Starting phenix.real_space_refine
on Tue Aug  4 15:25:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rjc_54011/08_2026/9rjc_54011_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rjc_54011/08_2026/9rjc_54011.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rjc_54011/08_2026/9rjc_54011.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rjc_54011/08_2026/9rjc_54011.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rjc_54011/08_2026/9rjc_54011_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rjc_54011/08_2026/9rjc_54011_neut.cif"
  }
  resolution = 4.2
  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=   0.031
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: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    2817      2.51       5
     N     709      2.21       5
     O     753      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4299
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1123
          Classifications: {'peptide': 140}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 134}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 524
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 524
          Classifications: {'peptide': 64}
          Link IDs: {'PTRANS': 5, 'TRANS': 58}
    Chain: "C"
      Number of atoms: 1335
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1335
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 4, 'TRANS': 159}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 1317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 166, 1317
          Classifications: {'peptide': 166}
          Link IDs: {'PTRANS': 6, 'TRANS': 159}
          Chain breaks: 1
  Time building chain proxies: 1.17, per 1000 atoms: 0.27
  Number of scatterers: 4299
  At special positions: 0
  Unit cell: (59.312, 75.488, 125.364, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O     753      8.00
     N     709      7.00
     C    2817      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: 0.31
  Conformation dependent library (CDL) restraints added in 98.9 milliseconds
  

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1002

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 3 sheets defined
      40.3% alpha, 15.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 44
      removed outlier: 3.602A  pdb=" N   VAL A  29 " --> pdb=" O   PHE A  25 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   LYS A  37 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ILE A  42 " --> pdb=" O   GLY A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 136
      No H-bonds generated for 'chain 'A' and resid 134 through 136'
    Processing helix  chain 'A' and resid 150 through 159
    Processing helix  chain 'B' and resid 84 through 110
    Processing helix  chain 'B' and resid 112 through 131
      removed outlier: 3.564A  pdb=" N   VAL B 116 " --> pdb=" O   PHE B 112 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 71
      removed outlier: 3.602A  pdb=" N   TYR C  71 " --> pdb=" O   LEU C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 77 through 104
    Processing helix  chain 'C' and resid 105 through 134
      Proline residue:  C 111  - end of helix
      removed outlier: 3.693A  pdb=" N   LEU C 115 " --> pdb=" O   PRO C 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 193 through 195
      No H-bonds generated for 'chain 'C' and resid 193 through 195'
    Processing helix  chain 'C' and resid 203 through 219
      removed outlier: 3.583A  pdb=" N   TYR C 207 " --> pdb=" O   VAL C 203 " (cutoff:3.500A)
      Proline residue:  C 209  - end of helix
    Processing helix  chain 'D' and resid 3 through 30
      removed outlier: 4.383A  pdb=" N   THR D  30 " --> pdb=" O   CYS D  26 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51
      removed outlier: 3.598A  pdb=" N   LEU A  67 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 66 through 70
    current: chain 'A' and resid 94 through 103
      removed outlier: 6.579A  pdb=" N   LEU A 112 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   ILE A 101 " --> pdb=" O   LYS A 110 " (cutoff:3.500A)
      removed outlier: 7.096A  pdb=" N   LYS A 110 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 109 through 113
    current: chain 'D' and resid 100 through 111
    Processing sheet with id=AA2, first strand: chain 'C' and resid 74 through 75
      removed outlier: 3.707A  pdb=" N   VAL C  74 " --> pdb=" O   HIS C 143 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   ILE C 138 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   SER C 160 " --> pdb=" O   ILE C 138 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   LEU C 140 " --> pdb=" O   LEU C 158 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASP C 154 " --> pdb=" O   ARG C 144 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA C 186 " --> pdb=" O   LEU C 173 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 40 through 50
      removed outlier: 4.020A  pdb=" N   ARG D  40 " --> pdb=" O   THR D  71 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   THR D  71 " --> pdb=" O   ARG D  40 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   HIS D  42 " --> pdb=" O   ASP D  69 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   THR D  67 " --> pdb=" O   SER D  44 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ILE D  46 " --> pdb=" O   PHE D  65 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   PHE D  65 " --> pdb=" O   ILE D  46 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   LEU D  48 " --> pdb=" O   LEU D  63 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   LEU D  63 " --> pdb=" O   LEU D  48 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   PHE D  68 " --> pdb=" O   ASP D 122 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASP D 122 " --> pdb=" O   PHE D  68 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ALA D  72 " --> pdb=" O   LEU D 118 " (cutoff:3.500A)

    186 hydrogen bonds defined for protein.
