Starting phenix.real_space_refine
on Tue Jun 10 09:22:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k41_62038/06_2025/9k41_62038.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k41_62038/06_2025/9k41_62038.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k41_62038/06_2025/9k41_62038.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k41_62038/06_2025/9k41_62038.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k41_62038/06_2025/9k41_62038.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k41_62038/06_2025/9k41_62038.cif"
  }
  resolution = 2.81
  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=  -0.002 sd=   0.052
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     289      5.49       5
     S      14      5.16       5
     C    6585      2.51       5
     N    2168      2.21       5
     O    2772      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 11828
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 783
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 644
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 785
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 783
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 644
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 785
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "H"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2950
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2992
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 6.91, per 1000 atoms: 0.58
  Number of scatterers: 11828
  At special positions: 0
  Unit cell: (121.136, 75.04, 114.704, 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      14     16.00
     P     289     15.00
     O    2772      8.00
     N    2168      7.00
     C    6585      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: 2.67
  Conformation dependent library (CDL) restraints added in 881.1 milliseconds
  

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1388

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 10 sheets defined
      72.3% alpha, 3.2% beta
      145 base pairs and 259 stacking pairs defined.
    Time for finding SS restraints: 5.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.559A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.677A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.644A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 25 through 31
      removed outlier: 3.546A  pdb=" N   ALA C  30 " --> pdb=" O   LYS C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 46
    Processing helix  chain 'C' and resid 55 through 82
    Processing helix  chain 'C' and resid 88 through 99
    Processing helix  chain 'C' and resid 99 through 106
    Processing helix  chain 'D' and resid 60 through 72
    Processing helix  chain 'D' and resid 78 through 107
    Processing helix  chain 'D' and resid 113 through 125
    Processing helix  chain 'D' and resid 127 through 147
    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 131
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.687A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.598A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 25 through 31
    Processing helix  chain 'G' and resid 35 through 46
    Processing helix  chain 'G' and resid 55 through 82
    Processing helix  chain 'G' and resid 88 through 98
    Processing helix  chain 'G' and resid 99 through 106
    Processing helix  chain 'H' and resid 60 through 72
    Processing helix  chain 'H' and resid 78 through 107
    Processing helix  chain 'H' and resid 113 through 125
    Processing helix  chain 'H' and resid 126 through 147
      removed outlier: 3.528A  pdb=" N   ALA H 130 " --> pdb=" O   PRO H 126 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.044A  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: 6.439A  pdb=" N   THR B  96 " --> pdb=" O   THR G 110 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 51 through 52
      removed outlier: 7.447A  pdb=" N   ARG C  51 " --> pdb=" O   ILE D 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 86 through 87
    Processing sheet with id=AA6, first strand: chain 'C' and resid 109 through 111
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.111A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 51 through 52
      removed outlier: 7.241A  pdb=" N   ARG G  51 " --> pdb=" O   ILE H 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 86 through 87

    405 hydrogen bonds defined for protein.
    1206 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      348 hydrogen bonds
      696 hydrogen bond angles
      0 basepair planarities
      145 basepair parallelities
      259 stacking parallelities
  Total time for adding SS restraints: 4.42

  Time building geometry restraints manager: 3.26 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2177
        1.33 -     1.45: 4095
        1.45 -     1.57: 5758
