Starting phenix.real_space_refine
on Fri Aug 22 14:00:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b33_44124/08_2025/9b33_44124.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b33_44124/08_2025/9b33_44124.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b33_44124/08_2025/9b33_44124.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b33_44124/08_2025/9b33_44124.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b33_44124/08_2025/9b33_44124.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b33_44124/08_2025/9b33_44124.cif"
  }
  resolution = 4.07
  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=   0.002 sd=   0.015
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: 6
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      2      6.06       5
     S       4      5.16       5
     C    2281      2.51       5
     N     604      2.21       5
     O     726      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3619
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "E"
      Number of atoms: 1806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1806
          Classifications: {'peptide': 237}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 225}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "F"
      Number of atoms: 1809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1809
          Classifications: {'peptide': 237}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 225}
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.01, per 1000 atoms: 0.28
  Number of scatterers: 3619
  At special positions: 0
  Unit cell: (70.1324, 67.435, 93.0603, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     Ca      2     19.99
     S       4     16.00
     O     726      8.00
     N     604      7.00
     C    2281      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: 0.21
  Conformation dependent library (CDL) restraints added in 103.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN E1001 "
        pdb="ZN    ZN E1001 " - pdb=" NE2 HIS E  24 "


  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  884

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 20.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'E' and resid 28 through 29
      removed outlier: 3.674A  pdb=" N   VAL E   5 " --> pdb=" O   ILE E 214 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   SER E  94 " --> pdb=" O   ALA E 211 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLY E  92 " --> pdb=" O   PHE E 213 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER E 215 " --> pdb=" O   ARG E  90 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA E  95 " --> pdb=" O   GLY E 171 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 24 through 26
    Processing sheet with id=AA3, first strand: chain 'E' and resid 49 through 52
    Processing sheet with id=AA4, first strand: chain 'E' and resid 60 through 61
      removed outlier: 3.851A  pdb=" N   TYR E  77 " --> pdb=" O   LEU E  61 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 154 through 155
    Processing sheet with id=AA6, first strand: chain 'E' and resid 110 through 111
      removed outlier: 3.517A  pdb=" N   PHE E 111 " --> pdb=" O   PHE E 128 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 28 through 29
      removed outlier: 3.685A  pdb=" N   SER F  94 " --> pdb=" O   ALA F 211 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   SER F 215 " --> pdb=" O   ARG F  90 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 24 through 26
    Processing sheet with id=AA9, first strand: chain 'F' and resid 47 through 48
      removed outlier: 3.583A  pdb=" N   PHE F 197 " --> pdb=" O   GLY F  48 " (cutoff:3.500A)
      removed outlier: 5.895A  pdb=" N   GLU F 192 " --> pdb=" O   PHE F 111 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   PHE F 111 " --> pdb=" O   GLU F 192 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   THR F 194 " --> pdb=" O   TRP F 109 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   TRP F 109 " --> pdb=" O   THR F 194 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   THR F 196 " --> pdb=" O   LEU F 107 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   PHE F 111 " --> pdb=" O   PHE F 128 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   PHE F 128 " --> pdb=" O   PHE F 111 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 47 through 48
      removed outlier: 3.583A  pdb=" N   PHE F 197 " --> pdb=" O   GLY F  48 " (cutoff:3.500A)
      removed outlier: 5.895A  pdb=" N   GLU F 192 " --> pdb=" O   PHE F 111 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   PHE F 111 " --> pdb=" O   GLU F 192 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   THR F 194 " --> pdb=" O   TRP F 109 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   TRP F 109 " --> pdb=" O   THR F 194 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   THR F 196 " --> pdb=" O   LEU F 107 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 50 through 53

    55 hydrogen bonds defined for protein.
