Starting phenix.real_space_refine
on Wed Mar  5 21:35:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b33_44124/03_2025/9b33_44124.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b33_44124/03_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_44124/03_2025/9b33_44124.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b33_44124/03_2025/9b33_44124.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b33_44124/03_2025/9b33_44124.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b33_44124/03_2025/9b33_44124.cif"
  }
  resolution = 4.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.76, per 1000 atoms: 0.76
  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: 0.79
  Conformation dependent library (CDL) restraints added in 413.8 milliseconds
  
  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: 0.40
  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: 0.80

  Time building geometry restraints manager: 0.95 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 237 or resid 1001 th \ 
rough 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:             1.090
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.210
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.370
-------------------------------------------------------------------------------
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   3699  Z= 0.476
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.042   0.008   TRP E 182 
 HIS   0.008   0.002   HIS F  24 
 PHE   0.047   0.006   PHE F 130 
 TYR   0.042   0.005   TYR E 176 
 ARG   0.013   0.002   ARG F  60 

*********************** 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  : 0.373 
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: 0.1634
  time to fit residues: 34.1051
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  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 34 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0970
   chunk 13 optimal weight:    0.2980
   chunk 21 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0970
   overall best weight:    0.4176

-------------------------------------------------------------------------------
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 = 0.4319 r_free = 0.4319 target = 0.166826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.142813 restraints weight = 7708.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.146758 restraints weight = 4846.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.149722 restraints weight = 3479.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.4104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6533
moved from start:          0.3876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3699  Z= 0.249
  Angle     :  1.028  16.424   5044  Z= 0.527
  Chirality :  0.055   0.277    580
  Planarity :  0.006   0.068    651
  Dihedral  : 11.255  54.648    500
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 19.08
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 19.36 %
    Favored  : 79.36 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  4.20 %
    Favored  : 95.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 4.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.60 (0.31), residues: 470
  helix:  None (None), residues: 0
  sheet: -3.96 (0.33), residues: 166
  loop : -3.75 (0.28), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP F 182 
 HIS   0.009   0.001   HIS F 180 
 PHE   0.031   0.003   PHE F 130 
 TYR   0.012   0.002   TYR F  54 
 ARG   0.005   0.001   ARG F 172 

*********************** 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
  152 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 150
  time to evaluate  : 0.371 
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   40 TRP cc_start: 0.7494 (t60) cc_final: 0.7255 (t60)
REVERT: E   51 HIS cc_start: 0.7567 (t-90) cc_final: 0.7052 (t70)
REVERT: E   60 ARG cc_start: 0.7972 (mmm160) cc_final: 0.7729 (mmm-85)
REVERT: E   79 VAL cc_start: 0.8478 (p) cc_final: 0.8158 (p)
REVERT: E   81 LEU cc_start: 0.8244 (mm) cc_final: 0.7951 (mm)
REVERT: E   90 ARG cc_start: 0.7344 (mtp180) cc_final: 0.6769 (mmm-85)
REVERT: E  138 LYS cc_start: 0.7451 (mtmt) cc_final: 0.6922 (mtmm)
REVERT: E  140 LEU cc_start: 0.8440 (mt) cc_final: 0.8115 (mt)
REVERT: E  174 LEU cc_start: 0.7645 (mp) cc_final: 0.7229 (mp)
REVERT: E  176 TYR cc_start: 0.7826 (t80) cc_final: 0.6877 (t80)
REVERT: F   16 ASP cc_start: 0.6631 (m-30) cc_final: 0.6328 (m-30)
REVERT: F   27 ILE cc_start: 0.7663 (tt) cc_final: 0.7389 (mt)
REVERT: F   93 LEU cc_start: 0.8601 (mt) cc_final: 0.8324 (mp)
REVERT: F  126 LEU cc_start: 0.8191 (tp) cc_final: 0.7693 (tp)
REVERT: F  176 TYR cc_start: 0.8375 (t80) cc_final: 0.7450 (t80)
REVERT: F  213 PHE cc_start: 0.7945 (p90) cc_final: 0.7737 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 151
  average time/residue: 0.1581
  time to fit residues: 28.8952
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  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0670
   chunk 23 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.8922