        1.57 -     1.69: 577
        1.69 -     1.81: 26
  Bond restraints: 12633
  Sorted by residual:
  bond pdb=" O3'  DC J -26 "
       pdb=" P    DA J -25 "
    ideal  model  delta    sigma   weight residual
    1.607  1.653 -0.046 1.50e-02 4.44e+03 9.38e+00
  bond pdb=" O3'  DA I  -9 "
       pdb=" P    DA I  -8 "
    ideal  model  delta    sigma   weight residual
    1.607  1.642 -0.035 1.50e-02 4.44e+03 5.56e+00
  bond pdb=" O3'  DC I  -6 "
       pdb=" P    DA I  -5 "
    ideal  model  delta    sigma   weight residual
    1.607  1.640 -0.033 1.50e-02 4.44e+03 4.78e+00
  bond pdb=" CA  ILE F  26 "
       pdb=" CB  ILE F  26 "
    ideal  model  delta    sigma   weight residual
    1.538  1.553 -0.015 1.37e-02 5.33e+03 1.25e+00
  bond pdb=" N   ASP B  24 "
       pdb=" CA  ASP B  24 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.014 1.29e-02 6.01e+03 1.22e+00
  ... (remaining 12628 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 17094
        1.03 -     2.07: 911
        2.07 -     3.10: 261
        3.10 -     4.13: 20
        4.13 -     5.17: 13
  Bond angle restraints: 18299
  Sorted by residual:
  angle pdb=" N   ASN B  25 "
        pdb=" CA  ASN B  25 "
        pdb=" C   ASN B  25 "
      ideal   model   delta    sigma   weight residual
     113.20  109.14    4.06 1.21e+00 6.83e-01 1.12e+01
  angle pdb=" N   ASP F  24 "
        pdb=" CA  ASP F  24 "
        pdb=" C   ASP F  24 "
      ideal   model   delta    sigma   weight residual
     111.17  115.78   -4.61 1.41e+00 5.03e-01 1.07e+01
  angle pdb=" O3'  DG J -27 "
        pdb=" C3'  DG J -27 "
        pdb=" C2'  DG J -27 "
      ideal   model   delta    sigma   weight residual
     111.50  106.84    4.66 1.50e+00 4.44e-01 9.67e+00
  angle pdb=" O3'  DA I  -8 "
        pdb=" C3'  DA I  -8 "
        pdb=" C2'  DA I  -8 "
      ideal   model   delta    sigma   weight residual
     111.50  106.95    4.55 1.50e+00 4.44e-01 9.22e+00
  angle pdb=" O3'  DC J -26 "
        pdb=" C3'  DC J -26 "
        pdb=" C2'  DC J -26 "
      ideal   model   delta    sigma   weight residual
     111.50  107.12    4.38 1.50e+00 4.44e-01 8.52e+00
  ... (remaining 18294 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.84: 4451
       20.84 -    41.69: 1347
       41.69 -    62.53: 1084
       62.53 -    83.38: 50
       83.38 -   104.22: 3
  Dihedral angle restraints: 6935
    sinusoidal: 4785
      harmonic: 2150
  Sorted by residual:
  dihedral pdb=" CA  PRO H 126 "
           pdb=" C   PRO H 126 "
           pdb=" N   GLY H 127 "
           pdb=" CA  GLY H 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.93   16.07     0      5.00e+00 4.00e-02 1.03e+01
  dihedral pdb=" CG  ARG A  49 "
           pdb=" CD  ARG A  49 "
           pdb=" NE  ARG A  49 "
           pdb=" CZ  ARG A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  132.97  -42.97     2      1.50e+01 4.44e-03 9.91e+00
  dihedral pdb=" C4'  DG J -17 "
           pdb=" C3'  DG J -17 "
           pdb=" O3'  DG J -17 "
           pdb=" P    DC J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00  -35.78 -104.22     1      3.50e+01 8.16e-04 9.76e+00
  ... (remaining 6932 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1640
       0.040 -    0.079: 364
       0.079 -    0.119: 68
       0.119 -    0.158: 11
       0.158 -    0.198: 4
  Chirality restraints: 2087
  Sorted by residual:
  chirality pdb=" C3'  DA I  -8 "
            pdb=" C4'  DA I  -8 "
            pdb=" O3'  DA I  -8 "
            pdb=" C2'  DA I  -8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.86    0.20 2.00e-01 2.50e+01 9.76e-01
  chirality pdb=" CA  ASP F  24 "
            pdb=" N   ASP F  24 "
            pdb=" C   ASP F  24 "
            pdb=" CB  ASP F  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.19e-01
  chirality pdb=" C3'  DG J -27 "
            pdb=" C4'  DG J -27 "
            pdb=" O3'  DG J -27 "
            pdb=" C2'  DG J -27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.85    0.19 2.00e-01 2.50e+01 8.99e-01
  ... (remaining 2084 not shown)

  Planarity restraints: 1304
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H 125 "    0.027 5.00e-02 4.00e+02   4.05e-02 2.63e+00
        pdb=" N   PRO H 126 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO H 126 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO H 126 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  44 "    0.011 2.00e-02 2.50e+03   1.07e-02 2.60e+00
        pdb=" N1   DC J  44 "   -0.013 2.00e-02 2.50e+03
        pdb=" C2   DC J  44 "    0.021 2.00e-02 2.50e+03
        pdb=" O2   DC J  44 "   -0.014 2.00e-02 2.50e+03
        pdb=" N3   DC J  44 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DC J  44 "    0.008 2.00e-02 2.50e+03
        pdb=" N4   DC J  44 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5   DC J  44 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DC J  44 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 125 "   -0.025 5.00e-02 4.00e+02   3.79e-02 2.29e+00
