Starting phenix.real_space_refine
on Fri Jul  3 02:30:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g86_29837/07_2026/8g86_29837.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g86_29837/07_2026/8g86_29837.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g86_29837/07_2026/8g86_29837.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g86_29837/07_2026/8g86_29837.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g86_29837/07_2026/8g86_29837.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g86_29837/07_2026/8g86_29837.map"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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     290      5.49       5
     S      12      5.16       5
     C    6637      2.51       5
     N    2229      2.21       5
     O    2804      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11972
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 646
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "C"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 648
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "G"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    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: 2995
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2995
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.16, per 1000 atoms: 0.18
  Number of scatterers: 11972
  At special positions: 0
  Unit cell: (74.865, 116.725, 114.31, 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     290     15.00
     O    2804      8.00
     N    2229      7.00
     C    6637      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: 0.82
  Conformation dependent library (CDL) restraints added in 266.4 milliseconds
  

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1424

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      73.4% alpha, 2.9% beta
      134 base pairs and 275 stacking pairs defined.
    Time for finding SS restraints: 1.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 4.145A  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
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.236A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 122
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.829A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
    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
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.387A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.003A  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: 6.691A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.144A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.769A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.764A  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 42 through 43
      removed outlier: 7.057A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    417 hydrogen bonds defined for protein.
    1227 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      319 hydrogen bonds
      634 hydrogen bond angles
      0 basepair planarities
      134 basepair parallelities
      275 stacking parallelities
  Total time for adding SS restraints: 2.07

  Time building geometry restraints manager: 1.07 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: 2227
        1.33 -     1.45: 4184
        1.45 -     1.57: 5764
        1.57 -     1.69: 578
        1.69 -     1.81: 22
  Bond restraints: 12775
  Sorted by residual:
  bond pdb=" C3'  DT J  41 "
       pdb=" C2'  DT J  41 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.15e+01
  bond pdb=" C3'  DC I -22 "
       pdb=" C2'  DC I -22 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.13e+01
  bond pdb=" C3'  DG I  68 "
       pdb=" C2'  DG I  68 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.12e+01
  bond pdb=" C3'  DA I -31 "
       pdb=" C2'  DA I -31 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.10e+01
  bond pdb=" C3'  DT J -11 "
       pdb=" C2'  DT J -11 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.06e+01
  ... (remaining 12770 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 17363
        1.41 -     2.83: 1103
        2.83 -     4.24: 23
        4.24 -     5.65: 6
        5.65 -     7.06: 3
  Bond angle restraints: 18498
  Sorted by residual:
  angle pdb=" N3   DT J -63 "
        pdb=" C4   DT J -63 "
        pdb=" O4   DT J -63 "
      ideal   model   delta    sigma   weight residual
     119.90  122.42   -2.52 6.00e-01 2.78e+00 1.76e+01
  angle pdb=" N3   DT I -71 "
        pdb=" C4   DT I -71 "
        pdb=" O4   DT I -71 "
      ideal   model   delta    sigma   weight residual