    552 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.35

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1323
        1.34 -     1.46: 1048
        1.46 -     1.58: 1995
        1.58 -     1.69: 0
        1.69 -     1.81: 35
  Bond restraints: 4401
  Sorted by residual:
  bond pdb=" N   TYR D 127 "
       pdb=" CA  TYR D 127 "
    ideal  model  delta    sigma   weight residual
    1.454  1.483 -0.029 1.15e-02 7.56e+03 6.25e+00
  bond pdb=" N   LYS A 114 "
       pdb=" CA  LYS A 114 "
    ideal  model  delta    sigma   weight residual
    1.461  1.485 -0.024 1.20e-02 6.94e+03 3.98e+00
  bond pdb=" CZ  TYR D 127 "
       pdb=" OH  TYR D 127 "
    ideal  model  delta    sigma   weight residual
    1.376  1.355  0.021 2.10e-02 2.27e+03 1.01e+00
  bond pdb=" C   THR A 113 "
       pdb=" N   LYS A 114 "
    ideal  model  delta    sigma   weight residual
    1.331  1.343 -0.012 1.23e-02 6.61e+03 9.32e-01
  bond pdb=" CA  TYR D 127 "
       pdb=" C   TYR D 127 "
    ideal  model  delta    sigma   weight residual
    1.524  1.512  0.012 1.31e-02 5.83e+03 9.10e-01
  ... (remaining 4396 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 5885
        2.60 -     5.20: 58
        5.20 -     7.80: 8
        7.80 -    10.40: 0
       10.40 -    13.00: 2
  Bond angle restraints: 5953
  Sorted by residual:
  angle pdb=" C   LYS A 114 "
        pdb=" CA  LYS A 114 "
        pdb=" CB  LYS A 114 "
      ideal   model   delta    sigma   weight residual
     110.34   99.37   10.97 1.40e+00 5.10e-01 6.14e+01
  angle pdb=" C   MET B  90 "
        pdb=" N   PHE B  91 "
        pdb=" CA  PHE B  91 "
      ideal   model   delta    sigma   weight residual
     120.31  114.43    5.88 1.52e+00 4.33e-01 1.50e+01
  angle pdb=" C   MET A  57 "
        pdb=" N   GLU A  58 "
        pdb=" CA  GLU A  58 "
      ideal   model   delta    sigma   weight residual
     122.15  109.15   13.00 3.47e+00 8.31e-02 1.40e+01
  angle pdb=" N   PHE B  91 "
        pdb=" CA  PHE B  91 "
        pdb=" CB  PHE B  91 "
      ideal   model   delta    sigma   weight residual
     110.28  115.56   -5.28 1.55e+00 4.16e-01 1.16e+01
  angle pdb=" N   ILE A 149 "
        pdb=" CA  ILE A 149 "
        pdb=" C   ILE A 149 "
      ideal   model   delta    sigma   weight residual
     112.96  109.72    3.24 1.00e+00 1.00e+00 1.05e+01
  ... (remaining 5948 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.40: 2325
       16.40 -    32.79: 213
       32.79 -    49.19: 37
       49.19 -    65.59: 7
       65.59 -    81.99: 5
  Dihedral angle restraints: 2587
    sinusoidal: 1039
      harmonic: 1548
  Sorted by residual:
  dihedral pdb=" C   LYS A 114 "
           pdb=" N   LYS A 114 "
           pdb=" CA  LYS A 114 "
           pdb=" CB  LYS A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.83  -11.77     0      2.50e+00 1.60e-01 2.22e+01
  dihedral pdb=" CA  ASP D  62 "
           pdb=" CB  ASP D  62 "
           pdb=" CG  ASP D  62 "
           pdb=" OD1 ASP D  62 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.19   54.19     1      2.00e+01 2.50e-03 9.96e+00
  dihedral pdb=" CG  ARG A 123 "
           pdb=" CD  ARG A 123 "
           pdb=" NE  ARG A 123 "
           pdb=" CZ  ARG A 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -132.63   42.63     2      1.50e+01 4.44e-03 9.78e+00
  ... (remaining 2584 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 521
       0.048 -    0.096: 118
       0.096 -    0.144: 33
       0.144 -    0.191: 0
       0.191 -    0.239: 1
  Chirality restraints: 673
  Sorted by residual:
  chirality pdb=" CA  LYS A 114 "
            pdb=" N   LYS A 114 "
            pdb=" C   LYS A 114 "
            pdb=" CB  LYS A 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CA  GLU C 208 "
            pdb=" N   GLU C 208 "
            pdb=" C   GLU C 208 "
            pdb=" CB  GLU C 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.96e-01
  chirality pdb=" CB  ILE C 155 "
            pdb=" CA  ILE C 155 "
            pdb=" CG1 ILE C 155 "
            pdb=" CG2 ILE C 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.52    0.13 2.00e-01 2.50e+01 4.17e-01
  ... (remaining 670 not shown)

  Planarity restraints: 734
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C 185 "   -0.006 2.00e-02 2.50e+03   1.30e-02 1.69e+00
        pdb=" CD  GLU C 185 "    0.023 2.00e-02 2.50e+03
        pdb=" OE1 GLU C 185 "   -0.008 2.00e-02 2.50e+03
        pdb=" OE2 GLU C 185 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D  12 "    0.008 2.00e-02 2.50e+03   9.79e-03 1.68e+00