    123 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: 0.34

  Time building geometry restraints manager: 0.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1083
        1.33 -     1.45: 668
        1.45 -     1.57: 1937
        1.57 -     1.69: 3
        1.69 -     1.81: 8
  Bond restraints: 3699
  Sorted by residual:
  bond pdb=" CA  ASN F  14 "
       pdb=" CB  ASN F  14 "
    ideal  model  delta    sigma   weight residual
    1.524  1.424  0.099 1.37e-02 5.33e+03 5.27e+01
  bond pdb=" C   SER E  21 "
       pdb=" N   TYR E  22 "
    ideal  model  delta    sigma   weight residual
    1.327  1.261  0.066 1.39e-02 5.18e+03 2.25e+01
  bond pdb=" C   LEU F  85 "
       pdb=" N   PRO F  86 "
    ideal  model  delta    sigma   weight residual
    1.331  1.365 -0.033 1.21e-02 6.83e+03 7.54e+00
  bond pdb=" CB  ASN E  69 "
       pdb=" CG  ASN E  69 "
    ideal  model  delta    sigma   weight residual
    1.516  1.577 -0.061 2.50e-02 1.60e+03 5.92e+00
  bond pdb=" CB  ASN F  69 "
       pdb=" CG  ASN F  69 "
    ideal  model  delta    sigma   weight residual
    1.516  1.576 -0.060 2.50e-02 1.60e+03 5.69e+00
  ... (remaining 3694 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.68: 4956
        4.68 -     9.37: 74
        9.37 -    14.05: 11
       14.05 -    18.73: 1
       18.73 -    23.42: 2
  Bond angle restraints: 5044
  Sorted by residual:
  angle pdb=" N   GLY E  48 "
        pdb=" CA  GLY E  48 "
        pdb=" C   GLY E  48 "
      ideal   model   delta    sigma   weight residual
     113.18  136.60  -23.42 2.37e+00 1.78e-01 9.76e+01
  angle pdb=" N   GLY F  48 "
        pdb=" CA  GLY F  48 "
        pdb=" C   GLY F  48 "
      ideal   model   delta    sigma   weight residual
     114.74  135.99  -21.25 2.54e+00 1.55e-01 7.00e+01
  angle pdb=" C   PRO E  68 "
        pdb=" N   ASN E  69 "
        pdb=" CA  ASN E  69 "
      ideal   model   delta    sigma   weight residual
     122.74  133.62  -10.88 1.44e+00 4.82e-01 5.71e+01
  angle pdb=" C   PRO F  68 "
        pdb=" N   ASN F  69 "
        pdb=" CA  ASN F  69 "
      ideal   model   delta    sigma   weight residual
     123.93  135.01  -11.08 1.54e+00 4.22e-01 5.18e+01
  angle pdb=" N   ALA F 207 "
        pdb=" CA  ALA F 207 "
        pdb=" C   ALA F 207 "
      ideal   model   delta    sigma   weight residual
     107.28  117.92  -10.64 1.75e+00 3.27e-01 3.69e+01
  ... (remaining 5039 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.13: 1985
       15.13 -    30.26: 133
       30.26 -    45.39: 48
       45.39 -    60.52: 12
       60.52 -    75.64: 4
  Dihedral angle restraints: 2182
    sinusoidal: 812
      harmonic: 1370
  Sorted by residual:
  dihedral pdb=" CA  ALA E 207 "
           pdb=" C   ALA E 207 "
           pdb=" N   ASP E 208 "
           pdb=" CA  ASP E 208 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  115.63   64.37     0      5.00e+00 4.00e-02 1.66e+02
  dihedral pdb=" CA  SER F 185 "
           pdb=" C   SER F 185 "
           pdb=" N   ALA F 186 "
           pdb=" CA  ALA F 186 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -118.77  -61.23     0      5.00e+00 4.00e-02 1.50e+02
  dihedral pdb=" CA  VAL E  47 "
           pdb=" C   VAL E  47 "
           pdb=" N   GLY E  48 "
           pdb=" CA  GLY E  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  120.27   59.73     0      5.00e+00 4.00e-02 1.43e+02
  ... (remaining 2179 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 422
       0.069 -    0.138: 119
       0.138 -    0.207: 28
       0.207 -    0.276: 5
       0.276 -    0.344: 6
  Chirality restraints: 580
  Sorted by residual:
  chirality pdb=" CB  VAL F 187 "
            pdb=" CA  VAL F 187 "
            pdb=" CG1 VAL F 187 "
            pdb=" CG2 VAL F 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.34 2.00e-01 2.50e+01 2.97e+00
  chirality pdb=" CB  VAL E 187 "
            pdb=" CA  VAL E 187 "
            pdb=" CG1 VAL E 187 "
            pdb=" CG2 VAL E 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.75e+00
  chirality pdb=" CB  VAL E 159 "
            pdb=" CA  VAL E 159 "
            pdb=" CG1 VAL E 159 "
            pdb=" CG2 VAL E 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.34e+00
  ... (remaining 577 not shown)

  Planarity restraints: 651
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F 177 "    0.058 5.00e-02 4.00e+02   8.78e-02 1.23e+01
        pdb=" N   PRO F 178 "   -0.152 5.00e-02 4.00e+02
        pdb=" CA  PRO F 178 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO F 178 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA E 177 "   -0.048 5.00e-02 4.00e+02   7.35e-02 8.65e+00
        pdb=" N   PRO E 178 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO E 178 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO E 178 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 130 "    0.017 2.00e-02 2.50e+03   2.17e-02 8.21e+00
        pdb=" CG  PHE E 130 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 130 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 130 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 130 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 130 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 130 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 648 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 182