     119.90  122.40   -2.50 6.00e-01 2.78e+00 1.73e+01
  angle pdb=" N3   DT J  64 "
        pdb=" C4   DT J  64 "
        pdb=" O4   DT J  64 "
      ideal   model   delta    sigma   weight residual
     119.90  122.40   -2.50 6.00e-01 2.78e+00 1.73e+01
  angle pdb=" N3   DT J  25 "
        pdb=" C4   DT J  25 "
        pdb=" O4   DT J  25 "
      ideal   model   delta    sigma   weight residual
     119.90  122.39   -2.49 6.00e-01 2.78e+00 1.72e+01
  angle pdb=" N3   DT J  58 "
        pdb=" C4   DT J  58 "
        pdb=" O4   DT J  58 "
      ideal   model   delta    sigma   weight residual
     119.90  122.38   -2.48 6.00e-01 2.78e+00 1.71e+01
  ... (remaining 18493 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.88: 5664
       35.88 -    71.77: 1344
       71.77 -   107.65: 13
      107.65 -   143.53: 0
      143.53 -   179.41: 1
  Dihedral angle restraints: 7022
    sinusoidal: 4817
      harmonic: 2205
  Sorted by residual:
  dihedral pdb=" C4'  DT I  20 "
           pdb=" C3'  DT I  20 "
           pdb=" O3'  DT I  20 "
           pdb=" P    DG I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.41 -179.41     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  ASP A  77 "
           pdb=" CB  ASP A  77 "
           pdb=" CG  ASP A  77 "
           pdb=" OD1 ASP A  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.37   58.37     1      2.00e+01 2.50e-03 1.14e+01
  dihedral pdb=" CB  GLU F  74 "
           pdb=" CG  GLU F  74 "
           pdb=" CD  GLU F  74 "
           pdb=" OE1 GLU F  74 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.78   88.78     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 7019 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1042
       0.026 -    0.052: 648
       0.052 -    0.078: 203
       0.078 -    0.104: 172
       0.104 -    0.130: 44
  Chirality restraints: 2109
  Sorted by residual:
  chirality pdb=" CA  ILE B  29 "
            pdb=" N   ILE B  29 "
            pdb=" C   ILE B  29 "
            pdb=" CB  ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" CA  ILE A  62 "
            pdb=" N   ILE A  62 "
            pdb=" C   ILE A  62 "
            pdb=" CB  ILE A  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.02e-01
  chirality pdb=" CA  ILE F  29 "
            pdb=" N   ILE F  29 "
            pdb=" C   ILE F  29 "
            pdb=" CB  ILE F  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 2106 not shown)

  Planarity restraints: 1335
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "    0.031 5.00e-02 4.00e+02   4.72e-02 3.57e+00
        pdb=" N   PRO G  80 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  79 "    0.030 5.00e-02 4.00e+02   4.52e-02 3.27e+00
        pdb=" N   PRO C  80 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  65 "    0.022 5.00e-02 4.00e+02   3.38e-02 1.82e+00
        pdb=" N   PRO A  66 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A  66 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  66 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1332 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2611
        2.81 -     3.33: 10262
        3.33 -     3.85: 24101
        3.85 -     4.38: 30291
        4.38 -     4.90: 40295
  Nonbonded interactions: 107560
  Sorted by model distance:
  nonbonded pdb=" OG  SER C  18 "
            pdb=" O   PHE C  25 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" NH1 ARG E  72 "
            pdb=" OP1  DT J -23 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" NH2 ARG C  20 "
            pdb=" OP1  DC I -42 "
     model   vdw
     2.386 3.120
  nonbonded pdb=" O2   DC I -42 "
            pdb=" N2   DG J  42 "
     model   vdw
     2.395 3.120
  nonbonded pdb=" O2   DC I -51 "
            pdb=" N2   DG J  51 "
     model   vdw
     2.425 2.496
  ... (remaining 107555 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' and resid 38 through 133)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 22 through 101)
  selection = (chain 'F' and resid 22 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             5.320
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.840
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  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:6.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
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   0.033  12775  Z= 0.514
  Angle     :  0.678   7.065  18498  Z= 0.623
  Chirality :  0.043   0.130   2109
  Planarity :  0.003   0.047   1335
  Dihedral  : 27.264 179.413   5598