        pdb=" CG  PHE D  12 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  12 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  12 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE D  12 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE D  12 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE D  12 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D  80 "   -0.010 2.00e-02 2.50e+03   8.09e-03 1.64e+00
        pdb=" CG  TRP D  80 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TRP D  80 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP D  80 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D  80 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP D  80 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP D  80 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D  80 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D  80 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP D  80 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 731 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 441
        2.75 -     3.29: 4094
        3.29 -     3.82: 6599
        3.82 -     4.36: 7226
        4.36 -     4.90: 12691
  Nonbonded interactions: 31051
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C  48 "
            pdb=" N   LYS C  49 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" OH  TYR D  93 "
            pdb=" OD1 ASP D 131 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   ILE B 136 "
            pdb=" NH1 ARG B 139 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" ND2 ASN D  50 "
            pdb=" OD1 ASP D  62 "
     model   vdw
     2.312 3.120
  nonbonded pdb=" OG  SER D  61 "
            pdb=" O   ASP D 131 "
     model   vdw
     2.313 3.040
  ... (remaining 31046 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             7.080
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.680
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:0.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
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      :  0.003   0.032   4401  Z= 0.155
  Angle     :  0.688  13.001   5953  Z= 0.366
  Chirality :  0.043   0.239    673
  Planarity :  0.004   0.029    734
  Dihedral  : 13.347  81.986   1585
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.37), residues: 517
  helix:  2.40 (0.38), residues: 187
  sheet:  0.48 (0.50), residues: 117
  loop : -1.81 (0.38), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  40 
 TYR   0.009   0.001   TYR C 130 
 PHE   0.023   0.002   PHE D  12 
 TRP   0.021   0.002   TRP D  80 
 HIS   0.003   0.001   HIS A 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.15 ( 4401)
  covalent geometry    : angle       0.68831 /  0.37 ( 5953)
  hydrogen bonds       : bond        0.17779 / 11.97 (  186)
  hydrogen bonds       : angle       6.07177 /  4.31 (  552)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 MET cc_start: 0.8686 (ttm) cc_final: 0.8416 (ttm)
REVERT: A   65 ASP cc_start: 0.8199 (m-30) cc_final: 0.7902 (m-30)
REVERT: A  156 MET cc_start: 0.8422 (tmm) cc_final: 0.8003 (tmm)
REVERT: C  100 TRP cc_start: 0.8786 (t-100) cc_final: 0.8323 (t-100)
REVERT: C  168 LYS cc_start: 0.8283 (mmtp) cc_final: 0.7828 (mmmt)
REVERT: D  147 SER cc_start: 0.8668 (m) cc_final: 0.8458 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0604
  time to fit residues: 9.9362
Evaluate side-chains
  114 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.143335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.114388 restraints weight = 8320.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.117352 restraints weight = 5664.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.119199 restraints weight = 4365.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.120550 restraints weight = 3680.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.121556 restraints weight = 3283.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4401  Z= 0.142
  Angle     :  0.542   7.843   5953  Z= 0.281
  Chirality :  0.041   0.138    673
  Planarity :  0.003   0.027    734
  Dihedral  :  3.781  14.086    569
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.37), residues: 517
  helix:  2.59 (0.37), residues: 190
  sheet:  0.47 (0.49), residues: 121
  loop : -1.75 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  16 
 TYR   0.014   0.001   TYR C 130 
 PHE   0.024   0.002   PHE B 125 
 TRP   0.017   0.001   TRP D  80 