        2.69 -     3.24: 3514
        3.24 -     3.80: 5946
        3.80 -     4.35: 7507
        4.35 -     4.90: 12463
  Nonbonded interactions: 29612
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP E  10 "
            pdb="ZN    ZN E1001 "
     model   vdw
     2.141 2.230
  nonbonded pdb=" OD2 ASP F  19 "
            pdb="ZN    ZN F1001 "
     model   vdw
     2.153 2.230
  nonbonded pdb=" OE1 GLU F   8 "
            pdb="ZN    ZN F1001 "
     model   vdw
     2.172 2.230
  nonbonded pdb=" OG1 THR F  97 "
            pdb=" O   TYR F 100 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OD2 ASP F  10 "
            pdb="ZN    ZN F1001 "
     model   vdw
     2.255 2.230
  ... (remaining 29607 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'E'
  selection = (chain 'F' and (resid 1 through 144 or (resid 145 through 146 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 147 through 1002))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     4.570
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6344
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   0.099   3700  Z= 0.386
  Angle     :  1.560  23.418   5044  Z= 0.849
  Chirality :  0.076   0.344    580
  Planarity :  0.010   0.088    651
  Dihedral  : 13.121  75.644   1298
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  1.49 %
    Allowed  : 23.19 %
    Favored  : 75.32 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  4.94 %
    Favored  : 94.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 3.78 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -6.09 (0.29), residues: 470
  helix:  None (None), residues: 0
  sheet: -4.52 (0.35), residues: 138
  loop : -4.12 (0.25), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG F  60 
 TYR   0.042   0.005   TYR E 176 
 PHE   0.047   0.006   PHE F 130 
 TRP   0.042   0.008   TRP E 182 
 HIS   0.008   0.002   HIS F  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00713 ( 3699)
  covalent geometry    : angle       1.55983 ( 5044)
  hydrogen bonds       : bond        0.30435 (   51)
  hydrogen bonds       : angle      14.50618 (  123)
  metal coordination   : bond        0.02331 (    1)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 174
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   17 ILE cc_start: 0.7824 (pt) cc_final: 0.7491 (mp)
REVERT: E   39 LYS cc_start: 0.8846 (tttt) cc_final: 0.8333 (tptp)
REVERT: E   40 TRP cc_start: 0.8120 (t60) cc_final: 0.7913 (t60)
REVERT: E   53 ILE cc_start: 0.7885 (pp) cc_final: 0.7357 (pt)
REVERT: E   60 ARG cc_start: 0.7374 (mmm160) cc_final: 0.6917 (mmm-85)
REVERT: E  133 PHE cc_start: 0.6780 (m-80) cc_final: 0.6445 (m-10)
REVERT: E  213 PHE cc_start: 0.7632 (p90) cc_final: 0.7422 (p90)
REVERT: F   16 ASP cc_start: 0.7386 (m-30) cc_final: 0.7002 (m-30)
REVERT: F   17 ILE cc_start: 0.8285 (pt) cc_final: 0.8038 (mm)
REVERT: F   93 LEU cc_start: 0.8459 (mt) cc_final: 0.8083 (mp)
REVERT: F  100 TYR cc_start: 0.7322 (m-10) cc_final: 0.6877 (m-80)
REVERT: F  106 ILE cc_start: 0.8591 (mm) cc_final: 0.8248 (mt)
REVERT: F  139 ASP cc_start: 0.7909 (p0) cc_final: 0.7700 (p0)
REVERT: F  170 VAL cc_start: 0.6780 (p) cc_final: 0.6147 (t)
  outliers start: 2
  outliers final: 0
  residues processed: 175
  average time/residue: 0.0624
  time to fit residues: 13.2895
Evaluate side-chains
  125 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    0.3980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0770
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0370
   overall best weight:    0.5016

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

Flipped N/Q/H residues before XYZ refinement:
E  14 ASN
E  41 ASN
** E 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 166 GLN
** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.165836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.141828 restraints weight = 7763.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.145600 restraints weight = 4880.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.148456 restraints weight = 3550.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.150395 restraints weight = 2797.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.152057 restraints weight = 2343.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6517
moved from start:          0.3818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3700  Z= 0.175
  Angle     :  1.027  16.484   5044  Z= 0.527
  Chirality :  0.055   0.282    580
  Planarity :  0.006   0.067    651
  Dihedral  : 11.334  54.998    500
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 19.50
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 18.94 %
    Favored  : 79.79 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  3.95 %
    Favored  : 95.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 4.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.60 (0.31), residues: 470
  helix:  None (None), residues: 0
  sheet: -3.97 (0.33), residues: 166
  loop : -3.75 (0.28), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F 172 
 TYR   0.017   0.002   TYR F  67 
 PHE   0.033   0.003   PHE F 130 
 TRP   0.030   0.003   TRP F 182 
 HIS   0.008   0.001   HIS F 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 3699)
  covalent geometry    : angle       1.02700 ( 5044)