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 16.30 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.28), residues: 743
  helix:  1.47 (0.20), residues: 551
  sheet:  None (None), residues: 0
  loop :  0.04 (0.39), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  83 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00553 /  0.51 (12775)
  covalent geometry    : angle       0.67758 /  0.62 (18498)
  hydrogen bonds       : bond        0.23805 / 16.33 (  736)
  hydrogen bonds       : angle       8.65357 /  6.37 ( 1861)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 160
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7789 (mtp85)
REVERT: A  120 MET cc_start: 0.8545 (mtt) cc_final: 0.8326 (mtp)
REVERT: B   79 LYS cc_start: 0.8392 (mtpt) cc_final: 0.8095 (mtmm)
REVERT: C  110 ASN cc_start: 0.8575 (t0) cc_final: 0.8350 (t0)
REVERT: D   73 GLU cc_start: 0.8617 (tp30) cc_final: 0.8383 (tp30)
REVERT: D  113 LYS cc_start: 0.8106 (ttmp) cc_final: 0.7756 (ttpp)
REVERT: E   59 GLU cc_start: 0.8053 (pm20) cc_final: 0.7844 (pm20)
REVERT: F   27 GLN cc_start: 0.8276 (mm110) cc_final: 0.7981 (mm110)
REVERT: G   15 LYS cc_start: 0.7400 (mtpt) cc_final: 0.6751 (tttt)
REVERT: G   71 ARG cc_start: 0.7091 (ttp-110) cc_final: 0.6668 (ttm-80)
REVERT: G   75 LYS cc_start: 0.8044 (mmtm) cc_final: 0.7803 (mmtp)
REVERT: H   54 LYS cc_start: 0.8614 (tptt) cc_final: 0.8385 (mmmm)
  outliers start: 6
  outliers final: 2
  residues processed: 163
  average time/residue: 0.8840
  time to fit residues: 151.5582
Evaluate side-chains
  142 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 140
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  118 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.7784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
D  44 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.177271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.134905 restraints weight = 10870.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 0.95
r_work: 0.3368 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3225 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  12775  Z= 0.195
  Angle     :  0.755  10.385  18498  Z= 0.424
  Chirality :  0.051   0.238   2109
  Planarity :  0.005   0.040   1335
  Dihedral  : 30.516 179.441   4097
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 15.82 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.46 (0.29), residues: 743
  helix:  2.19 (0.21), residues: 557
  sheet:  None (None), residues: 0
  loop : -0.05 (0.39), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  72 
 TYR   0.013   0.002   TYR B  51 
 PHE   0.015   0.002   PHE A  67 
 HIS   0.004   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00371 /  0.20 (12775)
  covalent geometry    : angle       0.75463 /  0.42 (18498)
  hydrogen bonds       : bond        0.06962 /  4.71 (  736)
  hydrogen bonds       : angle       3.33090 /  2.38 ( 1861)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8377 (mtt) cc_final: 0.8158 (mtp)
REVERT: A  131 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7465 (mtp180)
REVERT: B   79 LYS cc_start: 0.8757 (mtpt) cc_final: 0.8383 (mtmm)
REVERT: C  110 ASN cc_start: 0.8681 (t0) cc_final: 0.8350 (t0)
REVERT: D  113 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7904 (tttm)
REVERT: E   59 GLU cc_start: 0.8304 (pm20) cc_final: 0.8056 (pm20)
REVERT: F   27 GLN cc_start: 0.8551 (mm110) cc_final: 0.8196 (mm110)
REVERT: F   77 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8124 (mtpt)
REVERT: G   15 LYS cc_start: 0.7464 (mtpt) cc_final: 0.6802 (tttt)
REVERT: G   71 ARG cc_start: 0.7377 (ttp-110) cc_final: 0.6917 (ttm-80)
REVERT: G   75 LYS cc_start: 0.8255 (mmtm) cc_final: 0.7963 (mmtt)
REVERT: H  105 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7456 (mmtt)
  outliers start: 24
  outliers final: 8
  residues processed: 159
  average time/residue: 0.9462
  time to fit residues: 157.9915
Evaluate side-chains
  158 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain D residue  113 LYS
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   41 GLU
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain H residue   85 THR
Chi-restraints excluded: chain H residue  105 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 81 optimal weight:    9.9990
   chunk 85 optimal weight:   30.0000
   chunk 5 optimal weight:    0.6980
   chunk 90 optimal weight:   20.0000
   chunk 88 optimal weight:   20.0000
   chunk 26 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    2.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
C 104 GLN
D  44 GLN
