Starting phenix.real_space_refine
on Fri Aug 22 18:28:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gh8_40036/08_2025/8gh8_40036.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gh8_40036/08_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_40036/08_2025/8gh8_40036.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gh8_40036/08_2025/8gh8_40036.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gh8_40036/08_2025/8gh8_40036.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gh8_40036/08_2025/8gh8_40036.cif"
  }
  resolution = 4.3
  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=   0.001 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.83, per 1000 atoms: 0.26
  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: 0.60
  Conformation dependent library (CDL) restraints added in 298.3 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.75
  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: 0.89

  Time building geometry restraints manager: 0.80 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:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.250
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.940
-------------------------------------------------------------------------------
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= 0.212
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.006   0.001   ARG A 122 
 TYR   0.017   0.002   TYR A  60 
 PHE   0.021   0.002   PHE C  17 
 HIS   0.004   0.001   HIS B  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 7399)
  covalent geometry    : angle       0.79056 (10585)
  hydrogen bonds       : bond        0.18757 (   94)
  hydrogen bonds       : angle       5.41283 (  211)

*********************** 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  : 0.200 
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: 0.0892
  time to fit residues: 7.2508
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  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.7188

-------------------------------------------------------------------------------
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 = 0.5326 r_free = 0.5326 target = 0.312685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4829 r_free = 0.4829 target = 0.261245 restraints weight = 82003.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4853 r_free = 0.4853 target = 0.266862 restraints weight = 34925.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4844 r_free = 0.4844 target = 0.264833 restraints weight = 28276.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4845 r_free = 0.4845 target = 0.265211 restraints weight = 28965.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4846 r_free = 0.4846 target = 0.264800 restraints weight = 26131.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.4663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5292
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   7399  Z= 0.223
  Angle     :  0.791  11.745  10585  Z= 0.422
  Chirality :  0.040   0.178   1227
  Planarity :  0.006   0.069    871
  Dihedral  : 30.028 176.473   2143
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 13.61 %
    Favored  : 86.03 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 11.37 %
    Favored  : 88.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 aren not related in a simple way.
  whole: -3.99 (0.32), residues: 551
  helix: -2.34 (0.60), residues: 70
  sheet: -2.38 (1.26), residues: 16
  loop : -3.03 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C   3 
 TYR   0.019   0.004   TYR A  60 
 PHE   0.028   0.004   PHE D  17 
 HIS   0.007   0.001   HIS D  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 7399)
  covalent geometry    : angle       0.79095 (10585)
  hydrogen bonds       : bond        0.04799 (   94)
  hydrogen bonds       : angle       5.20753 (  211)

*********************** 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
  44 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.145 
Fit side-chains
REVERT: B   12 LYS cc_start: 0.8158 (tttm) cc_final: 0.7857 (ttpt)
REVERT: C    1 MET cc_start: 0.5191 (tpt) cc_final: 0.3913 (tpt)
REVERT: C   95 ARG cc_start: 0.6548 (mmt180) cc_final: 0.3710 (tpm170)
REVERT: D    1 MET cc_start: 0.5063 (tpt) cc_final: 0.3177 (tpt)
  outliers start: 2
  outliers final: 1
  residues processed: 44
  average time/residue: 0.0734
  time to fit residues: 4.3904
Evaluate side-chains
  37 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 64 optimal weight:   20.0000
   chunk 17 optimal weight:    0.5980
   chunk 36 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0770
   chunk 32 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 60 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.7140

-------------------------------------------------------------------------------
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**
B 134 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5331 r_free = 0.5331 target = 0.315346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4842 r_free = 0.4842 target = 0.264511 restraints weight = 80104.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4863 r_free = 0.4863 target = 0.269329 restraints weight = 32272.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4862 r_free = 0.4862 target = 0.268212 restraints weight = 27460.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4861 r_free = 0.4861 target = 0.268780 restraints weight = 27859.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4860 r_free = 0.4860 target = 0.267787 restraints weight = 25480.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.4695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5073
moved from start:          0.1521

