Starting phenix.real_space_refine
on Tue Jun 10 08:30:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k42_62040/06_2025/9k42_62040.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k42_62040/06_2025/9k42_62040.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k42_62040/06_2025/9k42_62040.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k42_62040/06_2025/9k42_62040.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k42_62040/06_2025/9k42_62040.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k42_62040/06_2025/9k42_62040.cif"
  }
  resolution = 3.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.043
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      12      5.16       5
     C    6552      2.51       5
     N    2191      2.21       5
     O    2780      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 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: 11824
  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: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 783
          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: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 783
          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: 2957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2957
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2985
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2985
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 7.25, per 1000 atoms: 0.61
  Number of scatterers: 11824
  At special positions: 0
  Unit cell: (88.976, 120.064, 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      12     16.00
     P     289     15.00
     O    2780      8.00
     N    2191      7.00
     C    6552      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: 2.74
  Conformation dependent library (CDL) restraints added in 864.3 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:  1396

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      75.1% alpha, 2.7% beta
      126 base pairs and 278 stacking pairs defined.
    Time for finding SS restraints: 6.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.596A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.859A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.571A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 23
    Processing helix  chain 'C' and resid 27 through 38
    Processing helix  chain 'C' and resid 46 through 75
      removed outlier: 4.584A  pdb=" N   VAL C  50 " --> pdb=" O   ALA C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 91
    Processing helix  chain 'C' and resid 91 through 98
    Processing helix  chain 'C' and resid 113 through 117
    Processing helix  chain 'D' and resid 60 through 72
    Processing helix  chain 'D' and resid 78 through 108
    Processing helix  chain 'D' and resid 113 through 125
    Processing helix  chain 'D' and resid 126 through 146
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.560A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.882A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.501A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 23
    Processing helix  chain 'G' and resid 27 through 38
    Processing helix  chain 'G' and resid 47 through 74
    Processing helix  chain 'G' and resid 80 through 91
    Processing helix  chain 'G' and resid 91 through 98
    Processing helix  chain 'G' and resid 113 through 117
    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
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.059A  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 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44
      removed outlier: 7.384A  pdb=" N   ARG C  43 " --> 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 78 through 79
    Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103
      removed outlier: 6.894A  pdb=" N   THR C 102 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.840A  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 43 through 44
      removed outlier: 7.258A  pdb=" N   ARG G  43 " --> 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 78 through 79

    417 hydrogen bonds defined for protein.
    1227 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      320 hydrogen bonds
      640 hydrogen bond angles
      0 basepair planarities
      126 basepair parallelities
      278 stacking parallelities
  Total time for adding SS restraints: 4.46

  Time building geometry restraints manager: 3.31 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2717
        1.34 -     1.45: 3756
        1.45 -     1.57: 5557
        1.57 -     1.69: 577
        1.69 -     1.81: 22
  Bond restraints: 12629
  Sorted by residual:
  bond pdb=" CA  VAL G  80 "
       pdb=" CB  VAL G  80 "
    ideal  model  delta    sigma   weight residual
    1.547  1.536  0.011 1.10e-02 8.26e+03 9.63e-01
  bond pdb=" C   SER G  19 "
       pdb=" O   SER G  19 "
    ideal  model  delta    sigma   weight residual
    1.236  1.225  0.011 1.15e-02 7.56e+03 9.59e-01
  bond pdb=" O3'  DG J  27 "
       pdb=" P    DA J  28 "
    ideal  model  delta    sigma   weight residual
    1.607  1.592  0.015 1.50e-02 4.44e+03 9.57e-01
  bond pdb=" CA  LYS C  75 "
       pdb=" CB  LYS C  75 "
    ideal  model  delta    sigma   weight residual
    1.531  1.545 -0.014 1.45e-02 4.76e+03 9.36e-01
  bond pdb=" O3'  DC I -56 "
