Starting phenix.real_space_refine
on Tue Aug  4 14:14:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lwo_63452/08_2026/9lwo_63452_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lwo_63452/08_2026/9lwo_63452.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lwo_63452/08_2026/9lwo_63452.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lwo_63452/08_2026/9lwo_63452.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lwo_63452/08_2026/9lwo_63452_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lwo_63452/08_2026/9lwo_63452_neut.cif"
  }
  resolution = 4.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.020
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      22      5.16       5
     C    2396      2.51       5
     N     634      2.21       5
     O     632      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 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: 3684
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1565
          Classifications: {'peptide': 183}
          Link IDs: {'PTRANS': 2, 'TRANS': 180}
    Chain: "B"
      Number of atoms: 1468
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 179, 1468
          Classifications: {'peptide': 179}
          Link IDs: {'PTRANS': 3, 'TRANS': 175}
    Chain: "C"
      Number of atoms: 651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 651
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Time building chain proxies: 1.09, per 1000 atoms: 0.30
  Number of scatterers: 3684
  At special positions: 0
  Unit cell: (78.264, 89.134, 93.482, 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      22     16.00
     O     632      8.00
     N     634      7.00
     C    2396      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: 0.28
  Conformation dependent library (CDL) restraints added in 125.9 milliseconds
  

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  842

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 0 sheets defined
      70.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 12
      removed outlier: 3.635A  pdb=" N   LEU A  12 " --> pdb=" O   LEU A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 37
      removed outlier: 3.639A  pdb=" N   ASP A  37 " --> pdb=" O   PHE A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 57
    Processing helix  chain 'A' and resid 60 through 71
    Processing helix  chain 'A' and resid 80 through 95
      removed outlier: 4.032A  pdb=" N   PHE A  84 " --> pdb=" O   GLY A  80 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   GLN A  95 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 103
    Processing helix  chain 'A' and resid 106 through 115
    Processing helix  chain 'A' and resid 123 through 128
      removed outlier: 3.954A  pdb=" N   PHE A 127 " --> pdb=" O   GLY A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 148
    Processing helix  chain 'A' and resid 157 through 168
    Processing helix  chain 'A' and resid 170 through 182
      removed outlier: 4.328A  pdb=" N   ARG A 182 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 73
    Processing helix  chain 'B' and resid 78 through 97
      removed outlier: 4.495A  pdb=" N   ARG B  82 " --> pdb=" O   SER B  78 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLY B  97 " --> pdb=" O   SER B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 104
      removed outlier: 3.544A  pdb=" N   ALA B 101 " --> pdb=" O   GLY B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 115
      removed outlier: 4.348A  pdb=" N   VAL B 111 " --> pdb=" O   TYR B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 138
      removed outlier: 3.783A  pdb=" N   LYS B 126 " --> pdb=" O   SER B 122 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   TYR B 138 " --> pdb=" O   ALA B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 147
    Processing helix  chain 'B' and resid 152 through 161
      removed outlier: 3.866A  pdb=" N   GLU B 161 " --> pdb=" O   ILE B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 188
      removed outlier: 3.753A  pdb=" N   ARG B 176 " --> pdb=" O   ILE B 172 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   VAL B 188 " --> pdb=" O   TYR B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 203
      removed outlier: 3.964A  pdb=" N   GLU B 199 " --> pdb=" O   ALA B 195 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   TYR B 203 " --> pdb=" O   GLU B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 216
    Processing helix  chain 'B' and resid 224 through 234
      removed outlier: 3.672A  pdb=" N   VAL B 228 " --> pdb=" O   ASN B 224 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLY B 234 " --> pdb=" O   TYR B 230 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 121
      No H-bonds generated for 'chain 'C' and resid 119 through 121'
    Processing helix  chain 'C' and resid 122 through 133
      removed outlier: 3.843A  pdb=" N   HIS C 126 " --> pdb=" O   LEU C 122 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   THR C 128 " --> pdb=" O   LYS C 124 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   TYR C 129 " --> pdb=" O   PRO C 125 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 146 through 164
    Processing helix  chain 'C' and resid 169 through 187
      removed outlier: 3.548A  pdb=" N   LYS C 187 " --> pdb=" O   LYS C 183 " (cutoff:3.500A)

    184 hydrogen bonds defined for protein.