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= 0.164
  Angle     :  0.724  11.273  10585  Z= 0.390
  Chirality :  0.038   0.188   1227
  Planarity :  0.006   0.064    871
  Dihedral  : 29.911 175.577   2143
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 11.62 %
    Favored  : 88.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 aren not related in a simple way.
  whole: -3.90 (0.32), residues: 551
  helix: -2.29 (0.61), residues: 70
  sheet: -2.61 (0.92), residues: 22
  loop : -2.93 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  99 
 TYR   0.013   0.002   TYR A  60 
 PHE   0.019   0.002   PHE C  17 
 HIS   0.006   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 7399)
  covalent geometry    : angle       0.72389 (10585)
  hydrogen bonds       : bond        0.03950 (   94)
  hydrogen bonds       : angle       5.02960 (  211)

*********************** 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
  43 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.187 
Fit side-chains
REVERT: B   12 LYS cc_start: 0.8164 (tttm) cc_final: 0.7858 (ttpt)
REVERT: C    1 MET cc_start: 0.5019 (tpt) cc_final: 0.3843 (tpt)
REVERT: D    1 MET cc_start: 0.5151 (tpt) cc_final: 0.3566 (tpt)
REVERT: D   60 TYR cc_start: 0.4606 (m-80) cc_final: 0.4090 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.0487
  time to fit residues: 3.2585
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  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 55 optimal weight:   30.0000
   chunk 40 optimal weight:   20.0000
   chunk 26 optimal weight:    0.3980
   chunk 61 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 66 optimal weight:   10.0000
   chunk 33 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    9.9990
   chunk 51 optimal weight:    9.9990
   overall best weight:    2.5784

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

Flipped N/Q/H residues before XYZ refinement:
** B  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 = 0.5275 r_free = 0.5275 target = 0.305446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.246980 restraints weight = 79448.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.252248 restraints weight = 34026.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.249629 restraints weight = 27606.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4704 r_free = 0.4704 target = 0.250487 restraints weight = 28857.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.250004 restraints weight = 25750.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.4512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5507
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.073   7399  Z= 0.282
  Angle     :  0.895  11.890  10585  Z= 0.463
  Chirality :  0.044   0.195   1227
  Planarity :  0.007   0.066    871
  Dihedral  : 29.957 177.868   2143
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  : 15.79 %
    Favored  : 83.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 aren not related in a simple way.
  whole: -4.18 (0.32), residues: 551
  helix: -2.04 (0.71), residues: 57
  sheet: -2.92 (1.20), residues: 18
  loop : -3.21 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D   6 
 TYR   0.020   0.004   TYR A  60 
 PHE   0.032   0.004   PHE C  17 
 HIS   0.010   0.002   HIS C  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00684 ( 7399)
  covalent geometry    : angle       0.89524 (10585)
  hydrogen bonds       : bond        0.05582 (   94)
  hydrogen bonds       : angle       5.76019 (  211)

*********************** 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
  42 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.130 
Fit side-chains
REVERT: B   12 LYS cc_start: 0.8141 (tttm) cc_final: 0.7875 (ttpt)
REVERT: C    1 MET cc_start: 0.4958 (tpt) cc_final: 0.3423 (tpt)
REVERT: C   95 ARG cc_start: 0.6607 (mmt180) cc_final: 0.3769 (tpm170)
REVERT: C  102 LEU cc_start: 0.4264 (tp) cc_final: 0.4056 (tp)
REVERT: C  131 VAL cc_start: 0.5045 (t) cc_final: 0.4824 (t)
REVERT: D    1 MET cc_start: 0.5041 (tpt) cc_final: 0.2816 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0656
  time to fit residues: 3.8643
Evaluate side-chains
  35 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 0 optimal weight:    0.5980
   chunk 63 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 24 optimal weight:    7.9990
   chunk 28 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 57 optimal weight:   10.0000
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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**
B  49 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5334 r_free = 0.5334 target = 0.315420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4815 r_free = 0.4815 target = 0.262664 restraints weight = 80617.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4821 r_free = 0.4821 target = 0.265186 restraints weight = 33279.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4826 r_free = 0.4826 target = 0.265495 restraints weight = 29588.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4820 r_free = 0.4820 target = 0.264578 restraints weight = 27515.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4825 r_free = 0.4825 target = 0.264413 restraints weight = 26073.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.4667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5158
moved from start:          0.2324