       pdb=" P    DG I -55 "
    ideal  model  delta    sigma   weight residual
    1.607  1.593  0.014 1.50e-02 4.44e+03 8.63e-01
  ... (remaining 12624 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 17678
        2.04 -     4.09: 554
        4.09 -     6.13: 59
        6.13 -     8.17: 9
        8.17 -    10.22: 3
  Bond angle restraints: 18303
  Sorted by residual:
  angle pdb=" O3'  DG I  54 "
        pdb=" C3'  DG I  54 "
        pdb=" C2'  DG I  54 "
      ideal   model   delta    sigma   weight residual
     111.50  101.28   10.22 1.50e+00 4.44e-01 4.64e+01
  angle pdb=" O3'  DT J -17 "
        pdb=" C3'  DT J -17 "
        pdb=" C2'  DT J -17 "
      ideal   model   delta    sigma   weight residual
     111.50  102.85    8.65 1.50e+00 4.44e-01 3.33e+01
  angle pdb=" O3'  DG I  26 "
        pdb=" C3'  DG I  26 "
        pdb=" C2'  DG I  26 "
      ideal   model   delta    sigma   weight residual
     111.50  103.91    7.59 1.50e+00 4.44e-01 2.56e+01
  angle pdb=" O3'  DT J  14 "
        pdb=" C3'  DT J  14 "
        pdb=" C2'  DT J  14 "
      ideal   model   delta    sigma   weight residual
     111.50  104.42    7.08 1.50e+00 4.44e-01 2.23e+01
  angle pdb=" O3'  DG I  25 "
        pdb=" C3'  DG I  25 "
        pdb=" C2'  DG I  25 "
      ideal   model   delta    sigma   weight residual
     111.50  104.51    6.99 1.50e+00 4.44e-01 2.17e+01
  ... (remaining 18298 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.09: 3992
       18.09 -    36.18: 997
       36.18 -    54.26: 1393
       54.26 -    72.35: 430
       72.35 -    90.44: 27
  Dihedral angle restraints: 6839
    sinusoidal: 4681
      harmonic: 2158
  Sorted by residual:
  dihedral pdb=" CA  ASN B  64 "
           pdb=" CB  ASN B  64 "
           pdb=" CG  ASN B  64 "
           pdb=" OD1 ASN B  64 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -165.78  -74.22     2      2.00e+01 2.50e-03 1.11e+01
  dihedral pdb=" CB  GLU D  99 "
           pdb=" CG  GLU D  99 "
           pdb=" CD  GLU D  99 "
           pdb=" OE1 GLU D  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -90.44   90.44     1      3.00e+01 1.11e-03 1.07e+01
  dihedral pdb=" CB  GLU C  65 "
           pdb=" CG  GLU C  65 "
           pdb=" CD  GLU C  65 "
           pdb=" OE1 GLU C  65 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.99  -89.99     1      3.00e+01 1.11e-03 1.07e+01
  ... (remaining 6836 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1591
       0.057 -    0.114: 384
       0.114 -    0.172: 89
       0.172 -    0.229: 23
       0.229 -    0.286: 2
  Chirality restraints: 2089
  Sorted by residual:
  chirality pdb=" C3'  DG I  54 "
            pdb=" C4'  DG I  54 "
            pdb=" O3'  DG I  54 "
            pdb=" C2'  DG I  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.95    0.29 2.00e-01 2.50e+01 2.05e+00
  chirality pdb=" C3'  DG J   4 "
            pdb=" C4'  DG J   4 "
            pdb=" O3'  DG J   4 "
            pdb=" C2'  DG J   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.89    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" C3'  DG I  -7 "
            pdb=" C4'  DG I  -7 "
            pdb=" O3'  DG I  -7 "
            pdb=" C2'  DG I  -7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.88    0.22 2.00e-01 2.50e+01 1.25e+00
  ... (remaining 2086 not shown)

  Planarity restraints: 1310
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  42 "   -0.036 5.00e-02 4.00e+02   5.44e-02 4.73e+00
        pdb=" N   PRO A  43 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  42 "    0.035 5.00e-02 4.00e+02   5.34e-02 4.56e+00
        pdb=" N   PRO E  43 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO E  43 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO E  43 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 125 "    0.031 5.00e-02 4.00e+02   4.62e-02 3.41e+00
        pdb=" N   PRO D 126 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO D 126 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 126 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1307 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 157
        2.62 -     3.19: 8833
        3.19 -     3.76: 21959
        3.76 -     4.33: 31580
        4.33 -     4.90: 43083
  Nonbonded interactions: 105612
  Sorted by model distance:
  nonbonded pdb=" C2'  DG I  11 "
            pdb=" O5'  DT I  12 "
     model   vdw
     2.050 3.440
  nonbonded pdb=" OG1 THR D  59 "
            pdb=" OD1 ASN D  86 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   THR D 142 "
            pdb=" OG  SER D 146 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OE1 GLU H  94 "
            pdb=" NE2 GLN H  98 "
     model   vdw
     2.282 3.120
  nonbonded pdb=" NH1 ARG F  92 "
            pdb=" OE1 GLU H  99 "
     model   vdw
     2.289 3.120
  ... (remaining 105607 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:             0.750
  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:             0.000
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     32.890
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.027  12629  Z= 0.256
  Angle     :  0.840  10.218  18303  Z= 0.532
  Chirality :  0.055   0.286   2089
  Planarity :  0.005   0.054   1310
  Dihedral  : 31.947  90.437   5443
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 13.27 %
    Favored  : 86.25 %
