Starting phenix.real_space_refine
on Tue Mar 11 23:18:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gh8_40036/03_2025/8gh8_40036.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gh8_40036/03_2025/8gh8_40036.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gh8_40036/03_2025/8gh8_40036.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gh8_40036/03_2025/8gh8_40036.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gh8_40036/03_2025/8gh8_40036.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gh8_40036/03_2025/8gh8_40036.cif"
  }
  resolution = 4.3
  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=   0.063
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     136      5.49       5
     S       4      5.16       5
     C    4084      2.51       5
     N    1216      2.21       5
     O    1551      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6991
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1053
          Classifications: {'peptide': 140}
          Link IDs: {'PTRANS': 8, 'TRANS': 131}
    Chain: "B"
      Number of atoms: 1044
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1044
          Classifications: {'peptide': 139}
          Link IDs: {'PTRANS': 8, 'TRANS': 130}
    Chain: "C"
      Number of atoms: 1053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1053
          Classifications: {'peptide': 140}
          Link IDs: {'PTRANS': 8, 'TRANS': 131}
    Chain: "D"
      Number of atoms: 1053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1053
          Classifications: {'peptide': 140}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 131}
    Chain: "E"
      Number of atoms: 693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 693
          Classifications: {'DNA': 34}
          Link IDs: {'rna3p': 33}
    Chain: "F"
      Number of atoms: 701
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 701
          Classifications: {'DNA': 34}
          Link IDs: {'rna3p': 33}
    Chain: "G"
      Number of atoms: 693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 693
          Classifications: {'DNA': 34}
          Link IDs: {'rna3p': 33}
    Chain: "H"
      Number of atoms: 701
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 701
          Classifications: {'DNA': 34}
          Link IDs: {'rna3p': 33}
  Time building chain proxies: 4.51, per 1000 atoms: 0.65
  Number of scatterers: 6991
  At special positions: 0
  Unit cell: (164.35, 167.2, 69.35, 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       4     16.00
     P     136     15.00
     O    1551      8.00
     N    1216      7.00
     C    4084      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: 1.65
  Conformation dependent library (CDL) restraints added in 646.2 milliseconds
  

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  982

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 5 sheets defined
      23.4% alpha, 5.2% beta
      16 base pairs and 56 stacking pairs defined.
    Time for finding SS restraints: 2.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 31 through 36
      removed outlier: 3.558A  pdb=" N   GLN A  36 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 75
    Processing helix  chain 'A' and resid 96 through 102
    Processing helix  chain 'A' and resid 104 through 111
    Processing helix  chain 'A' and resid 117 through 122
    Processing helix  chain 'A' and resid 124 through 129
      removed outlier: 4.400A  pdb=" N   LYS A 128 " --> pdb=" O   ALA A 124 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   GLY A 129 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 124 through 129'
    Processing helix  chain 'B' and resid 31 through 38
    Processing helix  chain 'B' and resid 70 through 75
    Processing helix  chain 'B' and resid 98 through 102
      removed outlier: 3.910A  pdb=" N   LEU B 102 " --> pdb=" O   ARG B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 124
      removed outlier: 3.978A  pdb=" N   ALA B 124 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 131
      removed outlier: 3.507A  pdb=" N   GLY B 129 " --> pdb=" O   GLU B 126 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 32 through 37
      removed outlier: 3.630A  pdb=" N   GLN C  36 " --> pdb=" O   PRO C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 74
      removed outlier: 3.936A  pdb=" N   PHE C  71 " --> pdb=" O   ASN C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 81 through 86
      removed outlier: 3.856A  pdb=" N   ALA C  85 " --> pdb=" O   GLY C  81 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   LEU C  86 " --> pdb=" O   PRO C  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 81 through 86'
    Processing helix  chain 'C' and resid 122 through 128
      removed outlier: 3.936A  pdb=" N   LYS C 128 " --> pdb=" O   ALA C 124 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 36
    Processing helix  chain 'D' and resid 67 through 75
      removed outlier: 3.788A  pdb=" N   PHE D  71 " --> pdb=" O   ASN D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 96 through 101
    Processing helix  chain 'D' and resid 106 through 110
      removed outlier: 3.788A  pdb=" N   THR D 110 " --> pdb=" O   ARG D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 124
      removed outlier: 3.906A  pdb=" N   ILE D 123 " --> pdb=" O   LEU D 119 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20
    Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 19
      removed outlier: 3.602A  pdb=" N   PHE B  26 " --> pdb=" O   LEU B  19 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   PHE B  27 " --> pdb=" O   LEU B  59 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 18 through 20
      removed outlier: 3.619A  pdb=" N   LEU C  59 " --> pdb=" O   PHE C  27 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLN C  29 " --> pdb=" O   LEU C  59 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 5 through 7
      removed outlier: 3.675A  pdb=" N   GLY D   7 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   VAL D  44 " --> pdb=" O   GLY D   7 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 17 through 19
      removed outlier: 5.622A  pdb=" N   PHE D  27 " --> pdb=" O   LEU D  59 " (cutoff:3.500A)