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

Flipped N/Q/H residues before XYZ refinement:
E  41 ASN
F 127 HIS
** F 180 HIS ** 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 = 0.4257 r_free = 0.4257 target = 0.161229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.136665 restraints weight = 7920.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.140299 restraints weight = 5110.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.143015 restraints weight = 3769.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6788
moved from start:          0.5374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3699  Z= 0.264
  Angle     :  0.981  16.149   5044  Z= 0.501
  Chirality :  0.056   0.318    580
  Planarity :  0.006   0.057    651
  Dihedral  : 10.877  56.710    500
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 18.24
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  : 22.77 %
    Favored  : 76.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.33 (0.32), residues: 470
  helix:  None (None), residues: 0
  sheet: -3.75 (0.34), residues: 166
  loop : -3.59 (0.29), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP F 182 
 HIS   0.005   0.001   HIS F 127 
 PHE   0.018   0.003   PHE F 111 
 TYR   0.012   0.002   TYR F  12 
 ARG   0.005   0.001   ARG F 172 

*********************** 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
  135 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.405 
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   60 ARG cc_start: 0.7769 (mmm160) cc_final: 0.7064 (mmm-85)
REVERT: E   78 ASP cc_start: 0.8456 (m-30) cc_final: 0.8084 (p0)
REVERT: E  104 ASN cc_start: 0.7855 (m-40) cc_final: 0.6916 (p0)
REVERT: E  137 GLN cc_start: 0.8409 (tt0) cc_final: 0.8141 (tt0)
REVERT: E  140 LEU cc_start: 0.8624 (mt) cc_final: 0.7901 (mt)
REVERT: E  174 LEU cc_start: 0.7784 (mp) cc_final: 0.7575 (mp)
REVERT: E  176 TYR cc_start: 0.8089 (t80) cc_final: 0.7325 (t80)
REVERT: F   67 TYR cc_start: 0.5578 (m-80) cc_final: 0.4758 (m-10)
REVERT: F   93 LEU cc_start: 0.8783 (mt) cc_final: 0.8460 (mp)
REVERT: F  126 LEU cc_start: 0.8222 (tp) cc_final: 0.7943 (tp)
REVERT: F  176 TYR cc_start: 0.8404 (t80) cc_final: 0.7840 (t80)
REVERT: F  208 ASP cc_start: 0.5708 (t70) cc_final: 0.5410 (t0)
REVERT: F  210 ILE cc_start: 0.7745 (mt) cc_final: 0.7488 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1535
  time to fit residues: 25.2716
Evaluate side-chains
  119 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 18 optimal weight:    0.0070
   chunk 33 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.6998

-------------------------------------------------------------------------------
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
F  51 HIS
F 127 HIS
F 137 GLN
F 180 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.162375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.137376 restraints weight = 7749.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.141359 restraints weight = 4945.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.144234 restraints weight = 3593.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.4031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6794
moved from start:          0.6190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3699  Z= 0.229
  Angle     :  0.899  13.170   5044  Z= 0.464
  Chirality :  0.055   0.242    580
  Planarity :  0.006   0.054    651
  Dihedral  : 10.227  51.567    500
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 18.24
  Ramachandran Plot:
    Outliers :  1.06 %
    Allowed  : 21.28 %
    Favored  : 77.66 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  2.96 %
    Favored  : 96.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.33 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.10 (0.33), residues: 470
  helix:  None (None), residues: 0
  sheet: -3.30 (0.37), residues: 158
  loop : -3.65 (0.29), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP F 182 
 HIS   0.003   0.001   HIS F 180 
 PHE   0.015   0.002   PHE F 111 
 TYR   0.012   0.001   TYR E  54 
 ARG   0.004   0.001   ARG F 158 