  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:  2.37 (0.30), residues: 730
  helix:  2.17 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.15 (0.39), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H 132 
 PHE   0.007   0.001   PHE E  67 
 TYR   0.018   0.002   TYR B  98 
 ARG   0.005   0.001   ARG C  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15768 (  737)
  hydrogen bonds       : angle       9.50804 ( 1867)
  covalent geometry    : bond        0.00580 (12629)
  covalent geometry    : angle       0.84001 (18303)

*********************** 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
  203 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 200
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8169 (m-10) cc_final: 0.7154 (m-80)
REVERT: F   88 TYR cc_start: 0.8177 (m-10) cc_final: 0.7359 (m-80)
REVERT: H   74 ASP cc_start: 0.7813 (p0) cc_final: 0.7498 (p0)
  outliers start: 3
  outliers final: 2
  residues processed: 202
  average time/residue: 0.3035
  time to fit residues: 81.0908
Evaluate side-chains
  155 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 153
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain F residue   23 ARG
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:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
B  64 ASN
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 GLN
D 107 ASN
E  39 HIS
E 108 ASN
G  25 GLN
G  85 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.077694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.054046 restraints weight = 52613.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 2.79
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  12629  Z= 0.176
  Angle     :  0.603   8.333  18303  Z= 0.362
  Chirality :  0.036   0.135   2089
  Planarity :  0.005   0.050   1310
  Dihedral  : 33.849  94.686   3984
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 18.61 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.90 (0.30), residues: 730
  helix:  2.58 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.22 (0.41), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.012   0.001   PHE A  67 
 TYR   0.016   0.002   TYR B  98 
 ARG   0.005   0.001   ARG A  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04480 (  737)
  hydrogen bonds       : angle       3.23527 ( 1867)
  covalent geometry    : bond        0.00383 (12629)
  covalent geometry    : angle       0.60344 (18303)

*********************** 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
  195 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 179
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8595 (tt0)
REVERT: C   93 GLU cc_start: 0.8669 (pm20) cc_final: 0.8464 (mt-10)
REVERT: D   91 ASP cc_start: 0.9018 (t0) cc_final: 0.8787 (t0)
REVERT: D  116 GLU cc_start: 0.8571 (mp0) cc_final: 0.8198 (mp0)
REVERT: E   42 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7612 (ttm-80)
REVERT: E   73 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8556 (tt0)
REVERT: G   93 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8402 (mm-30)
REVERT: H   74 ASP cc_start: 0.9013 (p0) cc_final: 0.8653 (p0)
REVERT: H   91 ASP cc_start: 0.8955 (t0) cc_final: 0.8678 (t0)
REVERT: H   94 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8419 (mm-30)
REVERT: H   98 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8776 (mm-40)
REVERT: H  116 GLU cc_start: 0.8473 (mp0) cc_final: 0.7985 (mp0)
  outliers start: 16
  outliers final: 12
  residues processed: 187
  average time/residue: 0.2756
  time to fit residues: 70.0005
Evaluate side-chains
  175 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 163
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain G residue   88 VAL
Chi-restraints excluded: chain G residue  102 THR
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 62 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 5 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
C  74 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.074360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.051295 restraints weight = 53928.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 2.74
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.3852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12629  Z= 0.168
  Angle     :  0.566   6.945  18303  Z= 0.338
  Chirality :  0.033   0.145   2089
  Planarity :  0.004   0.048   1310
  Dihedral  : 32.891  89.874   3980
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 17.96 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.24 (0.31), residues: 730
  helix:  2.78 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop :  0.08 (0.43), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.012   0.002   TYR H 106 
 ARG   0.004   0.000   ARG A  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03791 (  737)
  hydrogen bonds       : angle       3.02752 ( 1867)
  covalent geometry    : bond        0.00371 (12629)
  covalent geometry    : angle       0.56574 (18303)

*********************** 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
  198 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 178
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 PHE cc_start: 0.8515 (m-80) cc_final: 0.8303 (m-80)
REVERT: A   54 TYR cc_start: 0.8696 (m-80) cc_final: 0.8347 (m-80)
REVERT: A   73 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8618 (tt0)