    549 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: 0.55

  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:
        1.20 -     1.33: 655
        1.33 -     1.45: 1013
        1.45 -     1.57: 2069
        1.57 -     1.69: 0
        1.69 -     1.81: 35
  Bond restraints: 3772
  Sorted by residual:
  bond pdb=" CG1 ILE B  89 "
       pdb=" CD1 ILE B  89 "
    ideal  model  delta    sigma   weight residual
    1.513  1.397  0.116 3.90e-02 6.57e+02 8.88e+00
  bond pdb=" C   LYS C 124 "
       pdb=" N   PRO C 125 "
    ideal  model  delta    sigma   weight residual
    1.334  1.388 -0.054 2.34e-02 1.83e+03 5.38e+00
  bond pdb=" CG  LEU B 129 "
       pdb=" CD2 LEU B 129 "
    ideal  model  delta    sigma   weight residual
    1.521  1.453  0.068 3.30e-02 9.18e+02 4.30e+00
  bond pdb=" C   ILE B 153 "
       pdb=" N   PRO B 154 "
    ideal  model  delta    sigma   weight residual
    1.336  1.360 -0.024 1.23e-02 6.61e+03 3.85e+00
  bond pdb=" CD  GLU B  67 "
       pdb=" OE1 GLU B  67 "
    ideal  model  delta    sigma   weight residual
    1.249  1.213  0.036 1.90e-02 2.77e+03 3.69e+00
  ... (remaining 3767 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.28: 4902
        4.28 -     8.57: 140
        8.57 -    12.85: 32
       12.85 -    17.14: 4
       17.14 -    21.42: 2
  Bond angle restraints: 5080
  Sorted by residual:
  angle pdb=" N   GLU B  67 "
        pdb=" CA  GLU B  67 "
        pdb=" CB  GLU B  67 "
      ideal   model   delta    sigma   weight residual
     110.30  120.50  -10.20 1.54e+00 4.22e-01 4.38e+01
  angle pdb=" C   TRP C 123 "
        pdb=" N   LYS C 124 "
        pdb=" CA  LYS C 124 "
      ideal   model   delta    sigma   weight residual
     120.09  127.85   -7.76 1.25e+00 6.40e-01 3.85e+01
  angle pdb=" CA  LEU C 137 "
        pdb=" CB  LEU C 137 "
        pdb=" CG  LEU C 137 "
      ideal   model   delta    sigma   weight residual
     116.30  137.72  -21.42 3.50e+00 8.16e-02 3.75e+01
  angle pdb=" C   PHE A 134 "
        pdb=" N   ASN A 135 "
        pdb=" CA  ASN A 135 "
      ideal   model   delta    sigma   weight residual
     121.54  132.37  -10.83 1.91e+00 2.74e-01 3.22e+01
  angle pdb=" C   PHE A  68 "
        pdb=" N   ASP A  69 "
        pdb=" CA  ASP A  69 "
      ideal   model   delta    sigma   weight residual
     122.26  112.57    9.69 1.73e+00 3.34e-01 3.14e+01
  ... (remaining 5075 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.36: 1830
       13.36 -    26.73: 286
       26.73 -    40.09: 111
       40.09 -    53.45: 14
       53.45 -    66.82: 3
  Dihedral angle restraints: 2244
    sinusoidal: 949
      harmonic: 1295
  Sorted by residual:
  dihedral pdb=" CA  SER B 163 "
           pdb=" C   SER B 163 "
           pdb=" N   PHE B 164 "
           pdb=" CA  PHE B 164 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.31   31.69     0      5.00e+00 4.00e-02 4.02e+01
  dihedral pdb=" CA  LYS B 169 "
           pdb=" C   LYS B 169 "
           pdb=" N   THR B 170 "
           pdb=" CA  THR B 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.06   27.94     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CA  MET C 170 "
           pdb=" C   MET C 170 "
           pdb=" N   THR C 171 "
           pdb=" CA  THR C 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.49   24.51     0      5.00e+00 4.00e-02 2.40e+01
  ... (remaining 2241 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.097: 439
       0.097 -    0.193: 96
       0.193 -    0.290: 12
       0.290 -    0.386: 4
       0.386 -    0.483: 1
  Chirality restraints: 552
  Sorted by residual:
  chirality pdb=" CB  ILE B 153 "
            pdb=" CA  ILE B 153 "
            pdb=" CG1 ILE B 153 "
            pdb=" CG2 ILE B 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.16    0.48 2.00e-01 2.50e+01 5.82e+00
  chirality pdb=" CB  VAL B 188 "
            pdb=" CA  VAL B 188 "
            pdb=" CG1 VAL B 188 "
            pdb=" CG2 VAL B 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.25   -0.37 2.00e-01 2.50e+01 3.50e+00
  chirality pdb=" CB  ILE B 172 "
            pdb=" CA  ILE B 172 "
            pdb=" CG1 ILE B 172 "
            pdb=" CG2 ILE B 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.36 2.00e-01 2.50e+01 3.24e+00
  ... (remaining 549 not shown)

  Planarity restraints: 633
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 130 "   -0.039 2.00e-02 2.50e+03   3.30e-02 2.72e+01
        pdb=" CG  TRP C 130 "    0.089 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 130 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 130 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 130 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 130 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 130 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 130 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 130 "   -0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 130 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 190 "    0.024 2.00e-02 2.50e+03   2.33e-02 1.09e+01
        pdb=" CG  TYR C 190 "   -0.058 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 190 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 190 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 190 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 190 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 190 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 190 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 175 "   -0.225 9.50e-02 1.11e+02   1.02e-01 7.89e+00