*********************** 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
  134 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 132
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   25 ILE cc_start: 0.7977 (tt) cc_final: 0.7753 (tt)
REVERT: E   40 TRP cc_start: 0.7880 (t60) cc_final: 0.7430 (t60)
REVERT: E   55 ASN cc_start: 0.8230 (p0) cc_final: 0.7917 (p0)
REVERT: E   60 ARG cc_start: 0.7786 (mmm160) cc_final: 0.7207 (mmm-85)
REVERT: E   78 ASP cc_start: 0.8457 (m-30) cc_final: 0.8019 (p0)
REVERT: E  104 ASN cc_start: 0.7998 (m-40) cc_final: 0.7032 (p0)
REVERT: E  140 LEU cc_start: 0.8392 (mt) cc_final: 0.8150 (mt)
REVERT: E  154 LEU cc_start: 0.8654 (tp) cc_final: 0.8380 (tp)
REVERT: E  166 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6065 (mp10)
REVERT: E  176 TYR cc_start: 0.8285 (t80) cc_final: 0.7735 (t80)
REVERT: E  197 PHE cc_start: 0.8945 (p90) cc_final: 0.8568 (p90)
REVERT: F    7 VAL cc_start: 0.7478 (t) cc_final: 0.7189 (t)
REVERT: F   93 LEU cc_start: 0.8756 (mt) cc_final: 0.8533 (mp)
REVERT: F  126 LEU cc_start: 0.8246 (tp) cc_final: 0.8004 (tp)
REVERT: F  136 ASP cc_start: 0.7587 (t70) cc_final: 0.7238 (t0)
REVERT: F  176 TYR cc_start: 0.8504 (t80) cc_final: 0.8222 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1641
  time to fit residues: 26.7738
Evaluate side-chains
  113 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0770
   chunk 35 optimal weight:    9.9990
   chunk 23 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0020
   chunk 44 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.1748

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

Flipped N/Q/H residues before XYZ refinement:
** F  43 GLN ** 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 = 0.4211 r_free = 0.4211 target = 0.157152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.132545 restraints weight = 7879.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.136190 restraints weight = 5115.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.138917 restraints weight = 3775.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
moved from start:          0.6914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3699  Z= 0.284
  Angle     :  0.909  12.065   5044  Z= 0.473
  Chirality :  0.055   0.280    580
  Planarity :  0.006   0.054    651
  Dihedral  : 10.232  50.502    500
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 21.33
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 22.13 %
    Favored  : 76.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.33 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.06 (0.33), residues: 470
  helix:  None (None), residues: 0
  sheet: -3.16 (0.38), residues: 154
  loop : -3.70 (0.29), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP F 182 
 HIS   0.003   0.001   HIS E 180 
 PHE   0.015   0.003   PHE E 111 
 TYR   0.014   0.002   TYR F 176 
 ARG   0.004   0.001   ARG F 158 

*********************** 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
  135 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.410 
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: 0.8901 (pt) cc_final: 0.8691 (pt)
REVERT: E   55 ASN cc_start: 0.8232 (p0) cc_final: 0.7889 (p0)
REVERT: E   78 ASP cc_start: 0.8357 (m-30) cc_final: 0.8011 (p0)
REVERT: E   90 ARG cc_start: 0.7601 (mtp180) cc_final: 0.7044 (mmm-85)
REVERT: E  104 ASN cc_start: 0.7952 (m-40) cc_final: 0.6987 (p0)
REVERT: E  140 LEU cc_start: 0.8476 (mt) cc_final: 0.8218 (mt)
REVERT: E  154 LEU cc_start: 0.8563 (tp) cc_final: 0.8345 (tp)
REVERT: E  176 TYR cc_start: 0.8122 (t80) cc_final: 0.7397 (t80)
REVERT: F    7 VAL cc_start: 0.7543 (t) cc_final: 0.7222 (t)
REVERT: F  136 ASP cc_start: 0.7451 (t70) cc_final: 0.7128 (t0)
REVERT: F  137 GLN cc_start: 0.8553 (mt0) cc_final: 0.8286 (tt0)
REVERT: F  208 ASP cc_start: 0.4781 (t70) cc_final: 0.4283 (t70)
REVERT: F  215 SER cc_start: 0.7775 (p) cc_final: 0.7552 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1535
  time to fit residues: 25.3037
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  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 22 optimal weight:    0.0010
   chunk 36 optimal weight:    0.3980
   chunk 10 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 7 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.4786

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.162150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.137540 restraints weight = 7829.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.141475 restraints weight = 4999.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.144037 restraints weight = 3634.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6827
moved from start:          0.7468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3699  Z= 0.224
  Angle     :  0.880  12.975   5044  Z= 0.456
  Chirality :  0.055   0.266    580
  Planarity :  0.006   0.060    651
  Dihedral  :  9.757  45.495    500
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 17.96
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 21.28 %
    Favored  : 77.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.56 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.95 (0.33), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.98 (0.38), residues: 158
  loop : -3.67 (0.29), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP F  40 
 HIS   0.005   0.001   HIS F 180 
 PHE   0.015   0.002   PHE F 128 
 TYR   0.011   0.001   TYR E  54 
 ARG   0.004   0.001   ARG F 172 