    56 hydrogen bonds defined for protein.
    135 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      38 hydrogen bonds
      76 hydrogen bond angles
      0 basepair planarities
      16 basepair parallelities
      56 stacking parallelities
  Total time for adding SS restraints: 1.45

  Time building geometry restraints manager: 1.99 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: 1417
        1.33 -     1.45: 2040
        1.45 -     1.57: 3666
        1.57 -     1.68: 268
        1.68 -     1.80: 8
  Bond restraints: 7399
  Sorted by residual:
  bond pdb=" N   ALA B  91 "
       pdb=" CA  ALA B  91 "
    ideal  model  delta    sigma   weight residual
    1.457  1.504 -0.047 1.29e-02 6.01e+03 1.32e+01
  bond pdb=" N   LEU B  89 "
       pdb=" CA  LEU B  89 "
    ideal  model  delta    sigma   weight residual
    1.457  1.502 -0.044 1.29e-02 6.01e+03 1.18e+01
  bond pdb=" N   SER C  90 "
       pdb=" CA  SER C  90 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.29e-02 6.01e+03 9.66e+00
  bond pdb=" C   PRO C 132 "
       pdb=" N   PRO C 133 "
    ideal  model  delta    sigma   weight residual
    1.332  1.366 -0.034 1.12e-02 7.97e+03 9.08e+00
  bond pdb=" N   ALA C  91 "
       pdb=" CA  ALA C  91 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.039 1.31e-02 5.83e+03 8.89e+00
  ... (remaining 7394 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 10199
        2.03 -     4.06: 335
        4.06 -     6.09: 39
        6.09 -     8.11: 10
        8.11 -    10.14: 2
  Bond angle restraints: 10585
  Sorted by residual:
  angle pdb=" N   SER B  90 "
        pdb=" CA  SER B  90 "
        pdb=" C   SER B  90 "
      ideal   model   delta    sigma   weight residual
     113.18  103.04   10.14 1.21e+00 6.83e-01 7.03e+01
  angle pdb=" C   GLU D  66 "
        pdb=" CA  GLU D  66 "
        pdb=" CB  GLU D  66 "
      ideal   model   delta    sigma   weight residual
     116.34  110.40    5.94 1.40e+00 5.10e-01 1.80e+01
  angle pdb=" O   LEU C  89 "
        pdb=" C   LEU C  89 "
        pdb=" N   SER C  90 "
      ideal   model   delta    sigma   weight residual
     121.79  117.64    4.15 9.80e-01 1.04e+00 1.79e+01
  angle pdb=" N   ALA C  91 "
        pdb=" CA  ALA C  91 "
        pdb=" C   ALA C  91 "
      ideal   model   delta    sigma   weight residual
     113.18  108.06    5.12 1.21e+00 6.83e-01 1.79e+01
  angle pdb=" CA  ALA B  91 "
        pdb=" C   ALA B  91 "
        pdb=" O   ALA B  91 "
      ideal   model   delta    sigma   weight residual
     120.51  115.14    5.37 1.43e+00 4.89e-01 1.41e+01
  ... (remaining 10580 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.99: 3523
       34.99 -    69.97: 580
       69.97 -   104.96: 23
      104.96 -   139.94: 1
      139.94 -   174.93: 6
  Dihedral angle restraints: 4133
    sinusoidal: 2588
      harmonic: 1545
  Sorted by residual:
  dihedral pdb=" CA  SER B  90 "
           pdb=" C   SER B  90 "
           pdb=" N   ALA B  91 "
           pdb=" CA  ALA B  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.15  -24.85     0      5.00e+00 4.00e-02 2.47e+01
  dihedral pdb=" CA  TYR A  60 "
           pdb=" C   TYR A  60 "
           pdb=" N   GLY A  61 "
           pdb=" CA  GLY A  61 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.63   24.37     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  PRO D  93 "
           pdb=" C   PRO D  93 "
           pdb=" N   PRO D  94 "
           pdb=" CA  PRO D  94 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.18  -21.82     0      5.00e+00 4.00e-02 1.90e+01
  ... (remaining 4130 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 1208
       0.113 -    0.226: 16
       0.226 -    0.338: 0
       0.338 -    0.451: 0
       0.451 -    0.564: 3
  Chirality restraints: 1227
  Sorted by residual:
  chirality pdb=" P    DG F  28 "
            pdb=" OP1  DG F  28 "
            pdb=" OP2  DG F  28 "
            pdb=" O5'  DG F  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.91   -0.56 2.00e-01 2.50e+01 7.95e+00
  chirality pdb=" P    DA F  30 "
            pdb=" OP1  DA F  30 "
            pdb=" OP2  DA F  30 "
            pdb=" O5'  DA F  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.85   -0.50 2.00e-01 2.50e+01 6.37e+00
  chirality pdb=" P    DA F  29 "
            pdb=" OP1  DA F  29 "
            pdb=" OP2  DA F  29 "
            pdb=" O5'  DA F  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.82   -0.48 2.00e-01 2.50e+01 5.69e+00
  ... (remaining 1224 not shown)