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= 0.163
  Angle     :  0.735  12.381  10585  Z= 0.395
  Chirality :  0.038   0.177   1227
  Planarity :  0.006   0.065    871
  Dihedral  : 29.821 175.784   2143
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 11.80 %
    Favored  : 88.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 aren not related in a simple way.
  whole: -4.07 (0.33), residues: 551
  helix: -2.35 (0.60), residues: 76
  sheet: -3.49 (1.14), residues: 12
  loop : -3.06 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  95 
 TYR   0.014   0.002   TYR A  60 
 PHE   0.027   0.003   PHE C  26 
 HIS   0.006   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 7399)
  covalent geometry    : angle       0.73471 (10585)
  hydrogen bonds       : bond        0.03559 (   94)
  hydrogen bonds       : angle       5.24103 (  211)

*********************** 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
  44 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   64 ASP cc_start: 0.6422 (t70) cc_final: 0.5488 (t70)
REVERT: B   12 LYS cc_start: 0.8278 (tttm) cc_final: 0.7893 (ttpp)
REVERT: C    1 MET cc_start: 0.5379 (tpt) cc_final: 0.4305 (tpt)
REVERT: D    1 MET cc_start: 0.4656 (tpt) cc_final: 0.3179 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.0572
  time to fit residues: 3.7967
Evaluate side-chains
  36 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 10 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    8.9990
   chunk 13 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   chunk 42 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    2.0786

-------------------------------------------------------------------------------
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 = 0.5283 r_free = 0.5283 target = 0.307529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.250086 restraints weight = 80354.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4739 r_free = 0.4739 target = 0.255137 restraints weight = 33573.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4733 r_free = 0.4733 target = 0.253712 restraints weight = 29644.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4732 r_free = 0.4732 target = 0.253808 restraints weight = 28672.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4730 r_free = 0.4730 target = 0.253276 restraints weight = 26132.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.4554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5436
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   7399  Z= 0.243
  Angle     :  0.848  12.773  10585  Z= 0.444
  Chirality :  0.041   0.213   1227
  Planarity :  0.007   0.065    871
  Dihedral  : 29.844 177.486   2143
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 16.15 %
    Favored  : 83.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 aren not related in a simple way.
  whole: -4.28 (0.32), residues: 551
  helix: -2.43 (0.61), residues: 71
  sheet: -2.07 (1.58), residues: 12
  loop : -3.28 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D   6 
 TYR   0.031   0.004   TYR D  60 
 PHE   0.053   0.005   PHE C  26 
 HIS   0.007   0.002   HIS D  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00588 ( 7399)
  covalent geometry    : angle       0.84753 (10585)
  hydrogen bonds       : bond        0.04995 (   94)
  hydrogen bonds       : angle       5.83572 (  211)

*********************** 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
  41 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A  126 GLU cc_start: 0.7191 (pm20) cc_final: 0.6943 (tp30)
REVERT: B   12 LYS cc_start: 0.8271 (tttm) cc_final: 0.7908 (ttpt)
REVERT: C    1 MET cc_start: 0.5217 (tpt) cc_final: 0.3904 (tpt)
REVERT: C   48 THR cc_start: 0.6299 (p) cc_final: 0.6031 (p)
REVERT: D    1 MET cc_start: 0.5151 (tpt) cc_final: 0.3235 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0590
  time to fit residues: 3.6004
Evaluate side-chains
  34 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 56 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 30 optimal weight:    0.5980
   chunk 37 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0050
   chunk 24 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.5194

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5328 r_free = 0.5328 target = 0.314607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4876 r_free = 0.4876 target = 0.270427 restraints weight = 82733.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4893 r_free = 0.4893 target = 0.275056 restraints weight = 33799.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4892 r_free = 0.4892 target = 0.273718 restraints weight = 28088.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4891 r_free = 0.4891 target = 0.273584 restraints weight = 27721.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4895 r_free = 0.4895 target = 0.273557 restraints weight = 26365.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.4715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5038
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7399  Z= 0.157
  Angle     :  0.734  12.535  10585  Z= 0.392
  Chirality :  0.038   0.181   1227
  Planarity :  0.006   0.067    871
  Dihedral  : 29.701 175.688   2143
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 12.34 %
    Favored  : 87.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 aren not related in a simple way.
  whole: -4.08 (0.32), residues: 551
  helix: -2.24 (0.61), residues: 75
  sheet: -3.07 (1.61), residues: 6
  loop : -3.12 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  95 
 TYR   0.018   0.002   TYR D  60 
 PHE   0.024   0.003   PHE C  62 
 HIS   0.003   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 7399)
  covalent geometry    : angle       0.73392 (10585)
  hydrogen bonds       : bond        0.03778 (   94)
  hydrogen bonds       : angle       5.27270 (  211)