 HIS   0.002   0.001   HIS C 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.14 ( 4401)
  covalent geometry    : angle       0.54222 /  0.28 ( 5953)
  hydrogen bonds       : bond        0.04775 /  3.09 (  186)
  hydrogen bonds       : angle       4.28385 /  3.00 (  552)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A   65 ASP cc_start: 0.8318 (m-30) cc_final: 0.8025 (m-30)
REVERT: A  156 MET cc_start: 0.8487 (tmm) cc_final: 0.7905 (tmm)
REVERT: B   88 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7558 (tm-30)
REVERT: B   89 GLN cc_start: 0.9008 (mt0) cc_final: 0.8328 (mt0)
REVERT: C  123 MET cc_start: 0.8388 (ttm) cc_final: 0.7628 (ttm)
REVERT: C  168 LYS cc_start: 0.8441 (mmtp) cc_final: 0.7904 (mmmt)
REVERT: C  185 GLU cc_start: 0.7957 (mp0) cc_final: 0.7610 (mp0)
REVERT: D  124 LYS cc_start: 0.8977 (ptmt) cc_final: 0.8708 (ptmm)
REVERT: D  147 SER cc_start: 0.8736 (m) cc_final: 0.8530 (p)
REVERT: D  151 VAL cc_start: 0.9585 (t) cc_final: 0.9346 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.0552
  time to fit residues: 9.4204
Evaluate side-chains
  113 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0070
   chunk 17 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.6598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 130 GLN
C  76 ASN
C 143 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.141400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.112888 restraints weight = 8294.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.115732 restraints weight = 5708.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.117556 restraints weight = 4431.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.118906 restraints weight = 3752.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.119978 restraints weight = 3312.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4401  Z= 0.116
  Angle     :  0.480   4.585   5953  Z= 0.253
  Chirality :  0.040   0.126    673
  Planarity :  0.003   0.025    734
  Dihedral  :  3.649  14.141    569
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.37), residues: 517
  helix:  2.70 (0.37), residues: 191
  sheet:  0.49 (0.48), residues: 121
  loop : -1.77 (0.38), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  16 
 TYR   0.011   0.001   TYR C 130 
 PHE   0.020   0.001   PHE D  12 
 TRP   0.010   0.001   TRP D  80 
 HIS   0.013   0.001   HIS C 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.12 ( 4401)
  covalent geometry    : angle       0.47958 /  0.25 ( 5953)
  hydrogen bonds       : bond        0.04398 /  2.89 (  186)
  hydrogen bonds       : angle       4.02497 /  2.81 (  552)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASP cc_start: 0.8302 (m-30) cc_final: 0.7967 (m-30)
REVERT: A  156 MET cc_start: 0.8561 (tmm) cc_final: 0.7868 (tmm)
REVERT: A  157 ASN cc_start: 0.7833 (t0) cc_final: 0.7538 (t0)
REVERT: B   88 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7540 (tm-30)
REVERT: C  123 MET cc_start: 0.8394 (ttm) cc_final: 0.8190 (ttm)
REVERT: C  185 GLU cc_start: 0.7839 (mp0) cc_final: 0.7606 (mp0)
REVERT: D  124 LYS cc_start: 0.8937 (ptmt) cc_final: 0.8669 (ptmm)
REVERT: D  151 VAL cc_start: 0.9582 (t) cc_final: 0.9332 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0588
  time to fit residues: 10.1640
Evaluate side-chains
  112 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.136138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.108437 restraints weight = 8217.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.111026 restraints weight = 5695.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.112846 restraints weight = 4492.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.113946 restraints weight = 3801.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.114876 restraints weight = 3410.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.2799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4401  Z= 0.183
  Angle     :  0.583   6.358   5953  Z= 0.302
  Chirality :  0.042   0.129    673
  Planarity :  0.004   0.037    734
  Dihedral  :  4.019  14.770    569
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.36), residues: 517
  helix:  2.26 (0.36), residues: 191
  sheet: -0.22 (0.49), residues: 114
  loop : -1.97 (0.37), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 164 
 TYR   0.017   0.002   TYR C 130 
 PHE   0.016   0.002   PHE B 125 
 TRP   0.011   0.001   TRP D  80 
 HIS   0.005   0.001   HIS C 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.18 ( 4401)