E  76 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.173921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.132071 restraints weight = 10625.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 0.93
r_work: 0.3342 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076  12775  Z= 0.226
  Angle     :  0.732   8.448  18498  Z= 0.413
  Chirality :  0.049   0.226   2109
  Planarity :  0.006   0.042   1335
  Dihedral  : 31.145 178.324   4097
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 15.98 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.18 (0.29), residues: 743
  helix:  2.01 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.28 (0.39), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  77 
 TYR   0.013   0.002   TYR F  51 
 PHE   0.014   0.002   PHE A  67 
 HIS   0.006   0.002   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00464 /  0.23 (12775)
  covalent geometry    : angle       0.73193 /  0.41 (18498)
  hydrogen bonds       : bond        0.08757 /  5.98 (  736)
  hydrogen bonds       : angle       3.37940 /  2.41 ( 1861)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 151
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8567 (mtt) cc_final: 0.8357 (mtp)
REVERT: A  131 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7560 (mtp180)
REVERT: B   79 LYS cc_start: 0.8774 (mtpt) cc_final: 0.8426 (mtmm)
REVERT: C   36 LYS cc_start: 0.8550 (mmtm) cc_final: 0.8272 (mmpt)
REVERT: D  113 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8004 (tttm)
REVERT: F   27 GLN cc_start: 0.8589 (mm110) cc_final: 0.8225 (mm110)
REVERT: F   77 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8184 (mtpt)
REVERT: F   93 GLN cc_start: 0.8314 (mt0) cc_final: 0.7824 (mt0)
REVERT: G   15 LYS cc_start: 0.7604 (mtpt) cc_final: 0.6928 (tttt)
REVERT: G   71 ARG cc_start: 0.7560 (ttp-110) cc_final: 0.7059 (ttm-80)
REVERT: G   75 LYS cc_start: 0.8507 (mmtm) cc_final: 0.8253 (mmtm)
REVERT: G   95 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8427 (tmtm)
  outliers start: 24
  outliers final: 8
  residues processed: 159
  average time/residue: 0.9862
  time to fit residues: 164.4486
Evaluate side-chains
  156 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain D residue  113 LYS
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   41 GLU
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue   85 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:   30.0000
   chunk 59 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 94 optimal weight:   10.0000
   chunk 27 optimal weight:    0.5980
   chunk 77 optimal weight:   20.0000
   chunk 23 optimal weight:    3.9990
   chunk 78 optimal weight:    9.9990
   overall best weight:    2.4986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
C  24 GLN
C 104 GLN
D  44 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.174987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.131865 restraints weight = 10780.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 0.93
r_work: 0.3330 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.2705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  12775  Z= 0.200
  Angle     :  0.693   7.911  18498  Z= 0.393
  Chirality :  0.047   0.228   2109
  Planarity :  0.005   0.041   1335
  Dihedral  : 31.230 178.974   4097
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 16.93 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.27 (0.29), residues: 743
  helix:  2.09 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.28 (0.39), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  72 
 TYR   0.012   0.002   TYR E  54 
 PHE   0.015   0.002   PHE A  67 
 HIS   0.005   0.002   HIS H  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00402 /  0.20 (12775)
  covalent geometry    : angle       0.69329 /  0.39 (18498)
  hydrogen bonds       : bond        0.06683 /  4.51 (  736)
  hydrogen bonds       : angle       3.19983 /  2.28 ( 1861)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8537 (pm20) cc_final: 0.8297 (pm20)
REVERT: A  120 MET cc_start: 0.8538 (mtt) cc_final: 0.8320 (mtp)
REVERT: A  131 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7573 (mtp180)
REVERT: B   79 LYS cc_start: 0.8810 (mtpt) cc_final: 0.8437 (mtmm)
REVERT: C   36 LYS cc_start: 0.8519 (mmtm) cc_final: 0.8233 (mmpt)
REVERT: C   92 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8010 (mt-10)
REVERT: D  113 LYS cc_start: 0.8599 (ttmp) cc_final: 0.8030 (tttm)
REVERT: F   27 GLN cc_start: 0.8672 (mm110) cc_final: 0.8384 (mm110)
REVERT: F   77 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8162 (mtpt)
REVERT: G   15 LYS cc_start: 0.7638 (mtpt) cc_final: 0.6948 (tttt)