*********************** 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
  45 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.131 
Fit side-chains
REVERT: B   12 LYS cc_start: 0.8238 (tttm) cc_final: 0.7802 (ttpp)
REVERT: C    1 MET cc_start: 0.5022 (tpt) cc_final: 0.4004 (tpt)
REVERT: C   60 TYR cc_start: 0.4196 (m-80) cc_final: 0.3964 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0555
  time to fit residues: 3.7059
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  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 60 optimal weight:   10.0000
   chunk 8 optimal weight:    0.0670
   chunk 11 optimal weight:    8.9990
   chunk 16 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0980
   chunk 66 optimal weight:   20.0000
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.4318

-------------------------------------------------------------------------------
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 = 0.315562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4957 r_free = 0.4957 target = 0.275057 restraints weight = 82060.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4976 r_free = 0.4976 target = 0.279964 restraints weight = 38306.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4972 r_free = 0.4972 target = 0.278878 restraints weight = 29529.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4970 r_free = 0.4970 target = 0.278718 restraints weight = 30316.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4972 r_free = 0.4972 target = 0.278743 restraints weight = 28449.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.4842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4712
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7399  Z= 0.151
  Angle     :  0.704  11.411  10585  Z= 0.378
  Chirality :  0.037   0.164   1227
  Planarity :  0.006   0.069    871
  Dihedral  : 29.550 175.245   2143
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 13.79 %
    Favored  : 86.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 aren not related in a simple way.
  whole: -3.99 (0.33), residues: 551
  helix: -2.33 (0.62), residues: 71
  sheet: -3.10 (1.20), residues: 12
  loop : -3.00 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  95 
 TYR   0.013   0.002   TYR D  60 
 PHE   0.017   0.002   PHE D  62 
 HIS   0.003   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 7399)
  covalent geometry    : angle       0.70424 (10585)
  hydrogen bonds       : bond        0.03642 (   94)
  hydrogen bonds       : angle       5.22669 (  211)

*********************** 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
  42 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.117 
Fit side-chains
REVERT: B   12 LYS cc_start: 0.8113 (tttm) cc_final: 0.7858 (ttpt)
REVERT: C    1 MET cc_start: 0.4919 (tpt) cc_final: 0.3862 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0449
  time to fit residues: 2.8825
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  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0050
   chunk 35 optimal weight:    0.0370
   chunk 57 optimal weight:   10.0000
   chunk 63 optimal weight:    8.9990
   chunk 45 optimal weight:    0.0370
   chunk 10 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 62 optimal weight:    8.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.2950

-------------------------------------------------------------------------------
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 = 0.5336 r_free = 0.5336 target = 0.317725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4978 r_free = 0.4978 target = 0.279145 restraints weight = 79461.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4994 r_free = 0.4994 target = 0.282297 restraints weight = 35250.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4990 r_free = 0.4990 target = 0.281701 restraints weight = 29808.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4994 r_free = 0.4994 target = 0.281985 restraints weight = 27951.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4995 r_free = 0.4995 target = 0.282018 restraints weight = 27776.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.4882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4604
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   0.049   7399  Z= 0.145
  Angle     :  0.696  11.670  10585  Z= 0.371
  Chirality :  0.036   0.159   1227
  Planarity :  0.006   0.076    871
  Dihedral  : 29.451 175.043   2143
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.89 %
    Favored  : 88.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 aren not related in a simple way.
  whole: -3.90 (0.33), residues: 551
  helix: -2.21 (0.62), residues: 70
  sheet: -2.69 (1.14), residues: 12
  loop : -2.96 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 118 
 TYR   0.010   0.001   TYR D  60 
 PHE   0.017   0.002   PHE C  62 
 HIS   0.002   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 7399)
  covalent geometry    : angle       0.69591 (10585)
  hydrogen bonds       : bond        0.03523 (   94)
  hydrogen bonds       : angle       5.02288 (  211)