  Planarity restraints: 871
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C  89 "   -0.018 2.00e-02 2.50e+03   3.41e-02 1.16e+01
        pdb=" C   LEU C  89 "    0.059 2.00e-02 2.50e+03
        pdb=" O   LEU C  89 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   SER C  90 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D  93 "    0.045 5.00e-02 4.00e+02   6.77e-02 7.33e+00
        pdb=" N   PRO D  94 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO D  94 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO D  94 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B  93 "   -0.038 5.00e-02 4.00e+02   5.67e-02 5.15e+00
        pdb=" N   PRO B  94 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO B  94 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B  94 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 868 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 835
        2.76 -     3.29: 6239
        3.29 -     3.83: 11306
        3.83 -     4.36: 12441
        4.36 -     4.90: 19026
  Nonbonded interactions: 49847
  Sorted by model distance:
  nonbonded pdb=" O   ILE C   2 "
            pdb=" OG1 THR C  48 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   ALA A 106 "
            pdb=" OG1 THR A 110 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" N   LEU A   8 "
            pdb=" O   LEU A  20 "
     model   vdw
     2.294 3.120
  nonbonded pdb=" O   LEU A  88 "
            pdb=" NH1 ARG A 117 "
     model   vdw
     2.323 3.120
  nonbonded pdb=" NH2 ARG B   6 "
            pdb=" OE1 GLU B  43 "
     model   vdw
     2.327 3.120
  ... (remaining 49842 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 1 through 139)
  selection = chain 'B'
  selection = (chain 'C' and resid 1 through 139)
  selection = (chain 'D' and resid 1 through 139)
}
ncs_group {
  reference = chain 'E'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.840
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.470
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4247
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7399  Z= 0.254
  Angle     :  0.791  10.142  10585  Z= 0.443
  Chirality :  0.046   0.564   1227
  Planarity :  0.006   0.068    871
  Dihedral  : 26.603 174.929   3151
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  : 12.70 %
    Favored  : 86.75 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.00 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -3.65 (0.33), residues: 551
  helix: -2.08 (0.62), residues: 70
  sheet: -2.03 (1.10), residues: 18
  loop : -2.78 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  49 
 PHE   0.021   0.002   PHE C  17 
 TYR   0.017   0.002   TYR A  60 
 ARG   0.006   0.001   ARG A 122 