        pdb=" N   PRO D 126 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO D 126 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 126 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1301 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1308
        2.75 -     3.29: 10382
        3.29 -     3.82: 23519
        3.82 -     4.36: 27964
        4.36 -     4.90: 39816
  Nonbonded interactions: 102989
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS D  55 "
            pdb=" OP1  DT I -46 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" NH2 ARG G  41 "
            pdb=" OE1 GLU H  58 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" O   SER G  85 "
            pdb=" OG  SER G  85 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH1 ARG A 131 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH1 ARG E 131 "
     model   vdw
     2.309 3.120
  ... (remaining 102984 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=0.00 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:             1.100
  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:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     31.740
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.060
  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:13.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
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      :  0.004   0.046  12633  Z= 0.179
  Angle     :  0.561   5.167  18299  Z= 0.350
  Chirality :  0.036   0.198   2087
  Planarity :  0.004   0.041   1304
  Dihedral  : 28.881 104.221   5547
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 22.99 %
    Favored  : 75.72 %
  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:  1.93 (0.30), residues: 730
  helix:  1.71 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop :  0.08 (0.42), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 113 
 PHE   0.006   0.001   PHE C  34 
 TYR   0.010   0.002   TYR B  98 
 ARG   0.004   0.000   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12474 (  753)
  hydrogen bonds       : angle       4.65008 ( 1902)
  covalent geometry    : bond        0.00384 (12633)
  covalent geometry    : angle       0.56064 (18299)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 144
  time to evaluate  : 0.842 
Fit side-chains
REVERT: C   99 ASP cc_start: 0.8819 (t70) cc_final: 0.7585 (t0)
REVERT: C  121 ASN cc_start: 0.9301 (t0) cc_final: 0.8789 (t0)
REVERT: D   82 MET cc_start: 0.9307 (tpt) cc_final: 0.9096 (mmm)
REVERT: D   91 ASP cc_start: 0.9111 (t70) cc_final: 0.8801 (t0)
REVERT: G   81 ASP cc_start: 0.8985 (m-30) cc_final: 0.8775 (m-30)
REVERT: G   99 ASP cc_start: 0.8900 (t70) cc_final: 0.8635 (t0)
REVERT: G  121 ASN cc_start: 0.9264 (t0) cc_final: 0.8854 (t0)
REVERT: H   58 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8145 (mm-30)
REVERT: H   91 ASP cc_start: 0.9098 (t0) cc_final: 0.8782 (t0)
REVERT: H  128 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8131 (tm-30)
  outliers start: 8
  outliers final: 0
  residues processed: 148
  average time/residue: 1.6711
  time to fit residues: 262.0524
Evaluate side-chains
  110 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 75 optimal weight:    6.9990
   chunk 42 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 78 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 47 optimal weight:    4.9990
   chunk 58 optimal weight:    9.9990
   chunk 90 optimal weight:    6.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A 108 ASN
A 113 HIS
B  25 ASN
B  27 GLN
B  75 HIS
C  33 GLN
C  82 ASN
D  56 ASN
E  68 GLN
E 108 ASN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  75 HIS
G  33 GLN
G  77 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.054460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.038214 restraints weight = 52631.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 1.90
r_work: 0.2757 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8752
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12633  Z= 0.160
  Angle     :  0.567   8.134  18299  Z= 0.344
  Chirality :  0.033   0.128   2087
  Planarity :  0.004   0.038   1304
  Dihedral  : 30.984  99.735   4071
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 22.99 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.90 (0.31), residues: 730
  helix:  2.49 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.03 (0.44), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.006   0.001   PHE E  67 
 TYR   0.011   0.001   TYR H  63 
 ARG   0.007   0.001   ARG D 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04079 (  753)
  hydrogen bonds       : angle       2.76197 ( 1902)
  covalent geometry    : bond        0.00346 (12633)
  covalent geometry    : angle       0.56723 (18299)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