REVERT: B   22 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6705 (mt)
REVERT: B   88 TYR cc_start: 0.9254 (m-10) cc_final: 0.8942 (m-80)
REVERT: B   96 THR cc_start: 0.9378 (m) cc_final: 0.9100 (p)
REVERT: C   92 GLU cc_start: 0.9038 (tp30) cc_final: 0.8047 (tp30)
REVERT: C   96 LYS cc_start: 0.8936 (mmmt) cc_final: 0.8301 (mmmt)
REVERT: D   82 MET cc_start: 0.9182 (tpp) cc_final: 0.8905 (tpp)
REVERT: D   91 ASP cc_start: 0.9023 (t0) cc_final: 0.8750 (t0)
REVERT: D   94 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8107 (tp30)
REVERT: D   98 GLN cc_start: 0.9305 (mm-40) cc_final: 0.8757 (mm-40)
REVERT: D  112 ILE cc_start: 0.9289 (mt) cc_final: 0.8987 (mt)
REVERT: D  116 GLU cc_start: 0.8649 (mp0) cc_final: 0.8094 (mp0)
REVERT: E   42 ARG cc_start: 0.8148 (mtp180) cc_final: 0.7769 (ttm-80)
REVERT: E   54 TYR cc_start: 0.8657 (m-80) cc_final: 0.8417 (m-80)
REVERT: F   27 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8887 (mp10)
REVERT: G   91 ASP cc_start: 0.8657 (t0) cc_final: 0.8406 (t70)
REVERT: H   58 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7702 (mm-30)
REVERT: H   74 ASP cc_start: 0.8987 (p0) cc_final: 0.8601 (p0)
REVERT: H   91 ASP cc_start: 0.8990 (t0) cc_final: 0.8678 (t0)
REVERT: H   94 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8310 (tp30)
REVERT: H   98 GLN cc_start: 0.9294 (mm-40) cc_final: 0.8813 (mm110)
REVERT: H  112 ILE cc_start: 0.9552 (mt) cc_final: 0.9034 (mt)
REVERT: H  116 GLU cc_start: 0.8572 (mp0) cc_final: 0.8043 (mp0)
  outliers start: 20
  outliers final: 10
  residues processed: 188
  average time/residue: 0.2804
  time to fit residues: 71.9052
Evaluate side-chains
  179 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 168
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   88 VAL
Chi-restraints excluded: chain G residue  102 THR
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:   10.0000
   chunk 59 optimal weight:    0.8980
   chunk 50 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 79 optimal weight:    4.9990
   chunk 95 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  93 GLN
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.072389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.049882 restraints weight = 53149.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 2.75
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.4374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12629  Z= 0.167
  Angle     :  0.546   8.569  18303  Z= 0.328
  Chirality :  0.033   0.151   2089
  Planarity :  0.004   0.045   1310
  Dihedral  : 32.636  91.623   3980
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.90 %
    Favored  : 77.67 %
  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:  3.40 (0.31), residues: 730
  helix:  2.89 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop :  0.15 (0.45), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.011   0.001   PHE E  67 
 TYR   0.010   0.002   TYR H  63 
 ARG   0.006   0.000   ARG G  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03705 (  737)
  hydrogen bonds       : angle       2.98261 ( 1867)
  covalent geometry    : bond        0.00368 (12629)
  covalent geometry    : angle       0.54624 (18303)

*********************** 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
  195 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 180
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8618 (tt0)
REVERT: A   76 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8725 (pp30)
REVERT: B   22 LEU cc_start: 0.7089 (mt) cc_final: 0.6733 (mt)
REVERT: B   96 THR cc_start: 0.9391 (m) cc_final: 0.9154 (p)
REVERT: C   74 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8570 (t0)
REVERT: C   93 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8562 (mm-30)
REVERT: C   95 SER cc_start: 0.9573 (t) cc_final: 0.9338 (p)
REVERT: D   91 ASP cc_start: 0.9053 (t0) cc_final: 0.8773 (t0)
REVERT: D   94 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8419 (tp30)
REVERT: D   98 GLN cc_start: 0.9265 (mm-40) cc_final: 0.9003 (mm-40)
REVERT: D  116 GLU cc_start: 0.8658 (mp0) cc_final: 0.8100 (mp0)
REVERT: E   42 ARG cc_start: 0.8163 (mtp180) cc_final: 0.7782 (ttm-80)
REVERT: E   73 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8471 (tt0)
REVERT: E   76 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8805 (tm-30)
REVERT: F   22 LEU cc_start: 0.7028 (mt) cc_final: 0.6735 (mt)
REVERT: G   51 TYR cc_start: 0.9221 (t80) cc_final: 0.8944 (t80)
REVERT: G   57 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8619 (tt0)
REVERT: G   91 ASP cc_start: 0.8653 (t0) cc_final: 0.8285 (t0)
REVERT: H   58 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7874 (mm-30)
REVERT: H   74 ASP cc_start: 0.9049 (p0) cc_final: 0.8727 (p0)
REVERT: H   91 ASP cc_start: 0.8963 (t0) cc_final: 0.8688 (t0)
REVERT: H   94 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8159 (tp30)
REVERT: H   98 GLN cc_start: 0.9266 (mm-40) cc_final: 0.8817 (mm-40)
REVERT: H  116 GLU cc_start: 0.8621 (mp0) cc_final: 0.8042 (mp0)
  outliers start: 15
  outliers final: 7
  residues processed: 189
  average time/residue: 0.2614
  time to fit residues: 67.6206
Evaluate side-chains
  177 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 168
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   74 ASN
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain G residue  102 THR