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.551 
Fit side-chains
REVERT: B   12 LYS cc_start: 0.8310 (tttm) cc_final: 0.7868 (ttpt)
REVERT: C    1 MET cc_start: 0.4402 (tpt) cc_final: 0.3078 (tpt)
REVERT: D    1 MET cc_start: 0.4949 (tpt) cc_final: 0.3107 (tpt)
  outliers start: 1
  outliers final: 1
  residues processed: 60
  average time/residue: 0.1961
  time to fit residues: 15.8029
Evaluate side-chains
  40 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 50 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 17 optimal weight:    0.1980
   chunk 34 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 60 optimal weight:   10.0000
   overall best weight:    0.9786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5335 r_free = 0.5335 target = 0.315478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4829 r_free = 0.4829 target = 0.262521 restraints weight = 79974.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4847 r_free = 0.4847 target = 0.267427 restraints weight = 33649.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4848 r_free = 0.4848 target = 0.266645 restraints weight = 27774.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.4672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5136
moved from start:          0.1036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7399  Z= 0.250
  Angle     :  0.726  11.999  10585  Z= 0.392
  Chirality :  0.038   0.167   1227
  Planarity :  0.006   0.069    871
  Dihedral  : 30.008 175.583   2143
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 10.89 %
    Favored  : 88.75 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  8.35 %
    Favored  : 91.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -3.77 (0.32), residues: 551
  helix: -2.22 (0.60), residues: 69
  sheet: -3.04 (1.97), residues: 6
  loop : -2.85 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  49 
 PHE   0.020   0.003   PHE C  62 
 TYR   0.019   0.003   TYR C  60 
 ARG   0.004   0.000   ARG A 117 

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.490 
Fit side-chains
REVERT: B   12 LYS cc_start: 0.8089 (tttm) cc_final: 0.7814 (ttpt)
REVERT: C    1 MET cc_start: 0.4786 (tpt) cc_final: 0.3730 (tpt)
  outliers start: 1
  outliers final: 1
  residues processed: 46
  average time/residue: 0.1400
  time to fit residues: 9.5446
Evaluate side-chains
  38 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 33 optimal weight:    0.2980
   chunk 18 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 16 optimal weight:    0.2980
   chunk 60 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0570
   chunk 48 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.9302

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

Flipped N/Q/H residues before XYZ refinement:
B 134 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5336 r_free = 0.5336 target = 0.315831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4836 r_free = 0.4836 target = 0.263706 restraints weight = 80160.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4862 r_free = 0.4862 target = 0.269286 restraints weight = 32135.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4857 r_free = 0.4857 target = 0.268082 restraints weight = 27582.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.4669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5116
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7399  Z= 0.240
  Angle     :  0.724  11.104  10585  Z= 0.390
  Chirality :  0.038   0.160   1227
  Planarity :  0.006   0.063    871
  Dihedral  : 29.890 175.547   2143
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 11.62 %
    Favored  : 88.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -3.82 (0.33), residues: 551
  helix: -2.22 (0.62), residues: 69
  sheet: -2.56 (0.89), residues: 24
  loop : -2.87 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A  49 
 PHE   0.019   0.002   PHE C  17 
 TYR   0.014   0.002   TYR A  60 
 ARG   0.006   0.000   ARG D  95 

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.498 
Fit side-chains
REVERT: B   12 LYS cc_start: 0.8104 (tttm) cc_final: 0.7855 (ttpt)
REVERT: C    1 MET cc_start: 0.4870 (tpt) cc_final: 0.3637 (tpt)
REVERT: D    1 MET cc_start: 0.4793 (tpt) cc_final: 0.3178 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.1259
  time to fit residues: 8.8037
Evaluate side-chains
  41 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 40 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 64 optimal weight:   10.0000
   chunk 57 optimal weight:   10.0000
   chunk 17 optimal weight:    0.0370
   chunk 53 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0000
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.9466