REVERT: B   50 ILE cc_start: 0.9426 (mm) cc_final: 0.9176 (mp)
REVERT: C   99 ASP cc_start: 0.8689 (t70) cc_final: 0.7715 (t70)
REVERT: C  101 GLU cc_start: 0.8220 (pm20) cc_final: 0.7657 (pm20)
REVERT: C  121 ASN cc_start: 0.9268 (OUTLIER) cc_final: 0.8680 (t0)
REVERT: D   82 MET cc_start: 0.9410 (tpt) cc_final: 0.9146 (mmm)
REVERT: D   91 ASP cc_start: 0.9346 (t70) cc_final: 0.8958 (t0)
REVERT: D   94 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8721 (tp30)
REVERT: D  128 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8261 (tp30)
REVERT: G   81 ASP cc_start: 0.9181 (m-30) cc_final: 0.8924 (m-30)
REVERT: G   99 ASP cc_start: 0.9181 (t70) cc_final: 0.8630 (t0)
REVERT: G  121 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8679 (t0)
REVERT: H   58 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8383 (mm-30)
REVERT: H   91 ASP cc_start: 0.9273 (t0) cc_final: 0.8887 (t0)
REVERT: H   94 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8463 (tm-30)
REVERT: H  128 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8291 (tm-30)
  outliers start: 11
  outliers final: 3
  residues processed: 140
  average time/residue: 1.5502
  time to fit residues: 230.6444
Evaluate side-chains
  120 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 115
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 62 optimal weight:    0.0370
   chunk 23 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   chunk 93 optimal weight:    4.9990
   chunk 68 optimal weight:    0.8980
   chunk 85 optimal weight:   10.0000
   chunk 84 optimal weight:    7.9990
   chunk 77 optimal weight:    6.9990
   overall best weight:    1.3460

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

Flipped N/Q/H residues before XYZ refinement:
D  56 ASN
E 113 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.053538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.037528 restraints weight = 53205.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 1.91
r_work: 0.2728 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8789
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12633  Z= 0.165
  Angle     :  0.561   8.369  18299  Z= 0.339
  Chirality :  0.033   0.122   2087
  Planarity :  0.004   0.036   1304
  Dihedral  : 31.087  93.701   4071
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 22.83 %
    Favored  : 75.40 %
  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:  3.29 (0.31), residues: 730
  helix:  2.79 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.10 (0.45), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B  75 
 PHE   0.006   0.001   PHE C  34 
 TYR   0.009   0.001   TYR H  63 
 ARG   0.007   0.000   ARG H 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03896 (  753)
  hydrogen bonds       : angle       2.62099 ( 1902)
  covalent geometry    : bond        0.00361 (12633)
  covalent geometry    : angle       0.56077 (18299)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 1.003 
Fit side-chains
REVERT: C   99 ASP cc_start: 0.8711 (t70) cc_final: 0.7806 (t70)
REVERT: C  101 GLU cc_start: 0.8264 (pm20) cc_final: 0.7541 (pm20)
REVERT: C  121 ASN cc_start: 0.9230 (OUTLIER) cc_final: 0.8694 (t0)
REVERT: D   82 MET cc_start: 0.9492 (tpt) cc_final: 0.9159 (mmm)
REVERT: D   91 ASP cc_start: 0.9359 (t70) cc_final: 0.8992 (t0)
REVERT: D   94 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8552 (tm-30)
REVERT: D  106 TYR cc_start: 0.8821 (m-10) cc_final: 0.8393 (m-80)
REVERT: D  128 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8362 (tp30)
REVERT: F   92 ARG cc_start: 0.9447 (OUTLIER) cc_final: 0.9207 (mtp-110)
REVERT: G   99 ASP cc_start: 0.9196 (t70) cc_final: 0.8687 (t0)
REVERT: G  121 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8631 (t0)
REVERT: H   58 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8329 (mm-30)
REVERT: H   91 ASP cc_start: 0.9304 (t0) cc_final: 0.8927 (t0)
REVERT: H   94 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8474 (tm-30)
REVERT: H  128 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8326 (tm-30)
  outliers start: 11
  outliers final: 5
  residues processed: 132
  average time/residue: 1.7887
  time to fit residues: 249.6715
Evaluate side-chains
  119 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 19 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 93 optimal weight:    4.9990
   chunk 94 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 66 optimal weight:    5.9990
   chunk 78 optimal weight:    4.9990
   chunk 17 optimal weight:   10.0000
   overall best weight:    3.9388

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
D 107 ASN
E  39 HIS
F  25 ASN
G  82 ASN
H 107 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.049056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.033368 restraints weight = 53312.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.2749 rms_B_bonded: 1.92