  covalent geometry    : angle       0.58254 /  0.30 ( 5953)
  hydrogen bonds       : bond        0.05390 /  3.43 (  186)
  hydrogen bonds       : angle       4.23273 /  2.98 (  552)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A   65 ASP cc_start: 0.8358 (m-30) cc_final: 0.8001 (m-30)
REVERT: A  122 ASP cc_start: 0.8768 (m-30) cc_final: 0.8243 (m-30)
REVERT: A  126 TYR cc_start: 0.8332 (m-10) cc_final: 0.7848 (m-80)
REVERT: B   88 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7554 (tm-30)
REVERT: B   89 GLN cc_start: 0.8924 (mt0) cc_final: 0.8163 (mp10)
REVERT: C   60 ASP cc_start: 0.8342 (m-30) cc_final: 0.7935 (m-30)
REVERT: C  185 GLU cc_start: 0.7838 (mp0) cc_final: 0.7573 (mp0)
REVERT: D   67 THR cc_start: 0.8138 (m) cc_final: 0.7911 (t)
REVERT: D  124 LYS cc_start: 0.8968 (ptmt) cc_final: 0.8655 (ptmm)
REVERT: D  151 VAL cc_start: 0.9601 (t) cc_final: 0.9359 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.0585
  time to fit residues: 10.1677
Evaluate side-chains
  107 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0980
   chunk 48 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 130 GLN
C 198 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.140285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.112269 restraints weight = 8109.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.115160 restraints weight = 5517.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.117047 restraints weight = 4258.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.118361 restraints weight = 3583.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.119092 restraints weight = 3181.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4401  Z= 0.111
  Angle     :  0.522   6.450   5953  Z= 0.264
  Chirality :  0.040   0.123    673
  Planarity :  0.003   0.031    734
  Dihedral  :  3.705  14.460    569
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.37), residues: 517
  helix:  2.49 (0.37), residues: 190
  sheet: -0.18 (0.49), residues: 114
  loop : -1.86 (0.36), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 164 
 TYR   0.008   0.001   TYR C 130 
 PHE   0.018   0.001   PHE C 165 
 TRP   0.006   0.001   TRP D  80 
 HIS   0.005   0.001   HIS C 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 4401)
  covalent geometry    : angle       0.52197 /  0.26 ( 5953)
  hydrogen bonds       : bond        0.04238 /  2.75 (  186)
  hydrogen bonds       : angle       3.80304 /  2.66 (  552)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A   57 MET cc_start: 0.9058 (mmm) cc_final: 0.8339 (tpp)
REVERT: A   65 ASP cc_start: 0.8292 (m-30) cc_final: 0.7955 (m-30)
REVERT: A  116 ASP cc_start: 0.8255 (p0) cc_final: 0.8012 (p0)
REVERT: A  122 ASP cc_start: 0.8777 (m-30) cc_final: 0.8463 (m-30)
REVERT: C   60 ASP cc_start: 0.8351 (m-30) cc_final: 0.7863 (m-30)
REVERT: D   67 THR cc_start: 0.8151 (m) cc_final: 0.7926 (t)
REVERT: D  124 LYS cc_start: 0.8935 (ptmt) cc_final: 0.8595 (ptmm)
REVERT: D  151 VAL cc_start: 0.9580 (t) cc_final: 0.9357 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0527
  time to fit residues: 9.4743
Evaluate side-chains
  116 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 40 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 5 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0570
   chunk 51 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.7700

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.138633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.109875 restraints weight = 8284.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.112631 restraints weight = 5682.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.114467 restraints weight = 4428.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.115702 restraints weight = 3746.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.116236 restraints weight = 3347.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4401  Z= 0.127
  Angle     :  0.538   6.488   5953  Z= 0.278
  Chirality :  0.041   0.124    673
  Planarity :  0.003   0.030    734
  Dihedral  :  3.661  14.264    569
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.36), residues: 517
  helix:  2.29 (0.37), residues: 191
  sheet: -0.23 (0.49), residues: 114
  loop : -1.81 (0.36), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  16 
 TYR   0.011   0.001   TYR C 130 
 PHE   0.017   0.001   PHE D  12 
 TRP   0.040   0.001   TRP D  80 
 HIS   0.005   0.001   HIS C 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.13 ( 4401)