  hydrogen bonds       : bond        0.04849 (   51)
  hydrogen bonds       : angle       9.02521 (  123)
  metal coordination   : bond        0.00198 (    1)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 151
  time to evaluate  : 0.120 
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: E   51 HIS cc_start: 0.7489 (t-90) cc_final: 0.6927 (t70)
REVERT: E   81 LEU cc_start: 0.8236 (mm) cc_final: 0.7956 (mm)
REVERT: E   90 ARG cc_start: 0.7498 (mtp180) cc_final: 0.6877 (mmm-85)
REVERT: E  138 LYS cc_start: 0.7586 (mtmt) cc_final: 0.7074 (mtmm)
REVERT: E  140 LEU cc_start: 0.8469 (mt) cc_final: 0.8156 (mt)
REVERT: E  174 LEU cc_start: 0.7682 (mp) cc_final: 0.7298 (mp)
REVERT: E  176 TYR cc_start: 0.7889 (t80) cc_final: 0.6920 (t80)
REVERT: F   16 ASP cc_start: 0.6750 (m-30) cc_final: 0.6460 (m-30)
REVERT: F   27 ILE cc_start: 0.7661 (tt) cc_final: 0.7358 (mt)
REVERT: F   93 LEU cc_start: 0.8614 (mt) cc_final: 0.8326 (mp)
REVERT: F  126 LEU cc_start: 0.8230 (tp) cc_final: 0.7727 (tp)
REVERT: F  139 ASP cc_start: 0.7780 (p0) cc_final: 0.7573 (p0)
REVERT: F  166 GLN cc_start: 0.6639 (OUTLIER) cc_final: 0.6428 (mp10)
REVERT: F  176 TYR cc_start: 0.8396 (t80) cc_final: 0.7476 (t80)
REVERT: F  213 PHE cc_start: 0.8000 (p90) cc_final: 0.7798 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 152
  average time/residue: 0.0533
  time to fit residues: 9.8846
Evaluate side-chains
  124 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0170
   chunk 15 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    1.3822

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

Flipped N/Q/H residues before XYZ refinement:
** E  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 127 HIS
F 180 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.154379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.130074 restraints weight = 8018.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.133690 restraints weight = 5193.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.136181 restraints weight = 3814.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.138030 restraints weight = 3061.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.139220 restraints weight = 2585.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.5902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   3700  Z= 0.249
  Angle     :  1.024  14.560   5044  Z= 0.529
  Chirality :  0.058   0.314    580
  Planarity :  0.007   0.064    651
  Dihedral  : 11.109  58.269    500
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 23.72
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  : 24.47 %
    Favored  : 74.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.78 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.48 (0.32), residues: 470
  helix:  None (None), residues: 0
  sheet: -3.81 (0.34), residues: 164
  loop : -3.73 (0.29), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  60 
 TYR   0.014   0.002   TYR E  54 
 PHE   0.023   0.003   PHE E 130 
 TRP   0.026   0.004   TRP F 182 
 HIS   0.005   0.002   HIS F 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 3699)
  covalent geometry    : angle       1.02397 ( 5044)
  hydrogen bonds       : bond        0.04508 (   51)
  hydrogen bonds       : angle       8.97485 (  123)
  metal coordination   : bond        0.00611 (    1)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    4 ILE cc_start: 0.8856 (pt) cc_final: 0.8478 (pt)
REVERT: E   53 ILE cc_start: 0.8455 (mt) cc_final: 0.7872 (mt)
REVERT: E   60 ARG cc_start: 0.8705 (mmm-85) cc_final: 0.8006 (mmm-85)
REVERT: E   78 ASP cc_start: 0.8273 (m-30) cc_final: 0.7697 (p0)
REVERT: E   90 ARG cc_start: 0.7661 (mtp180) cc_final: 0.6839 (mmm-85)
REVERT: E  103 THR cc_start: 0.7685 (m) cc_final: 0.6908 (m)
REVERT: E  104 ASN cc_start: 0.7914 (m-40) cc_final: 0.7292 (p0)
REVERT: E  128 PHE cc_start: 0.8715 (p90) cc_final: 0.8422 (p90)
REVERT: E  140 LEU cc_start: 0.8791 (mt) cc_final: 0.8530 (mt)
REVERT: E  213 PHE cc_start: 0.8428 (p90) cc_final: 0.8124 (p90)
REVERT: F   93 LEU cc_start: 0.8841 (mt) cc_final: 0.8413 (mp)
REVERT: F  126 LEU cc_start: 0.8404 (tp) cc_final: 0.8156 (tp)
REVERT: F  139 ASP cc_start: 0.7922 (p0) cc_final: 0.7703 (p0)
REVERT: F  140 LEU cc_start: 0.8827 (mt) cc_final: 0.8601 (mp)
REVERT: F  176 TYR cc_start: 0.8672 (t80) cc_final: 0.8370 (t80)
REVERT: F  208 ASP cc_start: 0.5141 (t70) cc_final: 0.4603 (t70)
REVERT: F  210 ILE cc_start: 0.7748 (mt) cc_final: 0.7443 (mm)
REVERT: F  213 PHE cc_start: 0.8520 (p90) cc_final: 0.8031 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0697
  time to fit residues: 11.6253
Evaluate side-chains
  108 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0570
   chunk 34 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0870
   chunk 11 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0980
   chunk 24 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
E  41 ASN
** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  51 HIS
F 127 HIS
F 137 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.160869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.136227 restraints weight = 7877.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.140038 restraints weight = 5085.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.142824 restraints weight = 3753.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.144578 restraints weight = 2982.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.146156 restraints weight = 2528.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6787