r_work: 0.2580 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8916
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042  12633  Z= 0.315
  Angle     :  0.661   9.741  18299  Z= 0.387
  Chirality :  0.038   0.133   2087
  Planarity :  0.004   0.036   1304
  Dihedral  : 32.123  96.438   4071
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 23.95 %
    Favored  : 73.95 %
  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:  2.95 (0.32), residues: 730
  helix:  2.56 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.08 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.008   0.001   PHE D  65 
 TYR   0.011   0.002   TYR F  51 
 ARG   0.006   0.001   ARG D 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06158 (  753)
  hydrogen bonds       : angle       3.11330 ( 1902)
  covalent geometry    : bond        0.00708 (12633)
  covalent geometry    : angle       0.66106 (18299)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.973 
Fit side-chains
REVERT: A  115 LYS cc_start: 0.9538 (OUTLIER) cc_final: 0.9283 (mtpp)
REVERT: C   99 ASP cc_start: 0.9019 (t70) cc_final: 0.7944 (t0)
REVERT: C  101 GLU cc_start: 0.8313 (pm20) cc_final: 0.7663 (pm20)
REVERT: C  121 ASN cc_start: 0.9338 (OUTLIER) cc_final: 0.8812 (t0)
REVERT: D   82 MET cc_start: 0.9494 (tpt) cc_final: 0.9083 (mmm)
REVERT: D   91 ASP cc_start: 0.9375 (t70) cc_final: 0.9027 (t0)
REVERT: D   94 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8554 (tm-30)
REVERT: D  106 TYR cc_start: 0.8811 (m-10) cc_final: 0.8413 (m-80)
REVERT: D  128 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8506 (tp30)
REVERT: E  115 LYS cc_start: 0.9537 (OUTLIER) cc_final: 0.9285 (mtpp)
REVERT: G   99 ASP cc_start: 0.9222 (t70) cc_final: 0.8755 (t0)
REVERT: G  121 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.8696 (t0)
REVERT: H   58 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8477 (mm-30)
REVERT: H   91 ASP cc_start: 0.9349 (t0) cc_final: 0.8989 (t0)
REVERT: H   94 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8562 (tm-30)
REVERT: H  128 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8462 (tm-30)
  outliers start: 13
  outliers final: 4
  residues processed: 122
  average time/residue: 1.8088
  time to fit residues: 233.2673
Evaluate side-chains
  113 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 44 optimal weight:    0.5980
   chunk 53 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
C  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.050243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.034598 restraints weight = 52707.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.2802 rms_B_bonded: 1.88
r_work: 0.2640 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8868
moved from start:          0.3140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12633  Z= 0.191
  Angle     :  0.592   9.176  18299  Z= 0.354
  Chirality :  0.034   0.123   2087
  Planarity :  0.004   0.036   1304
  Dihedral  : 31.471  95.888   4071
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 24.12 %
    Favored  : 74.28 %
  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:  3.21 (0.31), residues: 730
  helix:  2.76 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.04 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D  72 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.009   0.001   TYR F  88 
 ARG   0.005   0.000   ARG D 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04174 (  753)
  hydrogen bonds       : angle       2.67936 ( 1902)
  covalent geometry    : bond        0.00426 (12633)
  covalent geometry    : angle       0.59168 (18299)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
REVERT: C   28 MET cc_start: 0.9221 (ptt) cc_final: 0.8903 (ppp)
REVERT: C   99 ASP cc_start: 0.8849 (t70) cc_final: 0.7771 (t0)
REVERT: C  101 GLU cc_start: 0.8253 (pm20) cc_final: 0.7712 (pm20)
REVERT: C  121 ASN cc_start: 0.9259 (OUTLIER) cc_final: 0.8757 (t0)
REVERT: D   82 MET cc_start: 0.9547 (tpt) cc_final: 0.9203 (mmm)
REVERT: D   91 ASP cc_start: 0.9351 (t70) cc_final: 0.8983 (t0)
REVERT: D   94 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8629 (tm-30)
REVERT: D  106 TYR cc_start: 0.8771 (m-10) cc_final: 0.8347 (m-80)
REVERT: D  128 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8417 (tp30)
REVERT: E   80 THR cc_start: 0.9505 (m) cc_final: 0.9304 (p)
REVERT: G   99 ASP cc_start: 0.9252 (t70) cc_final: 0.8773 (t0)
REVERT: G  121 ASN cc_start: 0.9195 (OUTLIER) cc_final: 0.8690 (t0)
REVERT: H   58 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8297 (mm-30)
REVERT: H   91 ASP cc_start: 0.9312 (t0) cc_final: 0.8931 (t0)
REVERT: H   94 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8548 (tm-30)
REVERT: H  128 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8392 (tm-30)
  outliers start: 10
  outliers final: 4
  residues processed: 123
  average time/residue: 1.7253
  time to fit residues: 224.7048