  covalent geometry    : angle       0.53775 /  0.28 ( 5953)
  hydrogen bonds       : bond        0.04380 /  2.81 (  186)
  hydrogen bonds       : angle       3.92709 /  2.74 (  552)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.100 
Fit side-chains
REVERT: A   27 MET cc_start: 0.8239 (tpt) cc_final: 0.7904 (tpt)
REVERT: A   57 MET cc_start: 0.9054 (mmm) cc_final: 0.8398 (tpp)
REVERT: A   65 ASP cc_start: 0.8306 (m-30) cc_final: 0.7960 (m-30)
REVERT: A  116 ASP cc_start: 0.8330 (p0) cc_final: 0.8078 (p0)
REVERT: A  122 ASP cc_start: 0.8780 (m-30) cc_final: 0.8437 (m-30)
REVERT: A  156 MET cc_start: 0.8538 (tpp) cc_final: 0.7590 (tmm)
REVERT: B   85 LYS cc_start: 0.8962 (ptmt) cc_final: 0.8661 (ttpt)
REVERT: B  131 LEU cc_start: 0.8624 (mt) cc_final: 0.8418 (mt)
REVERT: C   60 ASP cc_start: 0.8403 (m-30) cc_final: 0.7943 (m-30)
REVERT: C  123 MET cc_start: 0.8233 (ttm) cc_final: 0.7452 (ttm)
REVERT: C  185 GLU cc_start: 0.7320 (mp0) cc_final: 0.6996 (mp0)
REVERT: D   67 THR cc_start: 0.8199 (m) cc_final: 0.7945 (t)
REVERT: D  124 LYS cc_start: 0.8923 (ptmt) cc_final: 0.8580 (ptmm)
REVERT: D  132 ASP cc_start: 0.8158 (t70) cc_final: 0.7871 (t70)
REVERT: D  151 VAL cc_start: 0.9607 (t) cc_final: 0.9361 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.0574
  time to fit residues: 10.6104
Evaluate side-chains
  123 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 36 optimal weight:    0.0970
   chunk 43 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0170
   chunk 4 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0980
   chunk 21 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.2816

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.141464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.112773 restraints weight = 8148.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.115555 restraints weight = 5637.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.117477 restraints weight = 4392.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.118705 restraints weight = 3711.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.119489 restraints weight = 3314.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4401  Z= 0.099
  Angle     :  0.530   6.483   5953  Z= 0.265
  Chirality :  0.040   0.125    673
  Planarity :  0.003   0.029    734
  Dihedral  :  3.501  14.083    569
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.37), residues: 517
  helix:  2.45 (0.37), residues: 191
  sheet: -0.17 (0.49), residues: 114
  loop : -1.68 (0.37), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 164 
 TYR   0.005   0.001   TYR A 159 
 PHE   0.032   0.001   PHE C  77 
 TRP   0.020   0.001   TRP D  80 
 HIS   0.006   0.001   HIS C 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00215 /  0.10 ( 4401)
  covalent geometry    : angle       0.52973 /  0.27 ( 5953)
  hydrogen bonds       : bond        0.03603 /  2.34 (  186)
  hydrogen bonds       : angle       3.78522 /  2.64 (  552)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 MET cc_start: 0.9051 (mmm) cc_final: 0.8527 (tpp)
REVERT: A   65 ASP cc_start: 0.8245 (m-30) cc_final: 0.7935 (m-30)
REVERT: A  116 ASP cc_start: 0.8342 (p0) cc_final: 0.8137 (p0)
REVERT: A  122 ASP cc_start: 0.8783 (m-30) cc_final: 0.8393 (m-30)
REVERT: A  156 MET cc_start: 0.8548 (tpp) cc_final: 0.7621 (tmm)
REVERT: C   60 ASP cc_start: 0.8392 (m-30) cc_final: 0.7969 (m-30)
REVERT: C  100 TRP cc_start: 0.8807 (t-100) cc_final: 0.8336 (t-100)
REVERT: C  123 MET cc_start: 0.8253 (ttm) cc_final: 0.8052 (ttm)
REVERT: C  153 ASP cc_start: 0.6596 (m-30) cc_final: 0.6201 (t70)
REVERT: D   67 THR cc_start: 0.8160 (m) cc_final: 0.7904 (t)
REVERT: D  124 LYS cc_start: 0.8879 (ptmt) cc_final: 0.8538 (ptmm)
REVERT: D  132 ASP cc_start: 0.8199 (t70) cc_final: 0.7853 (t70)
REVERT: D  151 VAL cc_start: 0.9573 (t) cc_final: 0.9364 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.0488
  time to fit residues: 9.7467
Evaluate side-chains
  126 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 13 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.139734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.112077 restraints weight = 8126.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.114756 restraints weight = 5700.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.116501 restraints weight = 4467.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.117808 restraints weight = 3784.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.118704 restraints weight = 3361.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.3815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4401  Z= 0.144