moved from start:          0.6591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3700  Z= 0.158
  Angle     :  0.924  14.017   5044  Z= 0.475
  Chirality :  0.055   0.236    580
  Planarity :  0.006   0.054    651
  Dihedral  : 10.468  50.376    500
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 19.51
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  : 21.28 %
    Favored  : 77.87 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  3.46 %
    Favored  : 96.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.78 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.25 (0.32), residues: 470
  helix:  None (None), residues: 0
  sheet: -3.44 (0.36), residues: 158
  loop : -3.73 (0.28), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F 172 
 TYR   0.013   0.002   TYR E  54 
 PHE   0.016   0.002   PHE E 128 
 TRP   0.028   0.003   TRP F 182 
 HIS   0.005   0.001   HIS F 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3699)
  covalent geometry    : angle       0.92365 ( 5044)
  hydrogen bonds       : bond        0.03586 (   51)
  hydrogen bonds       : angle       8.69274 (  123)
  metal coordination   : bond        0.00104 (    1)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.094 
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: E    2 ASP cc_start: 0.8301 (p0) cc_final: 0.8007 (p0)
REVERT: E   40 TRP cc_start: 0.7577 (t60) cc_final: 0.7110 (t60)
REVERT: E   78 ASP cc_start: 0.8183 (m-30) cc_final: 0.7824 (p0)
REVERT: E  103 THR cc_start: 0.7537 (m) cc_final: 0.6858 (m)
REVERT: E  104 ASN cc_start: 0.7957 (m-40) cc_final: 0.6834 (p0)
REVERT: E  128 PHE cc_start: 0.8693 (p90) cc_final: 0.8358 (p90)
REVERT: E  140 LEU cc_start: 0.8695 (mt) cc_final: 0.8484 (mt)
REVERT: E  154 LEU cc_start: 0.8640 (tp) cc_final: 0.8334 (tp)
REVERT: F    7 VAL cc_start: 0.7317 (t) cc_final: 0.7049 (t)
REVERT: F   93 LEU cc_start: 0.8689 (mt) cc_final: 0.8255 (mp)
REVERT: F  126 LEU cc_start: 0.8406 (tp) cc_final: 0.8155 (tp)
REVERT: F  136 ASP cc_start: 0.7491 (t70) cc_final: 0.7283 (t0)
REVERT: F  208 ASP cc_start: 0.5244 (t70) cc_final: 0.5024 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0649
  time to fit residues: 10.8275
Evaluate side-chains
  110 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 13 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
E  41 ASN
** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 127 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.155289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.131261 restraints weight = 7943.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.135073 restraints weight = 5061.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.137784 restraints weight = 3646.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.139540 restraints weight = 2872.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.141063 restraints weight = 2421.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.7179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3700  Z= 0.199
  Angle     :  0.933  12.878   5044  Z= 0.484
  Chirality :  0.056   0.278    580
  Planarity :  0.006   0.052    651
  Dihedral  : 10.373  49.354    500
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 20.77
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 22.77 %
    Favored  : 75.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.78 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.06 (0.33), residues: 470
  helix:  None (None), residues: 0
  sheet: -3.09 (0.38), residues: 150
  loop : -3.74 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F 172 
 TYR   0.017   0.002   TYR F  67 
 PHE   0.016   0.003   PHE E 128 
 TRP   0.023   0.003   TRP F  40 
 HIS   0.004   0.001   HIS E  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 3699)
  covalent geometry    : angle       0.93312 ( 5044)
  hydrogen bonds       : bond        0.03344 (   51)
  hydrogen bonds       : angle       8.64872 (  123)
  metal coordination   : bond        0.00327 (    1)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  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: E    2 ASP cc_start: 0.8398 (p0) cc_final: 0.8181 (p0)
REVERT: E   40 TRP cc_start: 0.7728 (t60) cc_final: 0.7427 (t60)
REVERT: E   55 ASN cc_start: 0.8308 (p0) cc_final: 0.8003 (p0)
REVERT: E   78 ASP cc_start: 0.8281 (m-30) cc_final: 0.7930 (p0)
REVERT: E  104 ASN cc_start: 0.7861 (m-40) cc_final: 0.7070 (p0)
REVERT: E  128 PHE cc_start: 0.8922 (p90) cc_final: 0.8193 (p90)
REVERT: E  176 TYR cc_start: 0.8198 (t80) cc_final: 0.7487 (t80)
REVERT: F    7 VAL cc_start: 0.7567 (t) cc_final: 0.7276 (t)
REVERT: F  126 LEU cc_start: 0.8438 (tp) cc_final: 0.8230 (tp)
REVERT: F  176 TYR cc_start: 0.8771 (t80) cc_final: 0.8531 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0594
  time to fit residues: 9.4236
Evaluate side-chains
  107 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 35 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0470
   chunk 18 optimal weight:    7.9990
   chunk 1 optimal weight:    6.9990