*********************** 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: 0
    poor density    : 131
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   40 TRP cc_start: 0.7347 (t60) cc_final: 0.7047 (t60)
REVERT: E   55 ASN cc_start: 0.8249 (p0) cc_final: 0.7918 (p0)
REVERT: E   78 ASP cc_start: 0.8246 (m-30) cc_final: 0.7966 (p0)
REVERT: E   90 ARG cc_start: 0.7229 (mtp180) cc_final: 0.6522 (mmm-85)
REVERT: E  104 ASN cc_start: 0.7767 (m-40) cc_final: 0.6738 (p0)
REVERT: E  154 LEU cc_start: 0.8523 (tp) cc_final: 0.8264 (tp)
REVERT: E  176 TYR cc_start: 0.7903 (t80) cc_final: 0.7253 (t80)
REVERT: F    7 VAL cc_start: 0.7649 (t) cc_final: 0.7366 (t)
REVERT: F  103 THR cc_start: 0.7355 (m) cc_final: 0.7144 (m)
REVERT: F  107 LEU cc_start: 0.8620 (mm) cc_final: 0.8329 (mm)
REVERT: F  176 TYR cc_start: 0.8204 (t80) cc_final: 0.7732 (t80)
REVERT: F  208 ASP cc_start: 0.4704 (t70) cc_final: 0.3971 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1670
  time to fit residues: 26.3638
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  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0010
   chunk 40 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 44 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 35 optimal weight:    0.1980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.5786

-------------------------------------------------------------------------------
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 = 0.4255 r_free = 0.4255 target = 0.160881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.136158 restraints weight = 7899.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.140046 restraints weight = 5036.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.142887 restraints weight = 3683.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
moved from start:          0.7821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3699  Z= 0.224
  Angle     :  0.866  12.220   5044  Z= 0.449
  Chirality :  0.054   0.290    580
  Planarity :  0.005   0.052    651
  Dihedral  :  9.537  44.409    500
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 19.08
  Ramachandran Plot:
    Outliers :  1.06 %
    Allowed  : 22.55 %
    Favored  : 76.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.84 (0.33), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.69 (0.41), residues: 150
  loop : -3.73 (0.28), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP F  40 
 HIS   0.003   0.001   HIS E  24 
 PHE   0.016   0.003   PHE E 191 
 TYR   0.012   0.001   TYR E  54 
 ARG   0.003   0.001   ARG F  90 

*********************** 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
  129 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   55 ASN cc_start: 0.8138 (p0) cc_final: 0.7786 (p0)
REVERT: E   78 ASP cc_start: 0.8252 (m-30) cc_final: 0.7915 (p0)
REVERT: E   90 ARG cc_start: 0.7549 (mtp180) cc_final: 0.6691 (mmm-85)
REVERT: E  104 ASN cc_start: 0.7739 (m-40) cc_final: 0.6629 (p0)
REVERT: E  128 PHE cc_start: 0.8650 (p90) cc_final: 0.8343 (p90)
REVERT: E  140 LEU cc_start: 0.8585 (mt) cc_final: 0.8244 (mt)
REVERT: E  141 ILE cc_start: 0.8026 (mt) cc_final: 0.7689 (tt)
REVERT: E  176 TYR cc_start: 0.7946 (t80) cc_final: 0.7147 (t80)
REVERT: E  208 ASP cc_start: 0.5393 (t0) cc_final: 0.5179 (t0)
REVERT: F    7 VAL cc_start: 0.7785 (t) cc_final: 0.7514 (t)
REVERT: F  107 LEU cc_start: 0.8586 (mm) cc_final: 0.8197 (mm)
REVERT: F  126 LEU cc_start: 0.8479 (tp) cc_final: 0.8257 (tp)
REVERT: F  175 PHE cc_start: 0.8423 (t80) cc_final: 0.7971 (t80)
REVERT: F  208 ASP cc_start: 0.4773 (t70) cc_final: 0.4087 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1661
  time to fit residues: 26.1184
Evaluate side-chains
  109 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 25 optimal weight:    0.3980
   chunk 11 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0770
   chunk 14 optimal weight:    1.9990
   chunk 38 optimal weight:    0.1980
   chunk 27 optimal weight:    0.0270
   chunk 31 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.2796