REVERT: G   71 ARG cc_start: 0.7637 (ttp-110) cc_final: 0.7082 (ttm-80)
REVERT: G   75 LYS cc_start: 0.8474 (mmtm) cc_final: 0.8153 (mmtt)
REVERT: G   95 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8435 (tmtm)
  outliers start: 19
  outliers final: 8
  residues processed: 154
  average time/residue: 0.9539
  time to fit residues: 154.5368
Evaluate side-chains
  155 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 144
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue   85 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 97 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 76 optimal weight:   20.0000
   chunk 96 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9980
   overall best weight:    2.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
C 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.174489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.131439 restraints weight = 10755.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 0.93
r_work: 0.3328 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  12775  Z= 0.200
  Angle     :  0.688   7.923  18498  Z= 0.389
  Chirality :  0.047   0.236   2109
  Planarity :  0.005   0.041   1335
  Dihedral  : 31.282 177.922   4097
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.61 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.30 (0.29), residues: 743
  helix:  2.12 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.28 (0.39), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  42 
 TYR   0.016   0.002   TYR H  80 
 PHE   0.016   0.002   PHE A  67 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00402 /  0.20 (12775)
  covalent geometry    : angle       0.68765 /  0.39 (18498)
  hydrogen bonds       : bond        0.07117 /  4.81 (  736)
  hydrogen bonds       : angle       3.15816 /  2.25 ( 1861)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8527 (pm20) cc_final: 0.8309 (pm20)
REVERT: A  131 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7529 (mtp180)
REVERT: B   79 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8458 (mtmm)
REVERT: C   36 LYS cc_start: 0.8509 (mmtm) cc_final: 0.8227 (mmpt)
REVERT: C   41 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7755 (mm-30)
REVERT: C   92 GLU cc_start: 0.8251 (mt-10) cc_final: 0.8050 (mt-10)
REVERT: D  105 LYS cc_start: 0.8149 (mtmm) cc_final: 0.7904 (mtpt)
REVERT: D  113 LYS cc_start: 0.8603 (ttmp) cc_final: 0.8012 (tttm)
REVERT: F   27 GLN cc_start: 0.8657 (mm110) cc_final: 0.8353 (mm110)
REVERT: F   77 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8119 (mtpt)
REVERT: F   93 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7849 (mt0)
REVERT: G   15 LYS cc_start: 0.7693 (mtpt) cc_final: 0.6941 (tttt)
REVERT: G   71 ARG cc_start: 0.7667 (ttp-110) cc_final: 0.7092 (ttm-80)
REVERT: G   75 LYS cc_start: 0.8513 (mmtm) cc_final: 0.8226 (mmtt)
REVERT: G   95 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8392 (tmtm)
  outliers start: 20
  outliers final: 10
  residues processed: 155
  average time/residue: 0.8899
  time to fit residues: 145.0379
Evaluate side-chains
  158 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   71 ARG
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue   85 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 96 optimal weight:   10.0000
   chunk 65 optimal weight:    6.9990
   chunk 99 optimal weight:   30.0000
   chunk 63 optimal weight:    4.9990
   chunk 7 optimal weight:    0.5980
   chunk 87 optimal weight:   40.0000
   chunk 21 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 89 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    2.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
C 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.174728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.131741 restraints weight = 10791.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 0.93
r_work: 0.3329 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.2998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  12775  Z= 0.193
  Angle     :  0.678   7.996  18498  Z= 0.384
  Chirality :  0.046   0.231   2109
  Planarity :  0.005   0.042   1335
  Dihedral  : 31.314 178.697   4097
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.77 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.33 (0.29), residues: 743
  helix:  2.14 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.27 (0.39), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  72 
 TYR   0.012   0.002   TYR E  54 
 PHE   0.015   0.002   PHE A  67 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00385 /  0.19 (12775)