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 86 optimal weight:   10.0000
   chunk 45 optimal weight:    0.3980
   chunk 51 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
D 132 HIS
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.072306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.050464 restraints weight = 52956.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 2.66
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.4874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12629  Z= 0.144
  Angle     :  0.542   8.667  18303  Z= 0.322
  Chirality :  0.032   0.152   2089
  Planarity :  0.004   0.043   1310
  Dihedral  : 32.264  89.845   3980
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 20.71 %
    Favored  : 77.18 %
  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:  3.44 (0.31), residues: 730
  helix:  2.91 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop :  0.25 (0.46), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.028   0.002   TYR H 106 
 ARG   0.007   0.000   ARG G  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03307 (  737)
  hydrogen bonds       : angle       2.92188 ( 1867)
  covalent geometry    : bond        0.00308 (12629)
  covalent geometry    : angle       0.54159 (18303)

*********************** 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
  207 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 194
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8567 (tt0)
REVERT: A   76 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8717 (pp30)
REVERT: B   22 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6627 (mt)
REVERT: C   74 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8628 (t0)
REVERT: C   93 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8417 (mm-30)
REVERT: C   95 SER cc_start: 0.9527 (t) cc_final: 0.9301 (p)
REVERT: C  109 MET cc_start: 0.6155 (mpp) cc_final: 0.5231 (mpp)
REVERT: C  111 ASN cc_start: 0.8723 (t0) cc_final: 0.8364 (p0)
REVERT: D   91 ASP cc_start: 0.9016 (t0) cc_final: 0.8767 (t0)
REVERT: D   94 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8327 (tp30)
REVERT: D   98 GLN cc_start: 0.9297 (mm-40) cc_final: 0.8963 (mm-40)
REVERT: D  116 GLU cc_start: 0.8639 (mp0) cc_final: 0.8041 (mp0)
REVERT: E   76 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8792 (tm-30)
REVERT: F   88 TYR cc_start: 0.9196 (m-80) cc_final: 0.8499 (m-80)
REVERT: G   51 TYR cc_start: 0.9140 (t80) cc_final: 0.8840 (t80)
REVERT: G   65 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8610 (pp20)
REVERT: G   91 ASP cc_start: 0.8615 (t0) cc_final: 0.8230 (t0)
REVERT: G   96 LYS cc_start: 0.9583 (tppt) cc_final: 0.9375 (tptp)
REVERT: H   58 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7873 (mm-30)
REVERT: H   74 ASP cc_start: 0.9002 (p0) cc_final: 0.8670 (p0)
REVERT: H   91 ASP cc_start: 0.8927 (t0) cc_final: 0.8651 (t0)
REVERT: H   94 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8227 (tp30)
REVERT: H   98 GLN cc_start: 0.9267 (mm-40) cc_final: 0.8935 (mm-40)
REVERT: H  106 TYR cc_start: 0.8236 (m-10) cc_final: 0.7875 (m-80)
REVERT: H  116 GLU cc_start: 0.8591 (mp0) cc_final: 0.8072 (mp0)
  outliers start: 13
  outliers final: 6
  residues processed: 201
  average time/residue: 0.2678
  time to fit residues: 74.0187
Evaluate side-chains
  183 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 175
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   74 ASN
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 82 optimal weight:    6.9990
   chunk 5 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0970
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.071783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.049526 restraints weight = 53619.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 2.73
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.5150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12629  Z= 0.150
  Angle     :  0.548   9.998  18303  Z= 0.324
  Chirality :  0.033   0.210   2089
  Planarity :  0.004   0.044   1310
  Dihedral  : 32.244  89.492   3980
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 22.98 %
    Favored  : 74.92 %
  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:  3.44 (0.31), residues: 730
  helix:  2.89 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop :  0.32 (0.47), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.010   0.001   PHE A  67 
 TYR   0.022   0.002   TYR H 106 
 ARG   0.007   0.000   ARG G  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03457 (  737)
  hydrogen bonds       : angle       2.97550 ( 1867)
  covalent geometry    : bond        0.00325 (12629)
  covalent geometry    : angle       0.54808 (18303)

*********************** 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
  190 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 177
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8511 (tt0)
REVERT: B   22 LEU cc_start: 0.7267 (mt) cc_final: 0.6925 (mt)
REVERT: B   88 TYR cc_start: 0.9140 (m-80) cc_final: 0.8326 (m-80)
REVERT: C   74 ASN cc_start: 0.9024 (OUTLIER) cc_final: 0.8570 (t0)
REVERT: C   93 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8381 (mm-30)
REVERT: C   95 SER cc_start: 0.9547 (t) cc_final: 0.9325 (p)
REVERT: D   82 MET cc_start: 0.9181 (tpp) cc_final: 0.8969 (tpp)
REVERT: D   91 ASP cc_start: 0.9053 (t0) cc_final: 0.8814 (t0)