Evaluate side-chains
  116 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 76 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 85 optimal weight:   10.0000
   chunk 14 optimal weight:    6.9990
   chunk 46 optimal weight:    0.7980
   chunk 66 optimal weight:    5.9990
   chunk 78 optimal weight:    5.9990
   overall best weight:    1.3386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.051266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.035248 restraints weight = 53937.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.2833 rms_B_bonded: 1.96
r_work: 0.2672 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8844
moved from start:          0.3390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12633  Z= 0.166
  Angle     :  0.587  10.936  18299  Z= 0.348
  Chirality :  0.033   0.120   2087
  Planarity :  0.004   0.035   1304
  Dihedral  : 31.168  92.855   4071
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 25.24 %
    Favored  : 73.31 %
  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:  3.36 (0.31), residues: 730
  helix:  2.86 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.04 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.006   0.001   PHE A  67 
 TYR   0.009   0.001   TYR H  63 
 ARG   0.009   0.000   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03793 (  753)
  hydrogen bonds       : angle       2.55545 ( 1902)
  covalent geometry    : bond        0.00369 (12633)
  covalent geometry    : angle       0.58687 (18299)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
REVERT: C   28 MET cc_start: 0.9198 (ptt) cc_final: 0.8927 (ppp)
REVERT: C   99 ASP cc_start: 0.8809 (t70) cc_final: 0.7749 (t0)
REVERT: C  101 GLU cc_start: 0.8175 (pm20) cc_final: 0.7730 (pm20)
REVERT: C  121 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8726 (t0)
REVERT: D   91 ASP cc_start: 0.9391 (t70) cc_final: 0.9023 (t0)
REVERT: D   94 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8592 (tm-30)
REVERT: D  106 TYR cc_start: 0.8796 (m-10) cc_final: 0.8397 (m-80)
REVERT: D  128 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8366 (tp30)
REVERT: E  122 LYS cc_start: 0.9191 (ptpp) cc_final: 0.8963 (ptmm)
REVERT: G   99 ASP cc_start: 0.9224 (t70) cc_final: 0.8593 (t0)
REVERT: G  121 ASN cc_start: 0.9135 (OUTLIER) cc_final: 0.8637 (t0)
REVERT: H   58 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8346 (mm-30)
REVERT: H   91 ASP cc_start: 0.9324 (t0) cc_final: 0.8950 (t0)
REVERT: H   94 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8556 (tm-30)
REVERT: H  128 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8378 (tm-30)
  outliers start: 9
  outliers final: 3
  residues processed: 125
  average time/residue: 1.7932
  time to fit residues: 237.1444
Evaluate side-chains
  115 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 110
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 74 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 96 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 73 optimal weight:   10.0000
   overall best weight:    2.1986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.050261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.034181 restraints weight = 53868.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.2795 rms_B_bonded: 1.95
r_work: 0.2633 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8878
moved from start:          0.3503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  12633  Z= 0.207
  Angle     :  0.607  11.434  18299  Z= 0.357
  Chirality :  0.034   0.151   2087
  Planarity :  0.004   0.035   1304
  Dihedral  : 31.377  91.891   4071
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 26.21 %
    Favored  : 72.35 %
  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:  3.28 (0.31), residues: 730
  helix:  2.82 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.07 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.008   0.001   PHE E  78 
 TYR   0.012   0.002   TYR B  88 
 ARG   0.007   0.000   ARG H 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04300 (  753)
  hydrogen bonds       : angle       2.70515 ( 1902)
  covalent geometry    : bond        0.00465 (12633)
  covalent geometry    : angle       0.60738 (18299)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 1.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   99 ASP cc_start: 0.8886 (t70) cc_final: 0.7775 (t0)
REVERT: C  101 GLU cc_start: 0.8256 (pm20) cc_final: 0.7755 (pm20)
REVERT: C  121 ASN cc_start: 0.9205 (OUTLIER) cc_final: 0.8734 (t0)
REVERT: D   82 MET cc_start: 0.9547 (tpt) cc_final: 0.9070 (mmm)
REVERT: D   91 ASP cc_start: 0.9391 (t70) cc_final: 0.9040 (t0)
REVERT: D   94 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8610 (tm-30)
REVERT: D  128 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8470 (tp30)
REVERT: G   99 ASP cc_start: 0.9259 (t70) cc_final: 0.8841 (t0)