  covalent geometry    : angle       0.67840 /  0.38 (18498)
  hydrogen bonds       : bond        0.06611 /  4.44 (  736)
  hydrogen bonds       : angle       3.13441 /  2.24 ( 1861)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8529 (pm20) cc_final: 0.8296 (pm20)
REVERT: A  131 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7528 (mtp180)
REVERT: B   79 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8449 (mtmm)
REVERT: C   36 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8216 (mmpt)
REVERT: C   92 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8062 (mt-10)
REVERT: D  105 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7883 (mtpt)
REVERT: F   27 GLN cc_start: 0.8647 (mm110) cc_final: 0.8349 (mm110)
REVERT: F   77 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8126 (mtpt)
REVERT: F   93 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7869 (mt0)
REVERT: G   15 LYS cc_start: 0.7692 (mtpt) cc_final: 0.6935 (tttt)
REVERT: G   71 ARG cc_start: 0.7657 (ttp-110) cc_final: 0.7085 (ttm-80)
REVERT: G   75 LYS cc_start: 0.8509 (mmtm) cc_final: 0.8234 (mmtm)
REVERT: G   95 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8438 (tmtm)
  outliers start: 20
  outliers final: 9
  residues processed: 151
  average time/residue: 0.8657
  time to fit residues: 137.2661
Evaluate side-chains
  157 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue   85 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 98 optimal weight:   20.0000
   chunk 45 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0970
   chunk 24 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
C 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.175907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.133077 restraints weight = 10702.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 0.92
r_work: 0.3346 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.3022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  12775  Z= 0.143
  Angle     :  0.646   7.873  18498  Z= 0.370
  Chirality :  0.044   0.225   2109
  Planarity :  0.004   0.038   1335
  Dihedral  : 31.283 178.755   4097
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.77 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.54 (0.29), residues: 743
  helix:  2.31 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.25 (0.39), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  42 
 TYR   0.011   0.002   TYR B  51 
 PHE   0.014   0.001   PHE A  67 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.14 (12775)
  covalent geometry    : angle       0.64647 /  0.37 (18498)
  hydrogen bonds       : bond        0.05979 /  3.98 (  736)
  hydrogen bonds       : angle       3.11921 /  2.22 ( 1861)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8497 (mtt) cc_final: 0.8280 (mtp)
REVERT: A  131 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7529 (mtp180)
REVERT: B   52 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7683 (mp0)
REVERT: B   79 LYS cc_start: 0.8807 (mtpt) cc_final: 0.8453 (mtmm)
REVERT: C   36 LYS cc_start: 0.8494 (mmtm) cc_final: 0.8198 (mmpt)
REVERT: C   92 GLU cc_start: 0.8251 (mt-10) cc_final: 0.8026 (mt-10)
REVERT: F   27 GLN cc_start: 0.8623 (mm110) cc_final: 0.8323 (mm110)
REVERT: F   77 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8121 (mtpt)
REVERT: F   93 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7814 (mt0)
REVERT: G   15 LYS cc_start: 0.7709 (mtpt) cc_final: 0.6959 (tttt)
REVERT: G   75 LYS cc_start: 0.8477 (mmtm) cc_final: 0.8197 (mmtt)
REVERT: G   95 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8432 (tmtm)
  outliers start: 20
  outliers final: 8
  residues processed: 154
  average time/residue: 0.8435
  time to fit residues: 136.4222
Evaluate side-chains
  158 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain E residue   77 ASP
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue   85 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 96 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9990
   chunk 83 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 95 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9990
   chunk 72 optimal weight:   40.0000
   overall best weight:    1.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
C 104 GLN
E  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.175252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.132323 restraints weight = 10701.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 0.92
r_work: 0.3336 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.3109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12775  Z= 0.175