  Angle     :  0.580   6.406   5953  Z= 0.299
  Chirality :  0.042   0.151    673
  Planarity :  0.003   0.029    734
  Dihedral  :  3.736  14.207    569
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.36), residues: 517
  helix:  2.38 (0.36), residues: 191
  sheet: -0.24 (0.49), residues: 114
  loop : -1.69 (0.37), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 164 
 TYR   0.011   0.001   TYR C 130 
 PHE   0.020   0.002   PHE C  77 
 TRP   0.033   0.001   TRP D  80 
 HIS   0.005   0.001   HIS C 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.14 ( 4401)
  covalent geometry    : angle       0.58041 /  0.30 ( 5953)
  hydrogen bonds       : bond        0.04658 /  2.94 (  186)
  hydrogen bonds       : angle       3.91889 /  2.79 (  552)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   57 MET cc_start: 0.9106 (mmm) cc_final: 0.8508 (tpp)
REVERT: A   81 GLU cc_start: 0.8240 (tt0) cc_final: 0.8017 (tt0)
REVERT: A  122 ASP cc_start: 0.8759 (m-30) cc_final: 0.8064 (m-30)
REVERT: A  126 TYR cc_start: 0.8241 (m-10) cc_final: 0.7854 (m-80)
REVERT: A  156 MET cc_start: 0.8514 (tpp) cc_final: 0.7894 (tmm)
REVERT: C   60 ASP cc_start: 0.8525 (m-30) cc_final: 0.8130 (m-30)
REVERT: C  100 TRP cc_start: 0.8831 (t-100) cc_final: 0.8355 (t-100)
REVERT: C  123 MET cc_start: 0.8251 (ttm) cc_final: 0.7577 (ttm)
REVERT: C  153 ASP cc_start: 0.6690 (m-30) cc_final: 0.6291 (t70)
REVERT: D  124 LYS cc_start: 0.8859 (ptmt) cc_final: 0.8506 (ptmm)
REVERT: D  151 VAL cc_start: 0.9611 (t) cc_final: 0.9369 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0596
  time to fit residues: 11.6542
Evaluate side-chains
  122 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0470
   chunk 19 optimal weight:    0.0870
   overall best weight:    0.4056

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.142182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.113925 restraints weight = 8369.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.116915 restraints weight = 5609.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.118920 restraints weight = 4267.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.120190 restraints weight = 3553.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.121235 restraints weight = 3143.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.3916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4401  Z= 0.104
  Angle     :  0.542   6.591   5953  Z= 0.274
  Chirality :  0.041   0.124    673
  Planarity :  0.003   0.027    734
  Dihedral  :  3.527  14.188    569
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.37), residues: 517
  helix:  2.54 (0.37), residues: 191
  sheet: -0.13 (0.49), residues: 114
  loop : -1.67 (0.37), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 164 
 TYR   0.006   0.001   TYR C 130 
 PHE   0.021   0.001   PHE D  12 
 TRP   0.017   0.001   TRP D  80 
 HIS   0.004   0.001   HIS C 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00229 /  0.10 ( 4401)
  covalent geometry    : angle       0.54173 /  0.27 ( 5953)
  hydrogen bonds       : bond        0.03945 /  2.52 (  186)
  hydrogen bonds       : angle       3.77781 /  2.66 (  552)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.095 
Fit side-chains
REVERT: A   57 MET cc_start: 0.9056 (mmm) cc_final: 0.8329 (tpp)
REVERT: A   65 ASP cc_start: 0.8264 (m-30) cc_final: 0.7852 (m-30)
REVERT: A   81 GLU cc_start: 0.8235 (tt0) cc_final: 0.8008 (tt0)
REVERT: A  122 ASP cc_start: 0.8781 (m-30) cc_final: 0.8322 (m-30)
REVERT: A  156 MET cc_start: 0.8516 (tpp) cc_final: 0.7929 (tmm)
REVERT: B  131 LEU cc_start: 0.8648 (mt) cc_final: 0.8363 (mt)
REVERT: C   60 ASP cc_start: 0.8563 (m-30) cc_final: 0.8172 (m-30)
REVERT: C  100 TRP cc_start: 0.8787 (t-100) cc_final: 0.8337 (t-100)
REVERT: C  123 MET cc_start: 0.8272 (ttm) cc_final: 0.7629 (ttm)
REVERT: C  153 ASP cc_start: 0.6748 (m-30) cc_final: 0.6305 (t70)
REVERT: C  208 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8762 (tm-30)
REVERT: D   49 LYS cc_start: 0.8486 (mptt) cc_final: 0.8260 (mmtm)
REVERT: D  124 LYS cc_start: 0.8845 (ptmt) cc_final: 0.8602 (ptmt)
REVERT: D  151 VAL cc_start: 0.9594 (t) cc_final: 0.9393 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.0459
  time to fit residues: 8.4636
Evaluate side-chains
  119 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0770