        pdb=" NE  ARG A 175 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 175 "   -0.020 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 175 "    0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 175 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 630 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1149
        2.84 -     3.35: 3676
        3.35 -     3.87: 6487
        3.87 -     4.38: 7184
        4.38 -     4.90: 11120
  Nonbonded interactions: 29616
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 163 "
            pdb=" O   SER B 167 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" O   LEU A  53 "
            pdb=" OG1 THR A  57 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OG1 THR A  43 "
            pdb=" O   ILE A  79 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" OG1 THR A 151 "
            pdb=" O   LEU A 155 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" O   THR C 159 "
            pdb=" OG1 THR C 163 "
     model   vdw
     2.335 3.040
  ... (remaining 29611 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:                  0.010
  Normalize map: mean=0, sd=1:             6.190
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.600
  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:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
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      :  0.007   0.116   3772  Z= 0.325
  Angle     :  1.747  21.424   5080  Z= 0.853
  Chirality :  0.083   0.483    552
  Planarity :  0.010   0.102    633
  Dihedral  : 14.705  66.817   1402
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.50 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.48 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

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: -4.25 (0.33), residues: 431
  helix: -2.85 (0.23), residues: 277
  sheet:  None (None), residues: 0
  loop : -2.41 (0.47), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG A 175 
 TYR   0.058   0.004   TYR C 190 
 PHE   0.036   0.004   PHE C 120 
 TRP   0.089   0.005   TRP C 130 
 HIS   0.013   0.003   HIS A 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00666 /  0.33 ( 3772)
  covalent geometry    : angle       1.74740 /  0.85 ( 5080)
  hydrogen bonds       : bond        0.13116 /  7.82 (  184)
  hydrogen bonds       : angle       8.53387 /  6.08 (  549)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 CYS cc_start: 0.8871 (m) cc_final: 0.8343 (m)
REVERT: A   55 HIS cc_start: 0.9417 (t-90) cc_final: 0.9085 (t-90)
REVERT: A  101 HIS cc_start: 0.8742 (t-170) cc_final: 0.8333 (t-170)
REVERT: A  104 TYR cc_start: 0.9390 (t80) cc_final: 0.9051 (t80)
REVERT: A  159 LYS cc_start: 0.9584 (pptt) cc_final: 0.9336 (pptt)
REVERT: B   64 LYS cc_start: 0.9481 (ptpp) cc_final: 0.9134 (pttm)
REVERT: B   65 ILE cc_start: 0.9611 (pt) cc_final: 0.9301 (pt)
REVERT: B  103 PHE cc_start: 0.8807 (t80) cc_final: 0.8593 (t80)
REVERT: C  148 GLU cc_start: 0.9353 (pm20) cc_final: 0.9138 (pm20)
REVERT: C  151 ASP cc_start: 0.9372 (m-30) cc_final: 0.9141 (m-30)
REVERT: C  175 GLN cc_start: 0.9227 (tm-30) cc_final: 0.8998 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.0754
  time to fit residues: 14.5179
Evaluate side-chains
  132 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0470
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.3980
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.0781 > 50:)
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.3980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.4278

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  39 HIS
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 209 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.074446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.055094 restraints weight = 19210.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.057696 restraints weight = 12347.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.059671 restraints weight = 8899.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.061125 restraints weight = 6889.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.062255 restraints weight = 5626.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3772  Z= 0.140
  Angle     :  0.800  10.586   5080  Z= 0.409
  Chirality :  0.044   0.160    552
  Planarity :  0.005   0.039    633
  Dihedral  :  6.240  26.884    482
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.87 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  6.72 %
    Favored  : 92.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.54 (0.39), residues: 431
  helix: -1.46 (0.28), residues: 291
  sheet:  None (None), residues: 0
  loop : -1.81 (0.57), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 176 
 TYR   0.020   0.001   TYR A 130 
 PHE   0.021   0.002   PHE B 164 
 TRP   0.050   0.003   TRP C 130 
 HIS   0.011   0.002   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.14 ( 3772)
  covalent geometry    : angle       0.80041 /  0.41 ( 5080)
  hydrogen bonds       : bond        0.04162 /  2.52 (  184)
  hydrogen bonds       : angle       5.59223 /  3.85 (  549)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 155
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 CYS cc_start: 0.8991 (m) cc_final: 0.8593 (m)
REVERT: A   55 HIS cc_start: 0.9417 (t-90) cc_final: 0.9154 (t-90)
REVERT: A  101 HIS cc_start: 0.8923 (t-170) cc_final: 0.8654 (t-170)
REVERT: A  104 TYR cc_start: 0.9449 (t80) cc_final: 0.9078 (t80)