REVERT: G  121 ASN cc_start: 0.9163 (OUTLIER) cc_final: 0.8660 (t0)
REVERT: H   58 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8535 (mm-30)
REVERT: H   91 ASP cc_start: 0.9338 (t0) cc_final: 0.8964 (t0)
REVERT: H   94 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8579 (tm-30)
REVERT: H  128 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8407 (tm-30)
  outliers start: 9
  outliers final: 5
  residues processed: 121
  average time/residue: 2.5056
  time to fit residues: 321.1751
Evaluate side-chains
  118 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 111
  time to evaluate  : 2.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 74 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   chunk 98 optimal weight:    6.9990
   chunk 90 optimal weight:    6.9990
   chunk 95 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    2.9788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.049198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.033334 restraints weight = 54403.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.2757 rms_B_bonded: 1.91
r_work: 0.2596 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8902
moved from start:          0.3760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037  12633  Z= 0.251
  Angle     :  0.639  10.845  18299  Z= 0.372
  Chirality :  0.036   0.144   2087
  Planarity :  0.004   0.035   1304
  Dihedral  : 31.660  93.859   4071
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 25.40 %
    Favored  : 72.83 %
  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:  3.16 (0.31), residues: 730
  helix:  2.76 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.20 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.006   0.001   PHE G  34 
 TYR   0.014   0.002   TYR F  88 
 ARG   0.007   0.000   ARG C  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04847 (  753)
  hydrogen bonds       : angle       2.78055 ( 1902)
  covalent geometry    : bond        0.00568 (12633)
  covalent geometry    : angle       0.63883 (18299)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
REVERT: C   99 ASP cc_start: 0.8966 (t70) cc_final: 0.7871 (t0)
REVERT: C  101 GLU cc_start: 0.8239 (pm20) cc_final: 0.7831 (pm20)
REVERT: C  121 ASN cc_start: 0.9254 (OUTLIER) cc_final: 0.8739 (t0)
REVERT: D   91 ASP cc_start: 0.9370 (t70) cc_final: 0.9005 (t0)
REVERT: D   94 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8613 (tm-30)
REVERT: D  106 TYR cc_start: 0.8817 (m-10) cc_final: 0.8354 (m-80)
REVERT: D  128 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8487 (tp30)
REVERT: G   99 ASP cc_start: 0.9240 (t70) cc_final: 0.8788 (t0)
REVERT: G  121 ASN cc_start: 0.9223 (OUTLIER) cc_final: 0.8689 (t0)
REVERT: H   58 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8528 (mm-30)
REVERT: H   91 ASP cc_start: 0.9330 (t0) cc_final: 0.8966 (t0)
REVERT: H   94 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8567 (tm-30)
REVERT: H  106 TYR cc_start: 0.8753 (m-10) cc_final: 0.8449 (m-80)
REVERT: H  128 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8434 (tm-30)
  outliers start: 11
  outliers final: 6
  residues processed: 121
  average time/residue: 2.5919
  time to fit residues: 333.8221
Evaluate side-chains
  117 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 2.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 83 optimal weight:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 75 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 96 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    2.9988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.048953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.033276 restraints weight = 54260.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.2755 rms_B_bonded: 1.90
r_work: 0.2591 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8902
moved from start:          0.3982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038  12633  Z= 0.250
  Angle     :  0.643  12.315  18299  Z= 0.374
  Chirality :  0.036   0.146   2087
  Planarity :  0.004   0.034   1304
  Dihedral  : 31.678  95.693   4071
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 25.56 %
    Favored  : 72.67 %
  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:  3.19 (0.31), residues: 730
  helix:  2.78 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.19 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.009   0.001   PHE E  78 
 TYR   0.018   0.002   TYR F  88 
 ARG   0.007   0.000   ARG C  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04694 (  753)
  hydrogen bonds       : angle       2.75647 ( 1902)
  covalent geometry    : bond        0.00565 (12633)
  covalent geometry    : angle       0.64329 (18299)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
REVERT: C   99 ASP cc_start: 0.9009 (t70) cc_final: 0.7899 (t0)
REVERT: C  101 GLU cc_start: 0.8255 (pm20) cc_final: 0.7747 (pm20)