   chunk 28 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0370
   chunk 11 optimal weight:    0.0970
   chunk 51 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.3414

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.143404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.115709 restraints weight = 8203.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.118627 restraints weight = 5540.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.120542 restraints weight = 4247.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.121981 restraints weight = 3545.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.122724 restraints weight = 3113.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.4062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4401  Z= 0.102
  Angle     :  0.550   6.838   5953  Z= 0.278
  Chirality :  0.041   0.122    673
  Planarity :  0.003   0.031    734
  Dihedral  :  3.432  13.794    569
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.37), residues: 517
  helix:  2.33 (0.37), residues: 196
  sheet: -0.08 (0.50), residues: 114
  loop : -1.67 (0.38), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 164 
 TYR   0.008   0.001   TYR C 207 
 PHE   0.020   0.001   PHE D  12 
 TRP   0.016   0.001   TRP D  80 
 HIS   0.004   0.001   HIS C 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00226 /  0.10 ( 4401)
  covalent geometry    : angle       0.54953 /  0.28 ( 5953)
  hydrogen bonds       : bond        0.03789 /  2.40 (  186)
  hydrogen bonds       : angle       3.79876 /  2.66 (  552)

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

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

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1034 Ramachandran restraints generated.
    517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A   40 MET cc_start: 0.8740 (ttm) cc_final: 0.8488 (ttt)
REVERT: A   57 MET cc_start: 0.9008 (mmm) cc_final: 0.8363 (tpp)
REVERT: A   65 ASP cc_start: 0.8260 (m-30) cc_final: 0.7872 (m-30)
REVERT: A   81 GLU cc_start: 0.8204 (tt0) cc_final: 0.7985 (tt0)
REVERT: A  122 ASP cc_start: 0.8757 (m-30) cc_final: 0.8350 (m-30)
REVERT: A  156 MET cc_start: 0.8498 (tpp) cc_final: 0.7962 (tmm)
REVERT: B  131 LEU cc_start: 0.8656 (mt) cc_final: 0.8367 (mt)
REVERT: C   60 ASP cc_start: 0.8600 (m-30) cc_final: 0.8235 (m-30)
REVERT: C   61 ASP cc_start: 0.8092 (t70) cc_final: 0.7891 (t70)
REVERT: C  100 TRP cc_start: 0.8768 (t-100) cc_final: 0.8392 (t-100)
REVERT: C  153 ASP cc_start: 0.6750 (m-30) cc_final: 0.6340 (t70)
REVERT: C  208 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8687 (tm-30)
REVERT: D  124 LYS cc_start: 0.8692 (ptmt) cc_final: 0.8378 (ptmt)
REVERT: D  132 ASP cc_start: 0.8202 (t70) cc_final: 0.7997 (t0)
REVERT: D  151 VAL cc_start: 0.9593 (t) cc_final: 0.9390 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.0642
  time to fit residues: 12.1284
Evaluate side-chains
  121 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0980
   chunk 16 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.140093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.112810 restraints weight = 8458.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.115429 restraints weight = 5792.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.117383 restraints weight = 4514.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.118591 restraints weight = 3783.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.119384 restraints weight = 3356.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.4200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4401  Z= 0.121
  Angle     :  0.563   6.682   5953  Z= 0.285
  Chirality :  0.041   0.119    673
  Planarity :  0.003   0.027    734
  Dihedral  :  3.532  14.517    569
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.37), residues: 517
  helix:  2.33 (0.37), residues: 196
  sheet: -0.17 (0.49), residues: 114
  loop : -1.66 (0.38), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 164 
 TYR   0.009   0.001   TYR C 130 
 PHE   0.020   0.001   PHE D  12 
 TRP   0.025   0.001   TRP D  80 
 HIS   0.004   0.001   HIS C 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.12 ( 4401)
  covalent geometry    : angle       0.56334 /  0.28 ( 5953)
  hydrogen bonds       : bond        0.04212 /  2.68 (  186)
  hydrogen bonds       : angle       3.87130 /  2.72 (  552)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 907.05 seconds
wall clock time: 16 minutes 13.47 seconds (973.47 seconds total)