REVERT: B   64 LYS cc_start: 0.9409 (ptpp) cc_final: 0.9017 (pttm)
REVERT: B   65 ILE cc_start: 0.9653 (pt) cc_final: 0.9325 (pt)
REVERT: B  103 PHE cc_start: 0.8733 (t80) cc_final: 0.8432 (t80)
REVERT: B  225 PHE cc_start: 0.8831 (m-10) cc_final: 0.8412 (m-10)
REVERT: C  129 TYR cc_start: 0.9311 (m-80) cc_final: 0.9107 (m-80)
REVERT: C  151 ASP cc_start: 0.9413 (m-30) cc_final: 0.9196 (m-30)
REVERT: C  157 LEU cc_start: 0.9231 (mm) cc_final: 0.8911 (mm)
REVERT: C  175 GLN cc_start: 0.9342 (tm-30) cc_final: 0.9085 (tm-30)
  outliers start: 4
  outliers final: 0
  residues processed: 155
  average time/residue: 0.0717
  time to fit residues: 13.4865
Evaluate side-chains
  113 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 15 optimal weight:    0.2980
   chunk 33 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  25 ASN
B  74 ASN
** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.072097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.053219 restraints weight = 19873.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.055614 restraints weight = 13486.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.057333 restraints weight = 10037.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.058545 restraints weight = 7996.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.059518 restraints weight = 6710.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3772  Z= 0.151
  Angle     :  0.773   9.149   5080  Z= 0.398
  Chirality :  0.046   0.185    552
  Planarity :  0.004   0.034    633
  Dihedral  :  5.877  24.764    482
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 20.95
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.03 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  7.71 %
    Favored  : 92.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.41), residues: 431
  helix: -0.76 (0.29), residues: 291
  sheet:  None (None), residues: 0
  loop : -1.65 (0.59), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  41 
 TYR   0.019   0.002   TYR C 190 
 PHE   0.018   0.002   PHE B 164 
 TRP   0.052   0.003   TRP C 130 
 HIS   0.010   0.002   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.15 ( 3772)
  covalent geometry    : angle       0.77301 /  0.40 ( 5080)
  hydrogen bonds       : bond        0.03961 /  2.41 (  184)
  hydrogen bonds       : angle       5.20874 /  3.56 (  549)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 VAL cc_start: 0.9516 (t) cc_final: 0.9301 (t)
REVERT: A   55 HIS cc_start: 0.9421 (t-90) cc_final: 0.9183 (t-90)
REVERT: A  101 HIS cc_start: 0.8988 (t-170) cc_final: 0.8739 (t-170)
REVERT: A  104 TYR cc_start: 0.9447 (t80) cc_final: 0.9045 (t80)
REVERT: A  130 TYR cc_start: 0.9667 (m-80) cc_final: 0.9242 (m-80)
REVERT: A  141 LEU cc_start: 0.8944 (mm) cc_final: 0.8730 (mt)
REVERT: A  176 LYS cc_start: 0.9553 (tptp) cc_final: 0.9165 (mttt)
REVERT: B   65 ILE cc_start: 0.9671 (pt) cc_final: 0.9316 (pt)
REVERT: B   88 LYS cc_start: 0.9516 (mptt) cc_final: 0.9296 (mmtt)
REVERT: B  103 PHE cc_start: 0.9008 (t80) cc_final: 0.8529 (t80)
REVERT: B  107 TYR cc_start: 0.9295 (m-80) cc_final: 0.8899 (m-80)
REVERT: B  161 GLU cc_start: 0.9077 (mp0) cc_final: 0.8857 (mp0)
REVERT: B  188 VAL cc_start: 0.9149 (m) cc_final: 0.8903 (p)
REVERT: B  225 PHE cc_start: 0.8792 (m-10) cc_final: 0.8556 (m-10)
REVERT: B  229 LEU cc_start: 0.8961 (mm) cc_final: 0.8729 (mm)
REVERT: C  129 TYR cc_start: 0.9352 (m-80) cc_final: 0.9142 (m-80)
REVERT: C  151 ASP cc_start: 0.9453 (m-30) cc_final: 0.9216 (m-30)
REVERT: C  157 LEU cc_start: 0.9242 (mm) cc_final: 0.8899 (mm)
REVERT: C  175 GLN cc_start: 0.9402 (tm-30) cc_final: 0.9161 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0575
  time to fit residues: 10.8571
Evaluate side-chains
  118 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 41 optimal weight:    0.4980
   chunk 29 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:    0.4980
   chunk 28 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   chunk 25 optimal weight:    0.4980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.070768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.051843 restraints weight = 19627.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.054286 restraints weight = 12696.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.056141 restraints weight = 9183.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.057507 restraints weight = 7125.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.058522 restraints weight = 5835.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3772  Z= 0.150
  Angle     :  0.773   9.257   5080  Z= 0.395
  Chirality :  0.046   0.174    552
  Planarity :  0.004   0.035    633
  Dihedral  :  5.802  26.587    482
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 20.00
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.57 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  4.98 %
    Favored  : 94.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.41), residues: 431
  helix: -0.53 (0.29), residues: 291
  sheet:  None (None), residues: 0
  loop : -1.56 (0.60), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 166 
 TYR   0.011   0.001   TYR B 107 
 PHE   0.021   0.002   PHE C 169 
 TRP   0.038   0.002   TRP C 130 
 HIS   0.009   0.001   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.15 ( 3772)
  covalent geometry    : angle       0.77303 /  0.39 ( 5080)
  hydrogen bonds       : bond        0.03742 /  2.29 (  184)