-------------------------------------------------------------------------------
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 180 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.157091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.131183 restraints weight = 7441.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.135040 restraints weight = 4885.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.137914 restraints weight = 3614.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6771
moved from start:          0.8173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3699  Z= 0.229
  Angle     :  0.877  12.264   5044  Z= 0.457
  Chirality :  0.054   0.284    580
  Planarity :  0.006   0.051    651
  Dihedral  :  9.317  44.122    500
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 19.08
  Ramachandran Plot:
    Outliers :  1.06 %
    Allowed  : 21.70 %
    Favored  : 77.23 %
  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 : 3.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.68 (0.34), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.45 (0.43), residues: 136
  loop : -3.68 (0.28), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP F 182 
 HIS   0.023   0.002   HIS F 180 
 PHE   0.020   0.003   PHE E 128 
 TYR   0.026   0.002   TYR F 176 
 ARG   0.007   0.001   ARG F 172 

*********************** 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
  130 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   55 ASN cc_start: 0.8232 (p0) cc_final: 0.7926 (p0)
REVERT: E   78 ASP cc_start: 0.8478 (m-30) cc_final: 0.8097 (p0)
REVERT: E  104 ASN cc_start: 0.7674 (m-40) cc_final: 0.6439 (p0)
REVERT: E  128 PHE cc_start: 0.8632 (p90) cc_final: 0.8290 (p90)
REVERT: E  140 LEU cc_start: 0.8538 (mt) cc_final: 0.8290 (mt)
REVERT: E  141 ILE cc_start: 0.8240 (mt) cc_final: 0.8004 (tt)
REVERT: E  176 TYR cc_start: 0.7658 (t80) cc_final: 0.7113 (t80)
REVERT: E  208 ASP cc_start: 0.5672 (t0) cc_final: 0.5454 (t0)
REVERT: F    7 VAL cc_start: 0.7641 (t) cc_final: 0.7340 (t)
REVERT: F  101 LYS cc_start: 0.6243 (mtmm) cc_final: 0.5918 (mtmm)
REVERT: F  107 LEU cc_start: 0.8788 (mm) cc_final: 0.8371 (mm)
REVERT: F  208 ASP cc_start: 0.4574 (t70) cc_final: 0.3941 (t70)
REVERT: F  215 SER cc_start: 0.8035 (t) cc_final: 0.7832 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1679
  time to fit residues: 26.6295
Evaluate side-chains
  118 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 19 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 3 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
E 121 HIS
** F 124 ASN ** 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 = 0.4065 r_free = 0.4065 target = 0.146531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.121772 restraints weight = 7721.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.125195 restraints weight = 5131.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.127705 restraints weight = 3838.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7078
moved from start:          0.8719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   3699  Z= 0.349
  Angle     :  0.980  11.035   5044  Z= 0.506
  Chirality :  0.057   0.331    580
  Planarity :  0.007   0.057    651
  Dihedral  :  9.690  44.129    500
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 22.87
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  : 23.40 %
    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 : 3.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.86 (0.33), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.44 (0.46), residues: 132
  loop : -3.87 (0.27), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.004   TRP F  88 
 HIS   0.006   0.002   HIS E 180 
 PHE   0.021   0.003   PHE E 128 
 TYR   0.022   0.003   TYR E 176 
 ARG   0.009   0.002   ARG F  90 