  Angle     :  0.659   7.673  18498  Z= 0.376
  Chirality :  0.045   0.228   2109
  Planarity :  0.004   0.042   1335
  Dihedral  : 31.251 179.250   4096
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 17.41 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.50 (0.29), residues: 743
  helix:  2.27 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.24 (0.39), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  42 
 TYR   0.011   0.002   TYR B  51 
 PHE   0.014   0.002   PHE A  67 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.18 (12775)
  covalent geometry    : angle       0.65887 /  0.38 (18498)
  hydrogen bonds       : bond        0.06353 /  4.26 (  736)
  hydrogen bonds       : angle       3.09113 /  2.20 ( 1861)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8502 (pm20) cc_final: 0.8261 (pm20)
REVERT: A  120 MET cc_start: 0.8515 (mtt) cc_final: 0.8299 (mtp)
REVERT: A  131 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7557 (mtp180)
REVERT: B   52 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7717 (mp0)
REVERT: B   79 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8450 (mtmm)
REVERT: C   36 LYS cc_start: 0.8513 (mmtm) cc_final: 0.8232 (mmpt)
REVERT: C   92 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8053 (mt-10)
REVERT: F   27 GLN cc_start: 0.8640 (mm110) cc_final: 0.8334 (mm110)
REVERT: F   77 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8136 (mtpt)
REVERT: F   93 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7852 (mt0)
REVERT: G   15 LYS cc_start: 0.7722 (mtpt) cc_final: 0.6949 (tttt)
REVERT: G   71 ARG cc_start: 0.7691 (tmm-80) cc_final: 0.7289 (ttp80)
REVERT: G   75 LYS cc_start: 0.8466 (mmtm) cc_final: 0.8210 (mmtm)
REVERT: G   95 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8419 (tmtm)
  outliers start: 16
  outliers final: 9
  residues processed: 153
  average time/residue: 0.8051
  time to fit residues: 129.7141
Evaluate side-chains
  160 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue   85 THR
Chi-restraints excluded: chain H residue  109 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 80 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9980
   chunk 60 optimal weight:    0.5980
   chunk 68 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 84 optimal weight:   20.0000
   chunk 39 optimal weight:    0.6980
   chunk 79 optimal weight:    9.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
C 104 GLN
E  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.176369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.133582 restraints weight = 10762.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 0.91
r_work: 0.3353 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  12775  Z= 0.140
  Angle     :  0.634   7.656  18498  Z= 0.364
  Chirality :  0.043   0.219   2109
  Planarity :  0.004   0.039   1335
  Dihedral  : 31.229 179.231   4096
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 17.88 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.64 (0.29), residues: 743
  helix:  2.39 (0.21), residues: 557
  sheet:  None (None), residues: 0
  loop : -0.23 (0.39), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  42 
 TYR   0.012   0.002   TYR H  80 
 PHE   0.013   0.001   PHE A  67 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.14 (12775)
  covalent geometry    : angle       0.63374 /  0.36 (18498)
  hydrogen bonds       : bond        0.05713 /  3.79 (  736)
  hydrogen bonds       : angle       3.08484 /  2.20 ( 1861)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8446 (pm20) cc_final: 0.8186 (pm20)
REVERT: A  120 MET cc_start: 0.8495 (mtt) cc_final: 0.8274 (mtp)
REVERT: A  131 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7556 (mtp180)
REVERT: B   52 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7700 (mp0)
REVERT: B   79 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8443 (mtmm)
REVERT: C   36 LYS cc_start: 0.8496 (mmtm) cc_final: 0.8212 (mmpt)
REVERT: C   92 GLU cc_start: 0.8251 (mt-10) cc_final: 0.8024 (mt-10)
REVERT: F   27 GLN cc_start: 0.8619 (mm110) cc_final: 0.8312 (mm110)
REVERT: F   77 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8126 (mtpt)
REVERT: F   93 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7800 (mt0)
REVERT: G   15 LYS cc_start: 0.7722 (mtpt) cc_final: 0.6959 (tttt)
REVERT: G   71 ARG cc_start: 0.7673 (tmm-80) cc_final: 0.7264 (ttp80)
REVERT: G   75 LYS cc_start: 0.8454 (mmtm) cc_final: 0.8194 (mmtm)
REVERT: G   95 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8409 (tmtm)