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5331 r_free = 0.5331 target = 0.315261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4820 r_free = 0.4820 target = 0.263433 restraints weight = 79476.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4832 r_free = 0.4832 target = 0.266673 restraints weight = 32540.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4840 r_free = 0.4840 target = 0.267094 restraints weight = 27901.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.4632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5164
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7399  Z= 0.237
  Angle     :  0.717  11.633  10585  Z= 0.386
  Chirality :  0.038   0.186   1227
  Planarity :  0.006   0.066    871
  Dihedral  : 29.799 175.723   2143
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 12.16 %
    Favored  : 87.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -3.83 (0.33), residues: 551
  helix: -2.16 (0.62), residues: 70
  sheet: -2.65 (0.88), residues: 24
  loop : -2.89 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  49 
 PHE   0.020   0.002   PHE C  17 
 TYR   0.015   0.002   TYR C  60 
 ARG   0.004   0.000   ARG D  99 

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.538 
Fit side-chains
REVERT: B   12 LYS cc_start: 0.8104 (tttm) cc_final: 0.7873 (ttpt)
REVERT: C    1 MET cc_start: 0.4796 (tpt) cc_final: 0.3597 (tpt)
REVERT: D    1 MET cc_start: 0.4713 (tpt) cc_final: 0.3131 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.1325
  time to fit residues: 8.9033
Evaluate side-chains
  39 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0470
   chunk 55 optimal weight:   20.0000
   chunk 44 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 58 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0170
   chunk 12 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.6116

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  49 HIS ** 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 = 0.5338 r_free = 0.5338 target = 0.317044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4854 r_free = 0.4854 target = 0.267369 restraints weight = 79529.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4867 r_free = 0.4867 target = 0.269916 restraints weight = 32876.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4867 r_free = 0.4867 target = 0.269762 restraints weight = 28488.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.4698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5010
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7399  Z= 0.213
  Angle     :  0.699  11.769  10585  Z= 0.379
  Chirality :  0.037   0.166   1227
  Planarity :  0.006   0.067    871
  Dihedral  : 29.731 175.462   2143
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 12.52 %
    Favored  : 87.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -3.72 (0.33), residues: 551
  helix: -2.14 (0.62), residues: 69
  sheet: -2.46 (1.00), residues: 18
  loop : -2.81 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A  49 
 PHE   0.018   0.002   PHE D  17 
 TYR   0.018   0.002   TYR D  60 
 ARG   0.003   0.000   ARG D  99 

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.497 
Fit side-chains
REVERT: B   12 LYS cc_start: 0.8103 (tttm) cc_final: 0.7778 (ttpt)
REVERT: C    1 MET cc_start: 0.4611 (tpt) cc_final: 0.3586 (tpt)
REVERT: D    1 MET cc_start: 0.4605 (tpt) cc_final: 0.3127 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1324
  time to fit residues: 9.9010
Evaluate side-chains
  40 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 64 optimal weight:   10.0000
   chunk 53 optimal weight:    4.9990
   chunk 30 optimal weight:    0.2980
   chunk 5 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0270
   chunk 34 optimal weight:    3.9990
   chunk 62 optimal weight:    9.9990
   chunk 7 optimal weight:    1.9990
   chunk 36 optimal weight:    0.2980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.6440

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5329 r_free = 0.5329 target = 0.315165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4960 r_free = 0.4960 target = 0.274648 restraints weight = 80700.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4982 r_free = 0.4982 target = 0.279241 restraints weight = 35640.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4975 r_free = 0.4975 target = 0.278266 restraints weight = 30121.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.4819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4691
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7399  Z= 0.209
  Angle     :  0.691  11.316  10585  Z= 0.373
  Chirality :  0.037   0.164   1227
  Planarity :  0.006   0.068    871
  Dihedral  : 29.654 175.572   2143
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 11.25 %
    Favored  : 88.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -3.88 (0.33), residues: 551
  helix: -2.19 (0.62), residues: 70
  sheet: -4.39 (0.69), residues: 24
  loop : -2.81 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C  47 
 PHE   0.018   0.002   PHE D  17 
 TYR   0.015   0.002   TYR D  60 
 ARG   0.003   0.000   ARG D  99 