REVERT: D   94 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8448 (tp30)
REVERT: D   98 GLN cc_start: 0.9282 (mm-40) cc_final: 0.9077 (mm-40)
REVERT: D  106 TYR cc_start: 0.8096 (m-80) cc_final: 0.7504 (m-80)
REVERT: D  116 GLU cc_start: 0.8627 (mp0) cc_final: 0.8073 (mp0)
REVERT: E   76 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8736 (tm-30)
REVERT: F   88 TYR cc_start: 0.9206 (m-80) cc_final: 0.8824 (m-80)
REVERT: G   51 TYR cc_start: 0.9196 (t80) cc_final: 0.8950 (t80)
REVERT: G   91 ASP cc_start: 0.8599 (t0) cc_final: 0.8207 (t0)
REVERT: G   96 LYS cc_start: 0.9577 (tppt) cc_final: 0.9330 (tptp)
REVERT: H   58 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7828 (mm-30)
REVERT: H   74 ASP cc_start: 0.9016 (p0) cc_final: 0.8673 (p0)
REVERT: H   91 ASP cc_start: 0.8948 (t0) cc_final: 0.8702 (t0)
REVERT: H   94 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8265 (tp30)
REVERT: H   98 GLN cc_start: 0.9255 (mm-40) cc_final: 0.8888 (mm-40)
REVERT: H  116 GLU cc_start: 0.8633 (mp0) cc_final: 0.8014 (mp0)
  outliers start: 13
  outliers final: 6
  residues processed: 184
  average time/residue: 0.2671
  time to fit residues: 67.3372
Evaluate side-chains
  177 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 170
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   74 ASN
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:   10.0000
   chunk 98 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 84 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 105 ASN
D  98 GLN
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  72 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.068523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.045900 restraints weight = 53840.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 2.66
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.5596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038  12629  Z= 0.247
  Angle     :  0.611  10.121  18303  Z= 0.359
  Chirality :  0.036   0.180   2089
  Planarity :  0.004   0.043   1310
  Dihedral  : 32.395  90.145   3980
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 24.27 %
    Favored  : 73.46 %
  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:  2.71 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop :  0.09 (0.45), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS D  72 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.024   0.002   TYR H 106 
 ARG   0.009   0.001   ARG C  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04551 (  737)
  hydrogen bonds       : angle       3.27837 ( 1867)
  covalent geometry    : bond        0.00556 (12629)
  covalent geometry    : angle       0.61117 (18303)

*********************** 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
  180 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 166
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8532 (tt0)
REVERT: B   88 TYR cc_start: 0.9278 (m-10) cc_final: 0.9015 (m-80)
REVERT: C   39 LYS cc_start: 0.9536 (mmmm) cc_final: 0.9185 (mmmm)
REVERT: C   74 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8611 (t0)
REVERT: C   93 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8476 (mm-30)
REVERT: C   95 SER cc_start: 0.9516 (t) cc_final: 0.9276 (p)
REVERT: C  109 MET cc_start: 0.6905 (mpp) cc_final: 0.6590 (mpp)
REVERT: D   91 ASP cc_start: 0.9097 (t0) cc_final: 0.8777 (t0)
REVERT: D   94 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8259 (tp30)
REVERT: D   98 GLN cc_start: 0.9242 (mm110) cc_final: 0.8920 (mm-40)
REVERT: D  116 GLU cc_start: 0.8825 (mp0) cc_final: 0.8073 (mp0)
REVERT: E   73 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8504 (tt0)
REVERT: G   91 ASP cc_start: 0.8715 (t0) cc_final: 0.8330 (t0)
REVERT: G   96 LYS cc_start: 0.9571 (tppt) cc_final: 0.9285 (tptp)
REVERT: H   58 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7922 (mm-30)
REVERT: H   74 ASP cc_start: 0.9097 (p0) cc_final: 0.8775 (p0)
REVERT: H   82 MET cc_start: 0.9226 (tpp) cc_final: 0.8905 (tpp)
REVERT: H   91 ASP cc_start: 0.8977 (t0) cc_final: 0.8684 (t0)
REVERT: H   94 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8591 (tp30)
REVERT: H   98 GLN cc_start: 0.9257 (mm-40) cc_final: 0.8968 (mm110)
REVERT: H  106 TYR cc_start: 0.8247 (m-10) cc_final: 0.7956 (m-80)
REVERT: H  116 GLU cc_start: 0.8759 (mp0) cc_final: 0.8049 (mp0)
  outliers start: 14
  outliers final: 8
  residues processed: 175
  average time/residue: 0.2826
  time to fit residues: 68.0878
Evaluate side-chains
  168 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 159
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   74 ASN
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 80 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 90 optimal weight:    4.9990
   chunk 26 optimal weight:    8.9990
   chunk 15 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 88 optimal weight:    8.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  55 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.069192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.046772 restraints weight = 54504.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.2877 rms_B_bonded: 2.67
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.5770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12629  Z= 0.165
  Angle     :  0.574  10.395  18303  Z= 0.338
  Chirality :  0.033   0.171   2089