   chunk 0 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0970
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.8278

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

Flipped N/Q/H residues before XYZ refinement:
E  41 ASN
E 124 ASN
E 166 GLN
F 127 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.156042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.132257 restraints weight = 7943.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.135999 restraints weight = 5013.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.138743 restraints weight = 3610.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.140684 restraints weight = 2835.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.142015 restraints weight = 2358.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6877
moved from start:          0.7638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3700  Z= 0.179
  Angle     :  0.910  12.568   5044  Z= 0.473
  Chirality :  0.054   0.266    580
  Planarity :  0.006   0.058    651
  Dihedral  : 10.102  46.048    500
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 19.92
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 22.13 %
    Favored  : 76.60 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  1.73 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.56 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.01 (0.33), residues: 470
  helix:  None (None), residues: 0
  sheet: -3.02 (0.39), residues: 150
  loop : -3.73 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F 158 
 TYR   0.016   0.002   TYR E  54 
 PHE   0.016   0.003   PHE E 195 
 TRP   0.042   0.003   TRP F  40 
 HIS   0.018   0.002   HIS F 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 3699)
  covalent geometry    : angle       0.90975 ( 5044)
  hydrogen bonds       : bond        0.03309 (   51)
  hydrogen bonds       : angle       8.76890 (  123)
  metal coordination   : bond        0.00218 (    1)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   55 ASN cc_start: 0.8189 (p0) cc_final: 0.7905 (p0)
REVERT: E   78 ASP cc_start: 0.8236 (m-30) cc_final: 0.7850 (p0)
REVERT: E  104 ASN cc_start: 0.7774 (m-40) cc_final: 0.7055 (p0)
REVERT: E  128 PHE cc_start: 0.8949 (p90) cc_final: 0.8166 (p90)
REVERT: E  140 LEU cc_start: 0.8702 (mt) cc_final: 0.8359 (mt)
REVERT: E  176 TYR cc_start: 0.7916 (t80) cc_final: 0.7149 (t80)
REVERT: F    7 VAL cc_start: 0.7753 (t) cc_final: 0.7456 (t)
REVERT: F  126 LEU cc_start: 0.8411 (tp) cc_final: 0.8176 (tp)
REVERT: F  228 ARG cc_start: 0.5009 (mpt-90) cc_final: 0.4423 (mmt90)
  outliers start: 1
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0613
  time to fit residues: 9.8113
Evaluate side-chains
  110 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 127 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.148752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.125228 restraints weight = 8240.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.128883 restraints weight = 5154.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.131452 restraints weight = 3737.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.133218 restraints weight = 2945.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.134435 restraints weight = 2474.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
moved from start:          0.8453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   3700  Z= 0.264
  Angle     :  1.000  12.576   5044  Z= 0.521
  Chirality :  0.058   0.279    580
  Planarity :  0.007   0.051    651
  Dihedral  : 10.459  46.835    500
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 25.40
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 24.47 %
    Favored  : 74.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.78 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.19 (0.33), residues: 470
  helix:  None (None), residues: 0
  sheet: -3.16 (0.38), residues: 154
  loop : -3.85 (0.29), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  90 
 TYR   0.021   0.002   TYR E  54 
 PHE   0.020   0.003   PHE E 128 
 TRP   0.030   0.003   TRP E 182 
 HIS   0.007   0.002   HIS F 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00559 ( 3699)
  covalent geometry    : angle       1.00023 ( 5044)
  hydrogen bonds       : bond        0.03498 (   51)
  hydrogen bonds       : angle       9.32260 (  123)
  metal coordination   : bond        0.00782 (    1)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   40 TRP cc_start: 0.8618 (t60) cc_final: 0.8140 (t60)
REVERT: E   60 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.7415 (mmm-85)
REVERT: E   78 ASP cc_start: 0.8277 (m-30) cc_final: 0.7856 (p0)
REVERT: E  104 ASN cc_start: 0.7658 (m-40) cc_final: 0.7074 (p0)
REVERT: E  128 PHE cc_start: 0.8966 (p90) cc_final: 0.8462 (p90)
REVERT: E  140 LEU cc_start: 0.8764 (mt) cc_final: 0.8360 (mt)
REVERT: E  141 ILE cc_start: 0.8286 (mt) cc_final: 0.7984 (tt)
REVERT: E  166 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7796 (mm-40)
REVERT: E  176 TYR cc_start: 0.8161 (t80) cc_final: 0.7415 (t80)
REVERT: E  208 ASP cc_start: 0.5943 (t0) cc_final: 0.5685 (t0)
REVERT: E  213 PHE cc_start: 0.8535 (p90) cc_final: 0.8251 (p90)
REVERT: F  130 PHE cc_start: 0.6918 (m-80) cc_final: 0.6352 (m-80)
REVERT: F  175 PHE cc_start: 0.8366 (t80) cc_final: 0.7971 (t80)