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.588 
Fit side-chains
REVERT: B   12 LYS cc_start: 0.8141 (tttm) cc_final: 0.7912 (ttpt)
REVERT: C    1 MET cc_start: 0.4577 (tpt) cc_final: 0.3584 (tpt)
REVERT: D    1 MET cc_start: 0.4790 (tpt) cc_final: 0.3315 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1404
  time to fit residues: 10.2723
Evaluate side-chains
  41 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0470
   chunk 64 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   chunk 19 optimal weight:    0.0570
   chunk 12 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.4998

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5361 r_free = 0.5361 target = 0.321420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.5018 r_free = 0.5018 target = 0.283044 restraints weight = 82030.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.5026 r_free = 0.5026 target = 0.285662 restraints weight = 36243.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.5030 r_free = 0.5030 target = 0.285723 restraints weight = 30557.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.4876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4571
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7399  Z= 0.198
  Angle     :  0.677  11.470  10585  Z= 0.366
  Chirality :  0.036   0.155   1227
  Planarity :  0.006   0.070    871
  Dihedral  : 29.592 175.482   2143
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 11.43 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -3.76 (0.33), residues: 551
  helix: -2.12 (0.62), residues: 69
  sheet: -2.82 (0.84), residues: 24
  loop : -2.82 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B  49 
 PHE   0.024   0.002   PHE C  26 
 TYR   0.023   0.002   TYR C   4 
 ARG   0.002   0.000   ARG D  95 

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.523 
Fit side-chains
REVERT: B   12 LYS cc_start: 0.8078 (tttm) cc_final: 0.7857 (ttpt)
REVERT: C    1 MET cc_start: 0.4507 (tpt) cc_final: 0.3493 (tpt)
REVERT: D    1 MET cc_start: 0.4601 (tpt) cc_final: 0.3221 (tpt)
REVERT: D  128 LYS cc_start: 0.5511 (ptpp) cc_final: 0.3884 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.1373
  time to fit residues: 9.1527
Evaluate side-chains
  40 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 58 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 36 optimal weight:    0.2980
   chunk 26 optimal weight:    0.0670
   chunk 47 optimal weight:    0.8980
   overall best weight:    1.0522

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5322 r_free = 0.5322 target = 0.314109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4948 r_free = 0.4948 target = 0.273046 restraints weight = 81533.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4965 r_free = 0.4965 target = 0.277247 restraints weight = 37989.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4958 r_free = 0.4958 target = 0.275898 restraints weight = 30159.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.4806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4739
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7399  Z= 0.240
  Angle     :  0.708  11.385  10585  Z= 0.380
  Chirality :  0.037   0.164   1227
  Planarity :  0.006   0.073    871
  Dihedral  : 29.567 176.069   2143
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 13.43 %
    Favored  : 86.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -3.89 (0.33), residues: 551
  helix: -2.21 (0.62), residues: 71
  sheet: -2.90 (0.84), residues: 24
  loop : -2.92 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  47 
 PHE   0.035   0.003   PHE C  26 
 TYR   0.014   0.002   TYR D  60 
 ARG   0.003   0.000   ARG C 118 

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.502 
Fit side-chains
REVERT: B   12 LYS cc_start: 0.8195 (tttm) cc_final: 0.7905 (ttpt)
REVERT: C    1 MET cc_start: 0.4742 (tpt) cc_final: 0.3475 (tpt)
REVERT: D    1 MET cc_start: 0.4873 (tpt) cc_final: 0.3401 (tpt)
REVERT: D  128 LYS cc_start: 0.5522 (ptpp) cc_final: 0.3904 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1394
  time to fit residues: 10.0164
Evaluate side-chains
  41 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0770
   chunk 56 optimal weight:   10.0000
   chunk 59 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 63 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0170
   chunk 44 optimal weight:    0.7980
   chunk 66 optimal weight:   20.0000
   chunk 61 optimal weight:   10.0000
   overall best weight:    0.9778