  Planarity :  0.004   0.043   1310
  Dihedral  : 32.039  90.728   3979
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 24.92 %
    Favored  : 74.11 %
  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:  3.30 (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   0.003   0.001   HIS F  75 
 PHE   0.011   0.001   PHE A  67 
 TYR   0.023   0.002   TYR H 106 
 ARG   0.007   0.000   ARG C  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03615 (  737)
  hydrogen bonds       : angle       3.08082 ( 1867)
  covalent geometry    : bond        0.00368 (12629)
  covalent geometry    : angle       0.57386 (18303)

*********************** 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
  179 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 173
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8591 (tt0)
REVERT: B   22 LEU cc_start: 0.7036 (mt) cc_final: 0.6684 (mt)
REVERT: B   84 MET cc_start: 0.8632 (mmm) cc_final: 0.8215 (mmm)
REVERT: B   88 TYR cc_start: 0.9229 (m-10) cc_final: 0.8655 (m-80)
REVERT: C   74 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8585 (t0)
REVERT: C   93 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8486 (mm-30)
REVERT: C   95 SER cc_start: 0.9538 (t) cc_final: 0.9307 (p)
REVERT: D   91 ASP cc_start: 0.9092 (t0) cc_final: 0.8848 (t0)
REVERT: D   94 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8175 (tp30)
REVERT: D   98 GLN cc_start: 0.9161 (mm110) cc_final: 0.8877 (mm-40)
REVERT: D  116 GLU cc_start: 0.8708 (mp0) cc_final: 0.8008 (mp0)
REVERT: E   73 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8602 (tt0)
REVERT: E   97 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7814 (mt-10)
REVERT: F   22 LEU cc_start: 0.7238 (mp) cc_final: 0.7028 (mt)
REVERT: G   57 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8574 (tt0)
REVERT: G   91 ASP cc_start: 0.8709 (t0) cc_final: 0.8345 (t0)
REVERT: G   96 LYS cc_start: 0.9523 (tppt) cc_final: 0.9226 (tptp)
REVERT: H   58 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8026 (mm-30)
REVERT: H   74 ASP cc_start: 0.8957 (p0) cc_final: 0.8643 (p0)
REVERT: H   91 ASP cc_start: 0.8929 (t0) cc_final: 0.8700 (t0)
REVERT: H   94 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8242 (tp30)
REVERT: H   98 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8853 (mm-40)
REVERT: H  116 GLU cc_start: 0.8702 (mp0) cc_final: 0.8027 (mp0)
  outliers start: 6
  outliers final: 3
  residues processed: 178
  average time/residue: 0.2615
  time to fit residues: 63.9233
Evaluate side-chains
  172 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 167
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   74 ASN
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 99 optimal weight:   10.0000
   chunk 49 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 ASN
** E  55 GLN ** 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 = 0.3591 r_free = 0.3591 target = 0.069568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.047642 restraints weight = 54074.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 2.62
r_work: 0.2744 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.5958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12629  Z= 0.155
  Angle     :  0.577  10.775  18303  Z= 0.337
  Chirality :  0.033   0.208   2089
  Planarity :  0.004   0.044   1310
  Dihedral  : 31.957  89.925   3979
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 25.08 %
    Favored  : 73.46 %
  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:  3.32 (0.31), residues: 730
  helix:  2.82 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop :  0.18 (0.46), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.011   0.001   PHE A  67 
 TYR   0.022   0.002   TYR H 106 
 ARG   0.007   0.000   ARG C  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03506 (  737)
  hydrogen bonds       : angle       3.07246 ( 1867)
  covalent geometry    : bond        0.00338 (12629)
  covalent geometry    : angle       0.57724 (18303)

*********************** 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
  186 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 177
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8919 (tt0)
REVERT: B   22 LEU cc_start: 0.6959 (mt) cc_final: 0.6546 (mt)
REVERT: B   88 TYR cc_start: 0.9435 (m-10) cc_final: 0.9183 (m-80)
REVERT: C   74 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8697 (t0)
REVERT: C   93 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8427 (mm-30)
REVERT: C   95 SER cc_start: 0.9572 (t) cc_final: 0.9356 (p)
REVERT: C  109 MET cc_start: 0.7339 (mpp) cc_final: 0.6853 (mpp)
REVERT: C  111 ASN cc_start: 0.8901 (t0) cc_final: 0.8525 (p0)
REVERT: D   58 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6534 (tp30)
REVERT: D   91 ASP cc_start: 0.9140 (t0) cc_final: 0.8926 (t0)
REVERT: D   94 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8507 (tp30)
REVERT: D   98 GLN cc_start: 0.9264 (mm110) cc_final: 0.9057 (mm-40)
REVERT: D  116 GLU cc_start: 0.8925 (mp0) cc_final: 0.8386 (mp0)
REVERT: F   84 MET cc_start: 0.8896 (mmm) cc_final: 0.8630 (tpp)
REVERT: F   88 TYR cc_start: 0.9372 (m-80) cc_final: 0.8950 (m-80)
REVERT: G   91 ASP cc_start: 0.8540 (t0) cc_final: 0.8315 (t0)
REVERT: G   96 LYS cc_start: 0.9477 (tppt) cc_final: 0.9235 (tptp)
REVERT: H   58 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8147 (mm-30)