  hydrogen bonds       : angle       5.10355 /  3.47 (  549)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 151
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 CYS cc_start: 0.9112 (m) cc_final: 0.8845 (m)
REVERT: A   29 LEU cc_start: 0.9605 (mm) cc_final: 0.9365 (mm)
REVERT: A   55 HIS cc_start: 0.9421 (t-90) cc_final: 0.9191 (t-90)
REVERT: A  101 HIS cc_start: 0.8947 (t-170) cc_final: 0.8639 (t-170)
REVERT: A  104 TYR cc_start: 0.9462 (t80) cc_final: 0.9013 (t80)
REVERT: A  129 ASN cc_start: 0.9615 (p0) cc_final: 0.9409 (p0)
REVERT: A  130 TYR cc_start: 0.9674 (m-80) cc_final: 0.9277 (m-80)
REVERT: A  176 LYS cc_start: 0.9584 (tptp) cc_final: 0.9150 (mttt)
REVERT: B   65 ILE cc_start: 0.9667 (pt) cc_final: 0.9306 (pt)
REVERT: B   88 LYS cc_start: 0.9554 (mptt) cc_final: 0.9325 (mmtt)
REVERT: B  103 PHE cc_start: 0.8988 (t80) cc_final: 0.8598 (t80)
REVERT: B  107 TYR cc_start: 0.9335 (m-80) cc_final: 0.8899 (m-80)
REVERT: B  127 ILE cc_start: 0.8935 (pt) cc_final: 0.8525 (pt)
REVERT: B  161 GLU cc_start: 0.9148 (mp0) cc_final: 0.8790 (mp0)
REVERT: B  188 VAL cc_start: 0.9202 (m) cc_final: 0.8967 (p)
REVERT: B  225 PHE cc_start: 0.8758 (m-10) cc_final: 0.8509 (m-80)
REVERT: B  229 LEU cc_start: 0.8976 (mm) cc_final: 0.8692 (mm)
REVERT: C  129 TYR cc_start: 0.9319 (m-80) cc_final: 0.9092 (m-80)
REVERT: C  151 ASP cc_start: 0.9469 (m-30) cc_final: 0.9247 (m-30)
REVERT: C  175 GLN cc_start: 0.9440 (tm-30) cc_final: 0.9203 (tm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 152
  average time/residue: 0.0657
  time to fit residues: 12.1633
Evaluate side-chains
  120 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 35 optimal weight:    0.3980
   chunk 4 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  25 ASN
** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.069443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.051161 restraints weight = 19954.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.053581 restraints weight = 12838.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.055311 restraints weight = 9240.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.056635 restraints weight = 7193.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.057615 restraints weight = 5897.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.4286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3772  Z= 0.167
  Angle     :  0.799   9.353   5080  Z= 0.415
  Chirality :  0.047   0.188    552
  Planarity :  0.004   0.032    633
  Dihedral  :  5.826  26.665    482
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 23.92
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.03 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  4.48 %
    Favored  : 95.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.41), residues: 431
  helix: -0.40 (0.30), residues: 291
  sheet:  None (None), residues: 0
  loop : -1.68 (0.60), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 166 
 TYR   0.019   0.002   TYR A  32 
 PHE   0.034   0.003   PHE A 111 
 TRP   0.060   0.003   TRP C 130 
 HIS   0.008   0.002   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.17 ( 3772)
  covalent geometry    : angle       0.79850 /  0.42 ( 5080)
  hydrogen bonds       : bond        0.03746 /  2.27 (  184)
  hydrogen bonds       : angle       5.25438 /  3.57 (  549)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LEU cc_start: 0.9632 (mm) cc_final: 0.9336 (mm)
REVERT: A   31 VAL cc_start: 0.9505 (t) cc_final: 0.9278 (t)
REVERT: A  101 HIS cc_start: 0.9014 (t-170) cc_final: 0.8803 (t70)
REVERT: A  104 TYR cc_start: 0.9444 (t80) cc_final: 0.9024 (t80)
REVERT: A  130 TYR cc_start: 0.9702 (m-80) cc_final: 0.9297 (m-80)
REVERT: B   65 ILE cc_start: 0.9664 (pt) cc_final: 0.9316 (pt)
REVERT: B   88 LYS cc_start: 0.9601 (mptt) cc_final: 0.9347 (mmtt)
REVERT: B  103 PHE cc_start: 0.9053 (t80) cc_final: 0.8541 (t80)
REVERT: B  107 TYR cc_start: 0.9382 (m-80) cc_final: 0.8993 (m-80)
REVERT: B  161 GLU cc_start: 0.9172 (mp0) cc_final: 0.8882 (mp0)
REVERT: B  225 PHE cc_start: 0.8809 (m-10) cc_final: 0.8602 (m-10)
REVERT: B  229 LEU cc_start: 0.8958 (mm) cc_final: 0.8696 (mm)
REVERT: C  129 TYR cc_start: 0.9322 (m-80) cc_final: 0.9059 (m-80)
REVERT: C  151 ASP cc_start: 0.9529 (m-30) cc_final: 0.9287 (m-30)
REVERT: C  175 GLN cc_start: 0.9464 (tm-30) cc_final: 0.9215 (tm-30)
REVERT: C  177 TYR cc_start: 0.9188 (t80) cc_final: 0.8903 (t80)
REVERT: C  184 ARG cc_start: 0.9542 (mtm180) cc_final: 0.9145 (mtt180)
  outliers start: 1
  outliers final: 1
  residues processed: 141
  average time/residue: 0.0713
  time to fit residues: 12.0066
Evaluate side-chains
  109 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 18 optimal weight:    0.3980
   chunk 2 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 29 optimal weight:    0.4980
   chunk 32 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0970
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.070072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.051308 restraints weight = 20407.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.053612 restraints weight = 13669.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.055325 restraints weight = 10158.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.056571 restraints weight = 8053.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.057484 restraints weight = 6739.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.4511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3772  Z= 0.149
  Angle     :  0.798   9.343   5080  Z= 0.406
