 61 optimal weight:    0.4980
   chunk 57 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.2896

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

Flipped N/Q/H residues before XYZ refinement:
K 108 ASN
** M  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O  55 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.132209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.106548 restraints weight = 15878.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 1.54
r_work: 0.3429 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9282  Z= 0.201
  Angle     :  0.602  10.942  13477  Z= 0.351
  Chirality :  0.034   0.167   1536
  Planarity :  0.005   0.061    944
  Dihedral  : 30.269 173.181   2968
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 29.75 %
    Favored  : 66.13 %
  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:  2.83 (0.37), residues: 512
  helix:  2.59 (0.26), residues: 385
  sheet:  None (None), residues: 0
  loop : -0.45 (0.50), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS M  31 
 PHE   0.008   0.001   PHE K  78 
 TYR   0.010   0.001   TYR P  51 
 ARG   0.012   0.001   ARG M  20 

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 197
  time to evaluate  : 0.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  125 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7845 (mp10)
REVERT: K  131 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8372 (mtt-85)
REVERT: L   92 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7704 (ttm-80)
REVERT: M   64 GLU cc_start: 0.8088 (tp30) cc_final: 0.7687 (tp30)
REVERT: M   68 ASN cc_start: 0.8292 (m-40) cc_final: 0.7373 (m-40)
REVERT: N   64 ASN cc_start: 0.8809 (m-40) cc_final: 0.8549 (m-40)
REVERT: O  120 MET cc_start: 0.7936 (mtt) cc_final: 0.7699 (mtm)
REVERT: P   31 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8506 (tptm)
  outliers start: 18
  outliers final: 11
  residues processed: 202
  average time/residue: 1.5194
  time to fit residues: 322.3823
Evaluate side-chains
  211 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 196
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  100 LEU
Chi-restraints excluded: chain K residue  124 ILE
Chi-restraints excluded: chain K residue  125 GLN
Chi-restraints excluded: chain K residue  131 ARG
Chi-restraints excluded: chain L residue   47 SER
Chi-restraints excluded: chain L residue   92 ARG
Chi-restraints excluded: chain M residue  101 THR
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue   68 GLU
Chi-restraints excluded: chain N residue   75 SER
Chi-restraints excluded: chain O residue   57 SER
Chi-restraints excluded: chain O residue   65 LEU
Chi-restraints excluded: chain P residue   31 LYS
Chi-restraints excluded: chain P residue   86 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 69 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
K 108 ASN
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  55 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.128394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.102721 restraints weight = 15839.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.53
r_work: 0.3364 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   9282  Z= 0.321
  Angle     :  0.662  12.361  13477  Z= 0.383
  Chirality :  0.039   0.246   1536
  Planarity :  0.005   0.060    944
  Dihedral  : 30.340 168.264   2968
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 30.43 %
    Favored  : 64.99 %
  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:  2.54 (0.37), residues: 512
  helix:  2.40 (0.26), residues: 385
  sheet:  None (None), residues: 0
  loop : -0.63 (0.51), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS K 113 
 PHE   0.014   0.002   PHE K  78 
 TYR   0.011   0.001   TYR N 118 
 ARG   0.010   0.001   ARG M  35 

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 210
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
REVERT: K  125 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.7897 (mp10)
REVERT: K  131 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8404 (mtt-85)
REVERT: L   92 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7641 (ttm-80)
REVERT: M   61 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7942 (mp0)
REVERT: M   64 GLU cc_start: 0.8150 (tp30) cc_final: 0.7682 (tp30)
REVERT: M   68 ASN cc_start: 0.8417 (m-40) cc_final: 0.7565 (m-40)
REVERT: N   64 ASN cc_start: 0.8853 (m-40) cc_final: 0.8601 (m-40)
REVERT: N   76 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7880 (mtp180)
REVERT: O   70 LEU cc_start: 0.8928 (tp) cc_final: 0.8576 (tm)
REVERT: O  120 MET cc_start: 0.8003 (mtt) cc_final: 0.7716 (mtm)
REVERT: P   31 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8482 (tptm)
  outliers start: 20
  outliers final: 14
  residues processed: 214
  average time/residue: 1.4515
  time to fit residues: 326.2480
Evaluate side-chains
  228 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 209
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   90 MET
Chi-restraints excluded: chain K residue  100 LEU
Chi-restraints excluded: chain K residue  124 ILE
Chi-restraints excluded: chain K residue  125 GLN
Chi-restraints excluded: chain K residue  131 ARG
Chi-restraints excluded: chain L residue   47 SER
Chi-restraints excluded: chain L residue   92 ARG
Chi-restraints excluded: chain M residue  101 THR
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain N residue   33 SER
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue   68 GLU
Chi-restraints excluded: chain N residue   75 SER
Chi-restraints excluded: chain N residue   76 ARG
Chi-restraints excluded: chain O residue   57 SER
Chi-restraints excluded: chain O residue   65 LEU
Chi-restraints excluded: chain P residue   31 LYS
Chi-restraints excluded: chain P residue   86 VAL
Chi-restraints excluded: chain P residue   90 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 60 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 44 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0980
   chunk 47 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
K 108 ASN
** M  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  55 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.129209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.103687 restraints weight = 15705.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 1.51
r_work: 0.3389 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   9282  Z= 0.263
  Angle     :  0.641  12.725  13477  Z= 0.371
  Chirality :  0.037   0.222   1536
  Planarity :  0.005   0.063    944
  Dihedral  : 30.301 170.326   2968
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 30.66 %
    Favored  : 64.76 %
  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:  2.61 (0.37), residues: 512
  helix:  2.47 (0.26), residues: 385
  sheet:  None (None), residues: 0
  loop : -0.66 (0.50), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS M  31 
 PHE   0.011   0.001   PHE K  78 
 TYR   0.009   0.001   TYR N 118 
 ARG   0.011   0.001   ARG M  35 