*********************** 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
  125 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    2 ASP cc_start: 0.8560 (p0) cc_final: 0.8357 (p0)
REVERT: E   40 TRP cc_start: 0.7876 (t60) cc_final: 0.7623 (t60)
REVERT: E   55 ASN cc_start: 0.8326 (p0) cc_final: 0.7978 (p0)
REVERT: E   61 LEU cc_start: 0.8272 (tp) cc_final: 0.8049 (tt)
REVERT: E   78 ASP cc_start: 0.8370 (m-30) cc_final: 0.8073 (p0)
REVERT: E   90 ARG cc_start: 0.7773 (mtp180) cc_final: 0.7195 (tpt-90)
REVERT: E  104 ASN cc_start: 0.7854 (m-40) cc_final: 0.6920 (p0)
REVERT: E  140 LEU cc_start: 0.8490 (mt) cc_final: 0.8247 (mt)
REVERT: E  158 ARG cc_start: 0.7147 (mtm-85) cc_final: 0.6271 (tmt170)
REVERT: E  176 TYR cc_start: 0.8125 (t80) cc_final: 0.7777 (t80)
REVERT: E  208 ASP cc_start: 0.5974 (t0) cc_final: 0.5610 (t0)
REVERT: F    9 LEU cc_start: 0.8373 (mp) cc_final: 0.8157 (mp)
REVERT: F   36 LYS cc_start: 0.8816 (mmtm) cc_final: 0.8529 (mmmm)
REVERT: F   40 TRP cc_start: 0.5595 (t60) cc_final: 0.5133 (t60)
REVERT: F  208 ASP cc_start: 0.5397 (t70) cc_final: 0.4824 (t70)
REVERT: F  210 ILE cc_start: 0.8209 (mt) cc_final: 0.7849 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1670
  time to fit residues: 25.2104
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  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.4070 r_free = 0.4070 target = 0.146632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.122298 restraints weight = 7841.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.125831 restraints weight = 5151.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.128535 restraints weight = 3824.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.9093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   3699  Z= 0.312
  Angle     :  0.960  12.122   5044  Z= 0.497
  Chirality :  0.057   0.328    580
  Planarity :  0.006   0.052    651
  Dihedral  :  9.554  43.963    500
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 22.73
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 23.62 %
    Favored  : 75.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.89 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.83 (0.34), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.38 (0.48), residues: 132
  loop : -3.87 (0.27), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.004   TRP F 182 
 HIS   0.006   0.001   HIS F 127 
 PHE   0.023   0.003   PHE F 133 
 TYR   0.019   0.002   TYR F 176 
 ARG   0.008   0.001   ARG F  90 

********************** 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
  131 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   40 TRP cc_start: 0.7924 (t60) cc_final: 0.7564 (t60)
REVERT: E   55 ASN cc_start: 0.8375 (p0) cc_final: 0.8019 (p0)
REVERT: E   61 LEU cc_start: 0.8327 (tp) cc_final: 0.8077 (tt)
REVERT: E   78 ASP cc_start: 0.8323 (m-30) cc_final: 0.8035 (p0)
REVERT: E   90 ARG cc_start: 0.7709 (mtp180) cc_final: 0.6767 (mmm-85)
REVERT: E  104 ASN cc_start: 0.7674 (m-40) cc_final: 0.6875 (p0)
REVERT: E  128 PHE cc_start: 0.8599 (p90) cc_final: 0.8069 (p90)
REVERT: E  140 LEU cc_start: 0.8635 (mt) cc_final: 0.8323 (mt)
REVERT: E  176 TYR cc_start: 0.8135 (t80) cc_final: 0.7167 (t80)
REVERT: E  208 ASP cc_start: 0.5670 (t0) cc_final: 0.5254 (t0)
REVERT: F   36 LYS cc_start: 0.8787 (mmtm) cc_final: 0.8580 (mmmm)
REVERT: F  174 LEU cc_start: 0.9178 (tp) cc_final: 0.8854 (tp)
REVERT: F  176 TYR cc_start: 0.8158 (t80) cc_final: 0.7601 (t80)
REVERT: F  208 ASP cc_start: 0.4966 (t70) cc_final: 0.4143 (t70)
REVERT: F  210 ILE cc_start: 0.8164 (mt) cc_final: 0.7815 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1511
  time to fit residues: 24.4504
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  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 20 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.7588

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.148968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.125090 restraints weight = 8145.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.128521 restraints weight = 5350.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.130993 restraints weight = 3994.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.9640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   3699  Z= 0.363
  Angle     :  0.995  11.296   5044  Z= 0.514
  Chirality :  0.056   0.326    580
  Planarity :  0.007   0.059    651
  Dihedral  :  9.757  44.551    500
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 24.55
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  : 23.19 %
    Favored  : 75.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.67 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.94 (0.33), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.53 (0.46), residues: 132
  loop : -3.91 (0.27), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.004   TRP E 109 
 HIS   0.006   0.002   HIS E  24 
 PHE   0.021   0.003   PHE E 195 
 TYR   0.019   0.002   TYR F 176 
 ARG   0.010   0.001   ARG F  90 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1716.82 seconds
wall clock time: 30 minutes 26.30 seconds (1826.30 seconds total)