REVERT: C  121 ASN cc_start: 0.9256 (OUTLIER) cc_final: 0.8748 (t0)
REVERT: D   91 ASP cc_start: 0.9356 (t70) cc_final: 0.9009 (t0)
REVERT: D   94 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8618 (tm-30)
REVERT: D  106 TYR cc_start: 0.8815 (m-10) cc_final: 0.8342 (m-80)
REVERT: D  128 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8478 (tp30)
REVERT: G   99 ASP cc_start: 0.9247 (t70) cc_final: 0.8818 (t0)
REVERT: G  121 ASN cc_start: 0.9237 (OUTLIER) cc_final: 0.8685 (t0)
REVERT: H   58 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8532 (mm-30)
REVERT: H   91 ASP cc_start: 0.9338 (t0) cc_final: 0.8978 (t0)
REVERT: H   94 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8566 (tm-30)
REVERT: H  106 TYR cc_start: 0.8739 (m-10) cc_final: 0.8500 (m-80)
REVERT: H  128 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8422 (tm-30)
  outliers start: 11
  outliers final: 6
  residues processed: 118
  average time/residue: 1.6767
  time to fit residues: 210.2447
Evaluate side-chains
  114 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    1.6984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.049699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.034057 restraints weight = 53307.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.2785 rms_B_bonded: 1.88
r_work: 0.2625 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8877
moved from start:          0.4047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12633  Z= 0.182
  Angle     :  0.625  12.297  18299  Z= 0.364
  Chirality :  0.034   0.132   2087
  Planarity :  0.004   0.035   1304
  Dihedral  : 31.452  95.093   4071
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 26.05 %
    Favored  : 72.67 %
  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:  3.27 (0.31), residues: 730
  helix:  2.84 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.17 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.017   0.002   TYR F  88 
 ARG   0.008   0.000   ARG D 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03819 (  753)
  hydrogen bonds       : angle       2.62244 ( 1902)
  covalent geometry    : bond        0.00410 (12633)
  covalent geometry    : angle       0.62452 (18299)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   99 ASP cc_start: 0.8865 (t70) cc_final: 0.7827 (t0)
REVERT: C  101 GLU cc_start: 0.8279 (pm20) cc_final: 0.7874 (pm20)
REVERT: C  121 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.8746 (t0)
REVERT: D   82 MET cc_start: 0.9489 (tpt) cc_final: 0.9232 (mmm)
REVERT: D   91 ASP cc_start: 0.9345 (t70) cc_final: 0.8986 (t0)
REVERT: D   94 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8594 (tm-30)
REVERT: D  106 TYR cc_start: 0.8806 (m-10) cc_final: 0.8339 (m-80)
REVERT: D  128 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8495 (tp30)
REVERT: G   99 ASP cc_start: 0.9238 (t70) cc_final: 0.8834 (t0)
REVERT: G  121 ASN cc_start: 0.9214 (OUTLIER) cc_final: 0.8691 (t0)
REVERT: H   58 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8556 (mm-30)
REVERT: H   91 ASP cc_start: 0.9309 (t0) cc_final: 0.8947 (t0)
REVERT: H   94 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8566 (tm-30)
REVERT: H  128 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8398 (tm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 118
  average time/residue: 1.7100
  time to fit residues: 214.6124
Evaluate side-chains
  116 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 81 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 88 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   chunk 91 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    1.1786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.049965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.034411 restraints weight = 53548.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.2799 rms_B_bonded: 1.88
r_work: 0.2640 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.4048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12633  Z= 0.165
  Angle     :  0.622  13.326  18299  Z= 0.362
  Chirality :  0.034   0.138   2087
  Planarity :  0.004   0.035   1304
  Dihedral  : 31.418  94.905   4071
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 25.72 %
    Favored  : 72.51 %
  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:  3.27 (0.31), residues: 730
  helix:  2.83 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.13 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B  75 
 PHE   0.007   0.001   PHE E  67 
 TYR   0.021   0.001   TYR B  88 
 ARG   0.007   0.000   ARG D 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03746 (  753)
  hydrogen bonds       : angle       2.57695 ( 1902)
  covalent geometry    : bond        0.00369 (12633)
  covalent geometry    : angle       0.62217 (18299)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7946.21 seconds
wall clock time: 140 minutes 34.38 seconds (8434.38 seconds total)