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 203
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  125 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7841 (mp10)
REVERT: K  131 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8406 (mtt-85)
REVERT: L   92 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7579 (ttm-80)
REVERT: M   61 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7924 (mp0)
REVERT: M   64 GLU cc_start: 0.8118 (tp30) cc_final: 0.7676 (tp30)
REVERT: M   68 ASN cc_start: 0.8386 (m-40) cc_final: 0.7535 (m-40)
REVERT: N   64 ASN cc_start: 0.8823 (m-40) cc_final: 0.8568 (m-40)
REVERT: N   76 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7863 (mtp180)
REVERT: O   70 LEU cc_start: 0.8908 (tp) cc_final: 0.8582 (tm)
REVERT: O  116 ARG cc_start: 0.8682 (ttp80) cc_final: 0.8245 (ttp80)
REVERT: O  120 MET cc_start: 0.7962 (mtt) cc_final: 0.7557 (mtm)
REVERT: P   31 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8478 (tptm)
  outliers start: 20
  outliers final: 13
  residues processed: 208
  average time/residue: 1.4739
  time to fit residues: 321.8833
Evaluate side-chains
  220 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 202
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   90 MET
Chi-restraints excluded: chain K residue  100 LEU
Chi-restraints excluded: chain K residue  124 ILE
Chi-restraints excluded: chain K residue  125 GLN
Chi-restraints excluded: chain K residue  131 ARG
Chi-restraints excluded: chain L residue   47 SER
Chi-restraints excluded: chain L residue   92 ARG
Chi-restraints excluded: chain M residue  101 THR
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain N residue   33 SER
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue   68 GLU
Chi-restraints excluded: chain N residue   75 SER
Chi-restraints excluded: chain N residue   76 ARG
Chi-restraints excluded: chain O residue   57 SER
Chi-restraints excluded: chain O residue   65 LEU
Chi-restraints excluded: chain P residue   31 LYS
Chi-restraints excluded: chain P residue   86 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 67 optimal weight:    0.0970
   chunk 27 optimal weight:    0.9980
   chunk 58 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9990
   chunk 60 optimal weight:    0.5980
   chunk 62 optimal weight:    0.5980
   chunk 50 optimal weight:    0.4980
   chunk 64 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0670
   chunk 9 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.3316

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

Flipped N/Q/H residues before XYZ refinement:
K 108 ASN
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  31 HIS ** 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 = 0.3938 r_free = 0.3938 target = 0.130300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.104742 restraints weight = 15840.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 1.52
r_work: 0.3407 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9282  Z= 0.212
  Angle     :  0.632  12.382  13477  Z= 0.365
  Chirality :  0.036   0.211   1536
  Planarity :  0.006   0.074    944
  Dihedral  : 30.307 171.384   2968
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 31.58 %
    Favored  : 64.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.71 (0.37), residues: 512
  helix:  2.54 (0.26), residues: 385
  sheet:  None (None), residues: 0
  loop : -0.62 (0.50), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS M  31 
 PHE   0.014   0.001   PHE K  78 
 TYR   0.011   0.001   TYR P  51 
 ARG   0.011   0.001   ARG M  35 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8363.16 seconds
wall clock time: 147 minutes 35.02 seconds (8855.02 seconds total)