  outliers start: 15
  outliers final: 9
  residues processed: 151
  average time/residue: 0.8328
  time to fit residues: 132.3310
Evaluate side-chains
  158 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue   85 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 36 optimal weight:    8.9990
   chunk 90 optimal weight:   20.0000
   chunk 31 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 93 optimal weight:   10.0000
   chunk 5 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 88 optimal weight:   20.0000
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
C 104 GLN
E  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.175650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.132692 restraints weight = 10794.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 0.93
r_work: 0.3339 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.3184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  12775  Z= 0.168
  Angle     :  0.647   7.505  18498  Z= 0.370
  Chirality :  0.044   0.233   2109
  Planarity :  0.004   0.041   1335
  Dihedral  : 31.210 179.657   4096
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 18.04 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.60 (0.29), residues: 743
  helix:  2.35 (0.21), residues: 557
  sheet:  None (None), residues: 0
  loop : -0.22 (0.39), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  42 
 TYR   0.012   0.002   TYR G  57 
 PHE   0.014   0.002   PHE A  67 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.17 (12775)
  covalent geometry    : angle       0.64702 /  0.37 (18498)
  hydrogen bonds       : bond        0.06149 /  4.11 (  736)
  hydrogen bonds       : angle       3.07831 /  2.19 ( 1861)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8524 (pm20) cc_final: 0.8302 (pm20)
REVERT: A  120 MET cc_start: 0.8502 (mtt) cc_final: 0.8282 (mtp)
REVERT: A  131 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7523 (mtp180)
REVERT: B   52 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7711 (mp0)
REVERT: B   79 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8450 (mtmm)
REVERT: C   36 LYS cc_start: 0.8509 (mmtm) cc_final: 0.8230 (mmpt)
REVERT: C   92 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8049 (mt-10)
REVERT: F   27 GLN cc_start: 0.8624 (mm110) cc_final: 0.8305 (mm110)
REVERT: F   77 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8140 (mtpt)
REVERT: F   93 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7829 (mt0)
REVERT: G   15 LYS cc_start: 0.7730 (mtpt) cc_final: 0.6962 (tttt)
REVERT: G   71 ARG cc_start: 0.7676 (tmm-80) cc_final: 0.7263 (ttp80)
REVERT: G   75 LYS cc_start: 0.8467 (mmtm) cc_final: 0.8210 (mmtm)
REVERT: G   95 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8419 (tmtm)
  outliers start: 15
  outliers final: 8
  residues processed: 151
  average time/residue: 0.8483
  time to fit residues: 134.6933
Evaluate side-chains
  158 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue   85 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 74 optimal weight:    9.9990
   chunk 92 optimal weight:    9.9990
   chunk 62 optimal weight:    0.5980
   chunk 21 optimal weight:    4.9990
   chunk 90 optimal weight:   20.0000
   chunk 37 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 93 optimal weight:   10.0000
   overall best weight:    2.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
C 104 GLN
E  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.175076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.132137 restraints weight = 10694.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 0.92
r_work: 0.3334 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  12775  Z= 0.184
  Angle     :  0.667   7.467  18498  Z= 0.378
  Chirality :  0.046   0.249   2109
  Planarity :  0.005   0.041   1335
  Dihedral  : 31.323 178.636   4096
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 17.88 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.29), residues: 743
  helix:  2.21 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.19 (0.39), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  42 
 TYR   0.013   0.002   TYR H  80 
 PHE   0.014   0.002   PHE A  67 
 HIS   0.006   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.18 (12775)
  covalent geometry    : angle       0.66673 /  0.38 (18498)
  hydrogen bonds       : bond        0.06479 /  4.36 (  736)
  hydrogen bonds       : angle       3.12647 /  2.23 ( 1861)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4846.86 seconds
wall clock time: 82 minutes 56.72 seconds (4976.72 seconds total)