  Chirality :  0.047   0.222    552
  Planarity :  0.004   0.043    633
  Dihedral  :  5.763  27.403    482
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 20.54
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.64 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  5.22 %
    Favored  : 94.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.42), residues: 431
  helix: -0.32 (0.30), residues: 292
  sheet:  None (None), residues: 0
  loop : -1.59 (0.60), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 166 
 TYR   0.016   0.002   TYR C 190 
 PHE   0.027   0.002   PHE A 111 
 TRP   0.047   0.003   TRP C 130 
 HIS   0.011   0.001   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.15 ( 3772)
  covalent geometry    : angle       0.79788 /  0.41 ( 5080)
  hydrogen bonds       : bond        0.03719 /  2.28 (  184)
  hydrogen bonds       : angle       5.12371 /  3.48 (  549)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 TYR cc_start: 0.6170 (t80) cc_final: 0.5720 (t80)
REVERT: A   14 MET cc_start: 0.8610 (tpp) cc_final: 0.8086 (tpp)
REVERT: A   29 LEU cc_start: 0.9627 (mm) cc_final: 0.9415 (mm)
REVERT: A   31 VAL cc_start: 0.9520 (t) cc_final: 0.9307 (t)
REVERT: A   55 HIS cc_start: 0.9439 (t-90) cc_final: 0.9193 (t-90)
REVERT: A  101 HIS cc_start: 0.9089 (t-170) cc_final: 0.8866 (t70)
REVERT: A  104 TYR cc_start: 0.9461 (t80) cc_final: 0.9096 (t80)
REVERT: A  130 TYR cc_start: 0.9737 (m-80) cc_final: 0.9333 (m-80)
REVERT: A  143 ASP cc_start: 0.8096 (m-30) cc_final: 0.7892 (m-30)
REVERT: A  176 LYS cc_start: 0.9524 (tptp) cc_final: 0.9090 (mttt)
REVERT: B   65 ILE cc_start: 0.9672 (pt) cc_final: 0.9330 (pt)
REVERT: B   88 LYS cc_start: 0.9567 (mptt) cc_final: 0.9338 (mmtt)
REVERT: B  103 PHE cc_start: 0.9093 (t80) cc_final: 0.8669 (t80)
REVERT: B  107 TYR cc_start: 0.9360 (m-80) cc_final: 0.9030 (m-80)
REVERT: B  121 MET cc_start: 0.8802 (mpp) cc_final: 0.8602 (mpp)
REVERT: B  161 GLU cc_start: 0.9172 (mp0) cc_final: 0.8878 (mp0)
REVERT: B  188 VAL cc_start: 0.8885 (p) cc_final: 0.8662 (p)
REVERT: B  225 PHE cc_start: 0.8588 (m-10) cc_final: 0.8338 (m-10)
REVERT: B  229 LEU cc_start: 0.8963 (mm) cc_final: 0.8662 (mm)
REVERT: C  129 TYR cc_start: 0.9381 (m-80) cc_final: 0.9114 (m-80)
REVERT: C  151 ASP cc_start: 0.9480 (m-30) cc_final: 0.9274 (m-30)
REVERT: C  175 GLN cc_start: 0.9490 (tm-30) cc_final: 0.9275 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0707
  time to fit residues: 12.0683
Evaluate side-chains
  114 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0060
   chunk 21 optimal weight:    0.2980
   chunk 9 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.3796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 149 GLN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.071542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.052306 restraints weight = 19682.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.054770 restraints weight = 12820.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.056588 restraints weight = 9366.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.057906 restraints weight = 7320.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.058952 restraints weight = 6068.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.4665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   3772  Z= 0.141
  Angle     :  0.822   9.528   5080  Z= 0.414
  Chirality :  0.047   0.163    552
  Planarity :  0.004   0.031    633
  Dihedral  :  5.552  24.879    482
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 18.11
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.87 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  2.74 %
    Favored  : 97.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.41), residues: 431
  helix: -0.34 (0.30), residues: 291
  sheet:  None (None), residues: 0
  loop : -1.70 (0.58), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 166 
 TYR   0.017   0.001   TYR A  85 
 PHE   0.024   0.002   PHE C 120 
 TRP   0.065   0.003   TRP C 130 
 HIS   0.008   0.001   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.14 ( 3772)
  covalent geometry    : angle       0.82159 /  0.41 ( 5080)
  hydrogen bonds       : bond        0.03851 /  2.37 (  184)
  hydrogen bonds       : angle       5.20135 /  3.54 (  549)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 TYR cc_start: 0.5808 (t80) cc_final: 0.5396 (t80)
REVERT: A   14 MET cc_start: 0.8502 (tpp) cc_final: 0.8044 (tpp)
REVERT: A   29 LEU cc_start: 0.9555 (mm) cc_final: 0.9322 (mm)
REVERT: A   31 VAL cc_start: 0.9484 (t) cc_final: 0.9253 (t)
REVERT: A  101 HIS cc_start: 0.9045 (t-170) cc_final: 0.8831 (t70)
REVERT: A  104 TYR cc_start: 0.9434 (t80) cc_final: 0.9050 (t80)
REVERT: A  130 TYR cc_start: 0.9669 (m-80) cc_final: 0.9292 (m-80)
REVERT: A  143 ASP cc_start: 0.7964 (m-30) cc_final: 0.7763 (m-30)
REVERT: A  176 LYS cc_start: 0.9521 (tptp) cc_final: 0.9075 (mttt)
REVERT: B   65 ILE cc_start: 0.9646 (pt) cc_final: 0.9296 (pt)
REVERT: B  103 PHE cc_start: 0.8914 (t80) cc_final: 0.8545 (t80)
REVERT: B  107 TYR cc_start: 0.9308 (m-80) cc_final: 0.8901 (m-80)
REVERT: B  161 GLU cc_start: 0.9182 (mp0) cc_final: 0.8851 (mp0)
REVERT: B  229 LEU cc_start: 0.8984 (mm) cc_final: 0.8729 (mm)
REVERT: C  129 TYR cc_start: 0.9264 (m-80) cc_final: 0.8979 (m-80)
REVERT: C  148 GLU cc_start: 0.9557 (pm20) cc_final: 0.9197 (pm20)
REVERT: C  151 ASP cc_start: 0.9431 (m-30) cc_final: 0.9080 (m-30)
REVERT: C  175 GLN cc_start: 0.9536 (tm-30) cc_final: 0.9287 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 146