*********************** 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
  39 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.176 
Fit side-chains
REVERT: B   12 LYS cc_start: 0.8232 (tttm) cc_final: 0.7932 (ttpt)
REVERT: C    1 MET cc_start: 0.4684 (tpt) cc_final: 0.3855 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0451
  time to fit residues: 2.6804
Evaluate side-chains
  38 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 47 optimal weight:    0.4980
   chunk 21 optimal weight:    0.0370
   chunk 42 optimal weight:    0.9990
   chunk 54 optimal weight:    9.9990
   chunk 7 optimal weight:    0.0770
   overall best weight:    0.4816

-------------------------------------------------------------------------------
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 = 0.5329 r_free = 0.5329 target = 0.316498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4971 r_free = 0.4971 target = 0.277125 restraints weight = 81760.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4991 r_free = 0.4991 target = 0.282001 restraints weight = 36768.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4981 r_free = 0.4981 target = 0.280236 restraints weight = 29663.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4983 r_free = 0.4983 target = 0.280492 restraints weight = 29144.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4987 r_free = 0.4987 target = 0.280539 restraints weight = 27400.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.4862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4646
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7399  Z= 0.148
  Angle     :  0.693  11.564  10585  Z= 0.371
  Chirality :  0.036   0.161   1227
  Planarity :  0.006   0.074    871
  Dihedral  : 29.421 175.374   2143
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.28
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.94 (0.33), residues: 551
  helix: -2.25 (0.62), residues: 71
  sheet: -2.71 (0.84), residues: 24
  loop : -2.97 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 118 
 TYR   0.011   0.001   TYR A  60 
 PHE   0.015   0.002   PHE C  26 
 HIS   0.003   0.001   HIS B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 7399)
  covalent geometry    : angle       0.69275 (10585)
  hydrogen bonds       : bond        0.03650 (   94)
  hydrogen bonds       : angle       5.09115 (  211)

********************** 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
  39 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.123 
Fit side-chains
REVERT: B   12 LYS cc_start: 0.8137 (tttm) cc_final: 0.7884 (ttpt)
REVERT: C    1 MET cc_start: 0.4732 (tpt) cc_final: 0.3785 (tpt)
REVERT: D  128 LYS cc_start: 0.5611 (ptpp) cc_final: 0.4043 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0479
  time to fit residues: 2.8473
Evaluate side-chains
  36 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0370
   chunk 3 optimal weight:    0.3980
   chunk 15 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0370
   chunk 11 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0470
   overall best weight:    0.2634

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.5343 r_free = 0.5343 target = 0.318898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4945 r_free = 0.4945 target = 0.278276 restraints weight = 81087.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4975 r_free = 0.4975 target = 0.283854 restraints weight = 34079.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4965 r_free = 0.4965 target = 0.282361 restraints weight = 28643.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4970 r_free = 0.4970 target = 0.282908 restraints weight = 29085.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4968 r_free = 0.4968 target = 0.282031 restraints weight = 25928.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.4794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4805
moved from start:          0.3437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7399  Z= 0.143
  Angle     :  0.685  11.246  10585  Z= 0.366
  Chirality :  0.036   0.158   1227
  Planarity :  0.006   0.076    871
  Dihedral  : 29.383 175.373   2143
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.16 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 aren not related in a simple way.
  whole: -3.86 (0.33), residues: 551
  helix: -2.31 (0.61), residues: 71
  sheet: -2.77 (1.17), residues: 12
  loop : -2.90 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 118 
 TYR   0.007   0.001   TYR A  60 
 PHE   0.012   0.002   PHE D  62 
 HIS   0.003   0.001   HIS B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7399)
  covalent geometry    : angle       0.68515 (10585)
  hydrogen bonds       : bond        0.03562 (   94)
  hydrogen bonds       : angle       5.00758 (  211)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1034.10 seconds
wall clock time: 18 minutes 31.68 seconds (1111.68 seconds total)