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  49 HIS ** 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 = 0.5320 r_free = 0.5320 target = 0.313521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4934 r_free = 0.4934 target = 0.272601 restraints weight = 78923.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4952 r_free = 0.4952 target = 0.276493 restraints weight = 34999.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4949 r_free = 0.4949 target = 0.275318 restraints weight = 28699.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.4795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4774
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7399  Z= 0.240
  Angle     :  0.713  11.413  10585  Z= 0.381
  Chirality :  0.037   0.159   1227
  Planarity :  0.006   0.068    871
  Dihedral  : 29.520 176.188   2143
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 12.70 %
    Favored  : 87.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -3.88 (0.33), residues: 551
  helix: -2.15 (0.63), residues: 70
  sheet: -2.72 (0.88), residues: 24
  loop : -2.93 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C  47 
 PHE   0.042   0.003   PHE C  26 
 TYR   0.014   0.002   TYR C   4 
 ARG   0.003   0.000   ARG D  95 

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.507 
Fit side-chains
REVERT: B   12 LYS cc_start: 0.8097 (tttm) cc_final: 0.7759 (ttpt)
REVERT: C    1 MET cc_start: 0.4776 (tpt) cc_final: 0.3709 (tpt)
REVERT: D    1 MET cc_start: 0.4808 (tpt) cc_final: 0.3244 (tpt)
REVERT: D    2 ILE cc_start: 0.6137 (mt) cc_final: 0.5101 (pt)
REVERT: D  128 LYS cc_start: 0.5536 (ptpp) cc_final: 0.3972 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.1419
  time to fit residues: 9.7821
Evaluate side-chains
  42 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.1980
   chunk 41 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 56 optimal weight:   10.0000
   chunk 16 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0070
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  49 HIS ** 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 = 0.5332 r_free = 0.5332 target = 0.315950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4972 r_free = 0.4972 target = 0.276206 restraints weight = 81456.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4988 r_free = 0.4988 target = 0.280374 restraints weight = 37007.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4980 r_free = 0.4980 target = 0.278964 restraints weight = 29914.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.4839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4669
moved from start:          0.3009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7399  Z= 0.205
  Angle     :  0.692  11.459  10585  Z= 0.371
  Chirality :  0.036   0.154   1227
  Planarity :  0.006   0.067    871
  Dihedral  : 29.455 175.769   2143
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 11.98 %
    Favored  : 87.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -3.80 (0.33), residues: 551
  helix: -2.14 (0.63), residues: 70
  sheet: -2.60 (0.91), residues: 22
  loop : -2.87 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A  49 
 PHE   0.027   0.002   PHE C  26 
 TYR   0.014   0.002   TYR C   4 
 ARG   0.003   0.000   ARG D  95 

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.562 
Fit side-chains
REVERT: B   12 LYS cc_start: 0.8145 (tttm) cc_final: 0.7834 (ttpt)
REVERT: C    1 MET cc_start: 0.4550 (tpt) cc_final: 0.3653 (tpt)
REVERT: D    1 MET cc_start: 0.4494 (tpt) cc_final: 0.3152 (tpt)
REVERT: D  128 LYS cc_start: 0.5491 (ptpp) cc_final: 0.3940 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.1419
  time to fit residues: 9.4328
Evaluate side-chains
  41 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0010
   chunk 3 optimal weight:    0.7980
   chunk 38 optimal weight:    7.9990
   chunk 60 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 1 optimal weight:    0.4980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  49 HIS ** 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 = 0.5333 r_free = 0.5333 target = 0.316047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4922 r_free = 0.4922 target = 0.276839 restraints weight = 80424.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4948 r_free = 0.4948 target = 0.281063 restraints weight = 31718.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4940 r_free = 0.4940 target = 0.279829 restraints weight = 28354.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.4697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5048
moved from start:          0.3050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7399  Z= 0.208
  Angle     :  0.687  11.575  10585  Z= 0.369
  Chirality :  0.036   0.154   1227
  Planarity :  0.006   0.072    871
  Dihedral  : 29.439 175.768   2143
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 12.16 %
    Favored  : 87.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -3.80 (0.33), residues: 551
  helix: -2.11 (0.63), residues: 70
  sheet: -2.83 (1.18), residues: 12
  loop : -2.89 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  49 
 PHE   0.025   0.002   PHE C  26 
 TYR   0.010   0.002   TYR A  60 
 ARG   0.003   0.000   ARG D  95 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2026.99 seconds
wall clock time: 35 minutes 46.19 seconds (2146.19 seconds total)