  average time/residue: 0.0573
  time to fit residues: 10.2470
Evaluate side-chains
  119 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 21 optimal weight:    0.2980
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0770
   overall best weight:    0.4938

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.071586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.052452 restraints weight = 20878.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.054777 restraints weight = 14313.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.056543 restraints weight = 10727.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.057845 restraints weight = 8553.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.058792 restraints weight = 7178.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.4885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   3772  Z= 0.149
  Angle     :  0.838  10.877   5080  Z= 0.424
  Chirality :  0.048   0.181    552
  Planarity :  0.004   0.038    633
  Dihedral  :  5.608  25.788    482
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 20.27
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.34 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.41), residues: 431
  helix: -0.38 (0.30), residues: 292
  sheet:  None (None), residues: 0
  loop : -1.74 (0.57), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 175 
 TYR   0.018   0.001   TYR C 190 
 PHE   0.037   0.003   PHE B 180 
 TRP   0.059   0.003   TRP C 130 
 HIS   0.011   0.001   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.15 ( 3772)
  covalent geometry    : angle       0.83842 /  0.42 ( 5080)
  hydrogen bonds       : bond        0.03861 /  2.37 (  184)
  hydrogen bonds       : angle       5.16770 /  3.49 (  549)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.8649 (tpp) cc_final: 0.8430 (tpp)
REVERT: A   29 LEU cc_start: 0.9614 (mm) cc_final: 0.9413 (mm)
REVERT: A   31 VAL cc_start: 0.9497 (t) cc_final: 0.9289 (t)
REVERT: A   55 HIS cc_start: 0.9435 (t-90) cc_final: 0.9202 (t-90)
REVERT: A  130 TYR cc_start: 0.9708 (m-80) cc_final: 0.9333 (m-80)
REVERT: A  176 LYS cc_start: 0.9522 (tptp) cc_final: 0.9094 (mttt)
REVERT: B   65 ILE cc_start: 0.9658 (pt) cc_final: 0.9323 (pt)
REVERT: B   88 LYS cc_start: 0.9554 (mptt) cc_final: 0.9322 (mmtt)
REVERT: B  103 PHE cc_start: 0.9020 (t80) cc_final: 0.8647 (t80)
REVERT: B  107 TYR cc_start: 0.9371 (m-80) cc_final: 0.9009 (m-80)
REVERT: B  121 MET cc_start: 0.8852 (mpp) cc_final: 0.8625 (mpp)
REVERT: B  184 TYR cc_start: 0.8777 (t80) cc_final: 0.8499 (t80)
REVERT: B  229 LEU cc_start: 0.9010 (mm) cc_final: 0.8736 (mm)
REVERT: C  129 TYR cc_start: 0.9312 (m-80) cc_final: 0.9079 (m-80)
REVERT: C  148 GLU cc_start: 0.9606 (pm20) cc_final: 0.9344 (pm20)
REVERT: C  151 ASP cc_start: 0.9450 (m-30) cc_final: 0.9155 (m-30)
REVERT: C  175 GLN cc_start: 0.9513 (tm-30) cc_final: 0.9259 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.0552
  time to fit residues: 9.5912
Evaluate side-chains
  120 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 13 optimal weight:    0.4980
   chunk 12 optimal weight:    0.0570
   chunk 34 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 22 optimal weight:    0.4980
   overall best weight:    0.5298

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  61 HIS
** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.071254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.052931 restraints weight = 20236.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.055179 restraints weight = 13731.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.056849 restraints weight = 10241.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.058099 restraints weight = 8155.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.059036 restraints weight = 6823.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.5122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   3772  Z= 0.160
  Angle     :  0.882  10.820   5080  Z= 0.449
  Chirality :  0.049   0.208    552
  Planarity :  0.004   0.032    633
  Dihedral  :  5.673  25.436    482
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 21.49
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.57 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.40), residues: 431
  helix: -0.49 (0.29), residues: 293
  sheet:  None (None), residues: 0
  loop : -2.04 (0.54), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 175 
 TYR   0.018   0.001   TYR C 190 
 PHE   0.027   0.002   PHE C 120 
 TRP   0.054   0.004   TRP C 130 
 HIS   0.010   0.001   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.16 ( 3772)
  covalent geometry    : angle       0.88221 /  0.45 ( 5080)
  hydrogen bonds       : bond        0.04302 /  2.60 (  184)
  hydrogen bonds       : angle       5.58472 /  3.69 (  549)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 VAL cc_start: 0.9494 (t) cc_final: 0.9290 (t)
REVERT: A   55 HIS cc_start: 0.9420 (t-90) cc_final: 0.9186 (t-90)
REVERT: A  101 HIS cc_start: 0.9134 (t70) cc_final: 0.8677 (t-170)
REVERT: A  130 TYR cc_start: 0.9697 (m-80) cc_final: 0.9326 (m-80)
REVERT: A  161 PHE cc_start: 0.9721 (t80) cc_final: 0.9517 (t80)
REVERT: A  176 LYS cc_start: 0.9527 (tptp) cc_final: 0.9084 (mttt)
REVERT: A  178 ARG cc_start: 0.9443 (ptp-170) cc_final: 0.9172 (ptp-170)
REVERT: B   65 ILE cc_start: 0.9666 (pt) cc_final: 0.9353 (pt)
REVERT: B  103 PHE cc_start: 0.8992 (t80) cc_final: 0.8662 (t80)
REVERT: B  107 TYR cc_start: 0.9331 (m-80) cc_final: 0.8996 (m-80)