REVERT: F  208 ASP cc_start: 0.4922 (t70) cc_final: 0.4234 (t70)
REVERT: F  210 ILE cc_start: 0.8265 (mt) cc_final: 0.7938 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.0602
  time to fit residues: 9.5402
Evaluate side-chains
  108 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 44 optimal weight:    0.3980
   chunk 4 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
E  14 ASN
** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 127 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.153870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.130770 restraints weight = 8021.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.134495 restraints weight = 5057.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.137130 restraints weight = 3632.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.139072 restraints weight = 2839.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.140337 restraints weight = 2355.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.8677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3700  Z= 0.177
  Angle     :  0.932  12.297   5044  Z= 0.480
  Chirality :  0.056   0.298    580
  Planarity :  0.006   0.053    651
  Dihedral  :  9.915  43.563    500
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 22.59
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 22.55 %
    Favored  : 76.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.33 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.03 (0.33), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.87 (0.41), residues: 150
  loop : -3.84 (0.28), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F 158 
 TYR   0.018   0.001   TYR E  54 
 PHE   0.022   0.003   PHE E 195 
 TRP   0.038   0.003   TRP F  40 
 HIS   0.005   0.001   HIS E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 3699)
  covalent geometry    : angle       0.93249 ( 5044)
  hydrogen bonds       : bond        0.03271 (   51)
  hydrogen bonds       : angle       9.14645 (  123)
  metal coordination   : bond        0.00288 (    1)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  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: E    2 ASP cc_start: 0.8600 (p0) cc_final: 0.8391 (p0)
REVERT: E   78 ASP cc_start: 0.8224 (m-30) cc_final: 0.7925 (p0)
REVERT: E  104 ASN cc_start: 0.7476 (m-40) cc_final: 0.6580 (p0)
REVERT: E  128 PHE cc_start: 0.8996 (p90) cc_final: 0.8509 (p90)
REVERT: E  140 LEU cc_start: 0.8824 (mt) cc_final: 0.8498 (mt)
REVERT: E  141 ILE cc_start: 0.8179 (mt) cc_final: 0.7889 (tt)
REVERT: E  158 ARG cc_start: 0.6665 (mtp180) cc_final: 0.6454 (mtm180)
REVERT: E  176 TYR cc_start: 0.8089 (t80) cc_final: 0.7360 (t80)
REVERT: E  208 ASP cc_start: 0.5301 (t0) cc_final: 0.5079 (t0)
REVERT: F  175 PHE cc_start: 0.8300 (t80) cc_final: 0.7767 (t80)
REVERT: F  208 ASP cc_start: 0.4522 (t70) cc_final: 0.3730 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0695
  time to fit residues: 10.7604
Evaluate side-chains
  113 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0980
   chunk 2 optimal weight:    2.9990
   chunk 20 optimal weight:    0.3980
   chunk 38 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
E  14 ASN
E 121 HIS
F 124 ASN
F 127 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.153369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.130264 restraints weight = 7920.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.133933 restraints weight = 5052.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.136520 restraints weight = 3647.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.138429 restraints weight = 2869.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.139553 restraints weight = 2382.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
moved from start:          0.9072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3700  Z= 0.185
  Angle     :  0.941  13.308   5044  Z= 0.485
  Chirality :  0.057   0.308    580
  Planarity :  0.006   0.051    651
  Dihedral  :  9.603  43.559    500
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 22.45
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 22.98 %
    Favored  : 75.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.89 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.95 (0.33), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.67 (0.42), residues: 146
  loop : -3.86 (0.28), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F 158 
 TYR   0.019   0.001   TYR E  54 
 PHE   0.018   0.003   PHE F 191 
 TRP   0.048   0.003   TRP F  40 
 HIS   0.007   0.002   HIS E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 3699)
  covalent geometry    : angle       0.94056 ( 5044)
  hydrogen bonds       : bond        0.03200 (   51)
  hydrogen bonds       : angle       9.14421 (  123)
  metal coordination   : bond        0.00247 (    1)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    2 ASP cc_start: 0.8544 (p0) cc_final: 0.8287 (p0)
REVERT: E   78 ASP cc_start: 0.8164 (m-30) cc_final: 0.7875 (p0)
REVERT: E  104 ASN cc_start: 0.7660 (m-40) cc_final: 0.6928 (p0)
REVERT: E  128 PHE cc_start: 0.9004 (p90) cc_final: 0.8492 (p90)
REVERT: E  140 LEU cc_start: 0.8675 (mt) cc_final: 0.8064 (mt)
REVERT: E  158 ARG cc_start: 0.6636 (mtp180) cc_final: 0.5967 (tmt170)
REVERT: E  176 TYR cc_start: 0.8241 (t80) cc_final: 0.7567 (t80)