REVERT: H   74 ASP cc_start: 0.9058 (p0) cc_final: 0.8728 (p0)
REVERT: H   91 ASP cc_start: 0.9030 (t0) cc_final: 0.8798 (t0)
REVERT: H   94 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8583 (tp30)
REVERT: H   98 GLN cc_start: 0.9354 (mm-40) cc_final: 0.8930 (mm-40)
REVERT: H  116 GLU cc_start: 0.8963 (mp0) cc_final: 0.8422 (mp0)
  outliers start: 9
  outliers final: 5
  residues processed: 182
  average time/residue: 0.2686
  time to fit residues: 67.5064
Evaluate side-chains
  176 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 170
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   74 ASN
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 62 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  98 GLN
E  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.069077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.047246 restraints weight = 53896.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 2.62
r_work: 0.2728 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8733
moved from start:          0.6165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12629  Z= 0.172
  Angle     :  0.593  11.325  18303  Z= 0.345
  Chirality :  0.034   0.184   2089
  Planarity :  0.004   0.044   1310
  Dihedral  : 31.946  89.497   3979
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 25.73 %
    Favored  : 72.98 %
  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:  3.26 (0.31), residues: 730
  helix:  2.74 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.20 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS D  72 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.013   0.002   TYR H 106 
 ARG   0.007   0.001   ARG C  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03674 (  737)
  hydrogen bonds       : angle       3.12752 ( 1867)
  covalent geometry    : bond        0.00380 (12629)
  covalent geometry    : angle       0.59333 (18303)

********************** 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
  180 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 172
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8947 (tt0)
REVERT: B   22 LEU cc_start: 0.6886 (mt) cc_final: 0.6491 (mt)
REVERT: B   84 MET cc_start: 0.9038 (mmm) cc_final: 0.8718 (tmm)
REVERT: B   88 TYR cc_start: 0.9430 (m-10) cc_final: 0.8850 (m-80)
REVERT: C   36 LYS cc_start: 0.9498 (mmtm) cc_final: 0.9258 (mmtt)
REVERT: C   74 ASN cc_start: 0.9128 (OUTLIER) cc_final: 0.8711 (t0)
REVERT: C   93 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8407 (mm-30)
REVERT: D   56 ASN cc_start: 0.8788 (m-40) cc_final: 0.8193 (t0)
REVERT: D   91 ASP cc_start: 0.9135 (t0) cc_final: 0.8899 (t0)
REVERT: D   94 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8558 (tp30)
REVERT: D   98 GLN cc_start: 0.9342 (mm-40) cc_final: 0.9115 (mm-40)
REVERT: D  105 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.8174 (mtm-85)
REVERT: D  116 GLU cc_start: 0.8966 (mp0) cc_final: 0.8413 (mp0)
REVERT: F   84 MET cc_start: 0.8907 (mmm) cc_final: 0.8543 (tmm)
REVERT: F   88 TYR cc_start: 0.9362 (m-80) cc_final: 0.8637 (m-80)
REVERT: G   21 LYS cc_start: 0.9425 (tppt) cc_final: 0.9211 (tppt)
REVERT: G   91 ASP cc_start: 0.8506 (t0) cc_final: 0.8292 (t0)
REVERT: G   96 LYS cc_start: 0.9442 (tppt) cc_final: 0.9204 (tptp)
REVERT: H   74 ASP cc_start: 0.9026 (p0) cc_final: 0.8683 (p0)
REVERT: H   91 ASP cc_start: 0.9023 (t0) cc_final: 0.8813 (t0)
REVERT: H   94 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8732 (tp30)
REVERT: H   98 GLN cc_start: 0.9321 (mm-40) cc_final: 0.9056 (mm-40)
REVERT: H  116 GLU cc_start: 0.8985 (mp0) cc_final: 0.8438 (mp0)
  outliers start: 8
  outliers final: 7
  residues processed: 177
  average time/residue: 0.2550
  time to fit residues: 62.1488
Evaluate side-chains
  173 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 165
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   74 ASN
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 97 optimal weight:    6.9990
   chunk 49 optimal weight:    0.6980
   chunk 85 optimal weight:   10.0000
   chunk 90 optimal weight:    5.9990
   chunk 63 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 84 optimal weight:    8.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.069106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.047443 restraints weight = 54158.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 2.58
r_work: 0.2738 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.6318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12629  Z= 0.166
  Angle     :  0.593  11.289  18303  Z= 0.343
  Chirality :  0.034   0.194   2089
  Planarity :  0.004   0.044   1310
  Dihedral  : 31.895  88.992   3979
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 26.70 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.22 (0.31), residues: 730
  helix:  2.71 (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   0.005   0.001   HIS D  72 
 PHE   0.011   0.001   PHE E  67 
 TYR   0.012   0.002   TYR H 106 
 ARG   0.007   0.000   ARG G  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03579 (  737)
  hydrogen bonds       : angle       3.10123 ( 1867)
  covalent geometry    : bond        0.00367 (12629)
  covalent geometry    : angle       0.59254 (18303)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5245.61 seconds
wall clock time: 90 minutes 40.52 seconds (5440.52 seconds total)