REVERT: B  171 GLU cc_start: 0.8845 (tp30) cc_final: 0.8634 (tp30)
REVERT: B  229 LEU cc_start: 0.8846 (mm) cc_final: 0.8625 (mm)
REVERT: C  129 TYR cc_start: 0.9281 (m-80) cc_final: 0.9040 (m-80)
REVERT: C  148 GLU cc_start: 0.9621 (pm20) cc_final: 0.9280 (pm20)
REVERT: C  151 ASP cc_start: 0.9458 (m-30) cc_final: 0.9142 (m-30)
REVERT: C  175 GLN cc_start: 0.9415 (tm-30) cc_final: 0.9158 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.0659
  time to fit residues: 11.8762
Evaluate side-chains
  118 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 36 optimal weight:    0.4980
   chunk 22 optimal weight:    0.8980
   chunk 1 optimal weight:    0.1980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  61 HIS
** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.070961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.052639 restraints weight = 20449.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.054862 restraints weight = 13939.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.056513 restraints weight = 10472.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.057695 restraints weight = 8404.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.058627 restraints weight = 7112.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.5383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   3772  Z= 0.166
  Angle     :  0.905  10.595   5080  Z= 0.464
  Chirality :  0.051   0.226    552
  Planarity :  0.004   0.030    633
  Dihedral  :  5.590  25.774    482
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 22.43
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.64 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.39), residues: 431
  helix: -0.59 (0.29), residues: 292
  sheet:  None (None), residues: 0
  loop : -1.92 (0.55), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 175 
 TYR   0.018   0.002   TYR C 190 
 PHE   0.028   0.002   PHE C 120 
 TRP   0.076   0.004   TRP C 130 
 HIS   0.015   0.001   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.17 ( 3772)
  covalent geometry    : angle       0.90501 /  0.46 ( 5080)
  hydrogen bonds       : bond        0.04228 /  2.50 (  184)
  hydrogen bonds       : angle       5.57082 /  3.71 (  549)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 VAL cc_start: 0.9511 (t) cc_final: 0.9278 (t)
REVERT: A   55 HIS cc_start: 0.9424 (t-90) cc_final: 0.9188 (t-90)
REVERT: A  101 HIS cc_start: 0.9166 (t70) cc_final: 0.8720 (t-170)
REVERT: A  130 TYR cc_start: 0.9697 (m-80) cc_final: 0.9336 (m-80)
REVERT: A  143 ASP cc_start: 0.7988 (m-30) cc_final: 0.7788 (m-30)
REVERT: A  176 LYS cc_start: 0.9537 (tptp) cc_final: 0.9085 (mttt)
REVERT: B   65 ILE cc_start: 0.9673 (pt) cc_final: 0.9358 (pt)
REVERT: B  103 PHE cc_start: 0.9002 (t80) cc_final: 0.8488 (t80)
REVERT: B  106 GLU cc_start: 0.9659 (tm-30) cc_final: 0.9424 (pm20)
REVERT: B  107 TYR cc_start: 0.9365 (m-80) cc_final: 0.8197 (m-80)
REVERT: B  121 MET cc_start: 0.8849 (mpp) cc_final: 0.8639 (mpp)
REVERT: B  171 GLU cc_start: 0.8843 (tp30) cc_final: 0.8631 (tp30)
REVERT: B  229 LEU cc_start: 0.8811 (mm) cc_final: 0.8547 (mm)
REVERT: C  129 TYR cc_start: 0.9290 (m-80) cc_final: 0.9022 (m-80)
REVERT: C  148 GLU cc_start: 0.9630 (pm20) cc_final: 0.9305 (pm20)
REVERT: C  151 ASP cc_start: 0.9463 (m-30) cc_final: 0.9150 (m-30)
REVERT: C  175 GLN cc_start: 0.9437 (tm-30) cc_final: 0.9185 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0559
  time to fit residues: 9.4672
Evaluate side-chains
  114 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0980
   chunk 23 optimal weight:    0.0970
   chunk 5 optimal weight:    0.5980
   chunk 10 optimal weight:    0.1980
   chunk 34 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.3178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  25 ASN
B 149 GLN
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.073126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.054037 restraints weight = 19268.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.056544 restraints weight = 12573.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.058433 restraints weight = 9124.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.059868 restraints weight = 7113.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.060926 restraints weight = 5822.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.5445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   3772  Z= 0.150
  Angle     :  0.903  10.841   5080  Z= 0.453
  Chirality :  0.050   0.176    552
  Planarity :  0.004   0.031    633
  Dihedral  :  5.430  23.444    482
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 18.78
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.10 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  0.50 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.39), residues: 431
  helix: -0.59 (0.29), residues: 291
  sheet:  None (None), residues: 0
  loop : -2.06 (0.53), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 175 
 TYR   0.019   0.002   TYR A  32 
 PHE   0.028   0.002   PHE C 120 
 TRP   0.076   0.003   TRP C 130 
 HIS   0.012   0.001   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.15 ( 3772)
  covalent geometry    : angle       0.90305 /  0.45 ( 5080)
  hydrogen bonds       : bond        0.04247 /  2.53 (  184)
  hydrogen bonds       : angle       5.47599 /  3.67 (  549)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 920.11 seconds
wall clock time: 16 minutes 33.76 seconds (993.76 seconds total)