REVERT: E  208 ASP cc_start: 0.5774 (t0) cc_final: 0.5540 (t0)
REVERT: F    7 VAL cc_start: 0.8123 (t) cc_final: 0.7913 (t)
REVERT: F   40 TRP cc_start: 0.5001 (t60) cc_final: 0.4724 (t60)
REVERT: F   93 LEU cc_start: 0.8561 (mp) cc_final: 0.7936 (mp)
REVERT: F  138 LYS cc_start: 0.8189 (mtmm) cc_final: 0.7751 (mttp)
REVERT: F  172 ARG cc_start: 0.7497 (mmm-85) cc_final: 0.6970 (mmm-85)
REVERT: F  175 PHE cc_start: 0.8368 (t80) cc_final: 0.7820 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0629
  time to fit residues: 9.7451
Evaluate side-chains
  117 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 45 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
F 127 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.153837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.130174 restraints weight = 8104.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.134010 restraints weight = 5130.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.136755 restraints weight = 3695.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.138752 restraints weight = 2887.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.140203 restraints weight = 2385.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6949
moved from start:          0.9262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3700  Z= 0.173
  Angle     :  0.914  12.374   5044  Z= 0.467
  Chirality :  0.056   0.303    580
  Planarity :  0.006   0.057    651
  Dihedral  :  9.345  44.268    500
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 19.50
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 23.19 %
    Favored  : 75.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.67 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.71 (0.34), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.50 (0.46), residues: 136
  loop : -3.69 (0.28), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  90 
 TYR   0.017   0.001   TYR E  54 
 PHE   0.022   0.003   PHE E 195 
 TRP   0.043   0.003   TRP F  40 
 HIS   0.008   0.001   HIS E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 3699)
  covalent geometry    : angle       0.91406 ( 5044)
  hydrogen bonds       : bond        0.03164 (   51)
  hydrogen bonds       : angle       9.11470 (  123)
  metal coordination   : bond        0.00252 (    1)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    2 ASP cc_start: 0.8536 (p0) cc_final: 0.8303 (p0)
REVERT: E   61 LEU cc_start: 0.8513 (tt) cc_final: 0.8305 (tt)
REVERT: E   78 ASP cc_start: 0.8119 (m-30) cc_final: 0.7822 (p0)
REVERT: E  128 PHE cc_start: 0.8985 (p90) cc_final: 0.8704 (p90)
REVERT: E  137 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7827 (tm-30)
REVERT: E  140 LEU cc_start: 0.8160 (mt) cc_final: 0.7887 (mt)
REVERT: E  158 ARG cc_start: 0.6558 (mtp180) cc_final: 0.5993 (tmt170)
REVERT: E  176 TYR cc_start: 0.7958 (t80) cc_final: 0.7424 (t80)
REVERT: F  130 PHE cc_start: 0.6901 (m-80) cc_final: 0.6148 (m-80)
REVERT: F  172 ARG cc_start: 0.7289 (mmm-85) cc_final: 0.6967 (mmm-85)
REVERT: F  175 PHE cc_start: 0.8447 (t80) cc_final: 0.7804 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.0612
  time to fit residues: 9.3557
Evaluate side-chains
  110 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 15 optimal weight:    0.0010
   chunk 17 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0670
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.5324

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

Flipped N/Q/H residues before XYZ refinement:
E  14 ASN
E 131 ASN
** E 137 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 = 0.4189 r_free = 0.4189 target = 0.155657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.132519 restraints weight = 7893.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.136259 restraints weight = 5015.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.138886 restraints weight = 3625.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.140660 restraints weight = 2849.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.142208 restraints weight = 2388.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.9573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3700  Z= 0.162
  Angle     :  0.908  13.280   5044  Z= 0.462
  Chirality :  0.055   0.289    580
  Planarity :  0.006   0.055    651
  Dihedral  :  9.116  43.781    500
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 20.06
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 22.13 %
    Favored  : 76.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.89 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.55 (0.34), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.16 (0.47), residues: 132
  loop : -3.68 (0.28), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E 158 
 TYR   0.017   0.001   TYR E  54 
 PHE   0.018   0.003   PHE F 191 
 TRP   0.040   0.003   TRP F  40 
 HIS   0.008   0.001   HIS E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 3699)
  covalent geometry    : angle       0.90815 ( 5044)
  hydrogen bonds       : bond        0.03097 (   51)
  hydrogen bonds       : angle       9.04488 (  123)
  metal coordination   : bond        0.00160 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 804.08 seconds
wall clock time: 14 minutes 33.14 seconds (873.14 seconds total)