Starting phenix.real_space_refine
on Tue Mar  3 13:11:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f73_31484/03_2026/7f73_31484.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f73_31484/03_2026/7f73_31484.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f73_31484/03_2026/7f73_31484.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f73_31484/03_2026/7f73_31484.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f73_31484/03_2026/7f73_31484.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f73_31484/03_2026/7f73_31484.map"
  }
  resolution = 4.0
  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=   0.007 sd=   0.086
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    3248      2.51       5
     N     816      2.21       5
     O     848      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4934
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2467
          Classifications: {'peptide': 293}
          Link IDs: {'PTRANS': 4, 'TRANS': 288}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2467
          Classifications: {'peptide': 293}
          Link IDs: {'PTRANS': 4, 'TRANS': 288}
          Chain breaks: 1
  Time building chain proxies: 1.38, per 1000 atoms: 0.28
  Number of scatterers: 4934
  At special positions: 0
  Unit cell: (83.699, 118.483, 94.569, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      22     16.00
     O     848      8.00
     N     816      7.00
     C    3248      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: 0.36
  Conformation dependent library (CDL) restraints added in 323.4 milliseconds
  

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1132

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      87.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 64
    Processing helix  chain 'A' and resid 69 through 97
    Processing helix  chain 'A' and resid 103 through 110
    Processing helix  chain 'A' and resid 118 through 150
      removed outlier: 4.338A  pdb=" N   ALA A 146 " --> pdb=" O   LEU A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 182
      removed outlier: 3.724A  pdb=" N   ASP A 157 " --> pdb=" O   TYR A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 205
      removed outlier: 4.608A  pdb=" N   SER A 191 " --> pdb=" O   GLY A 187 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   MET A 203 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   THR A 205 " --> pdb=" O   GLY A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 235
      removed outlier: 3.549A  pdb=" N   GLN A 213 " --> pdb=" O   GLY A 209 " (cutoff:3.500A)
      removed outlier: 5.312A  pdb=" N   ASN A 217 " --> pdb=" O   GLN A 213 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   GLN A 218 " --> pdb=" O   LYS A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 296
      removed outlier: 3.948A  pdb=" N   SER A 294 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLU A 296 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 329
      removed outlier: 3.567A  pdb=" N   PHE A 310 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ASN A 317 " --> pdb=" O   LEU A 313 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LEU A 319 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 64
    Processing helix  chain 'B' and resid 69 through 97
    Processing helix  chain 'B' and resid 103 through 110
    Processing helix  chain 'B' and resid 118 through 150
      removed outlier: 4.338A  pdb=" N   ALA B 146 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 182
      removed outlier: 3.724A  pdb=" N   ASP B 157 " --> pdb=" O   TYR B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 205
      removed outlier: 4.608A  pdb=" N   SER B 191 " --> pdb=" O   GLY B 187 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   MET B 203 " --> pdb=" O   LEU B 199 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU B 204 " --> pdb=" O   SER B 200 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   THR B 205 " --> pdb=" O   GLY B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 235
      removed outlier: 3.549A  pdb=" N   GLN B 213 " --> pdb=" O   GLY B 209 " (cutoff:3.500A)
      removed outlier: 5.312A  pdb=" N   ASN B 217 " --> pdb=" O   GLN B 213 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   GLN B 218 " --> pdb=" O   LYS B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 296
      removed outlier: 3.948A  pdb=" N   SER B 294 " --> pdb=" O   PHE B 290 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU B 296 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 329
      removed outlier: 3.566A  pdb=" N   PHE B 310 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ASN B 317 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LEU B 319 " --> pdb=" O   LEU B 315 " (cutoff:3.500A)

    411 hydrogen bonds defined for protein.
    1233 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: 0.72

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1078
        1.33 -     1.45: 1216
        1.45 -     1.57: 2742
        1.57 -     1.69: 0
        1.69 -     1.81: 28
  Bond restraints: 5064
  Sorted by residual:
  bond pdb=" N   THR B 205 "
       pdb=" CA  THR B 205 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.10e-02 8.26e+03 1.11e+01
  bond pdb=" N   THR A 205 "
       pdb=" CA  THR A 205 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.10e-02 8.26e+03 1.10e+01
  bond pdb=" N   VAL A 202 "
       pdb=" CA  VAL A 202 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.036 1.19e-02 7.06e+03 9.05e+00
  bond pdb=" N   VAL B 202 "
       pdb=" CA  VAL B 202 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.19e-02 7.06e+03 8.70e+00
  bond pdb=" N   PHE A 149 "
       pdb=" CA  PHE A 149 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.27e-02 6.20e+03 8.22e+00
  ... (remaining 5059 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 6370
        2.00 -     4.00: 393
        4.00 -     6.00: 69
        6.00 -     8.00: 10
        8.00 -    10.00: 2
  Bond angle restraints: 6844
  Sorted by residual:
  angle pdb=" C   PHE A 149 "
        pdb=" N   VAL A 150 "
        pdb=" CA  VAL A 150 "
      ideal   model   delta    sigma   weight residual
     122.97  117.47    5.50 9.80e-01 1.04e+00 3.14e+01
  angle pdb=" C   PHE B 149 "
        pdb=" N   VAL B 150 "
        pdb=" CA  VAL B 150 "
      ideal   model   delta    sigma   weight residual
     122.97  117.51    5.46 9.80e-01 1.04e+00 3.11e+01
  angle pdb=" CA  GLN B  78 "
        pdb=" CB  GLN B  78 "
        pdb=" CG  GLN B  78 "
      ideal   model   delta    sigma   weight residual
     114.10  124.10  -10.00 2.00e+00 2.50e-01 2.50e+01
  angle pdb=" CA  GLN A  78 "
        pdb=" CB  GLN A  78 "
        pdb=" CG  GLN A  78 "
      ideal   model   delta    sigma   weight residual
     114.10  124.09   -9.99 2.00e+00 2.50e-01 2.49e+01
  angle pdb=" N   PHE B 149 "
        pdb=" CA  PHE B 149 "
        pdb=" C   PHE B 149 "
      ideal   model   delta    sigma   weight residual
     113.41  118.88   -5.47 1.22e+00 6.72e-01 2.01e+01
  ... (remaining 6839 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.01: 2566
       17.01 -    34.02: 300
       34.02 -    51.03: 68
       51.03 -    68.04: 15
       68.04 -    85.05: 3
  Dihedral angle restraints: 2952
    sinusoidal: 1208
      harmonic: 1744
  Sorted by residual:
  dihedral pdb=" CA  TRP B 188 "
           pdb=" C   TRP B 188 "
           pdb=" N   TRP B 189 "
           pdb=" CA  TRP B 189 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.03  -20.97     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  TRP A 188 "
           pdb=" C   TRP A 188 "
           pdb=" N   TRP A 189 "
           pdb=" CA  TRP A 189 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.03  -20.97     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  ARG B 299 "
           pdb=" C   ARG B 299 "
           pdb=" N   GLU B 300 "
           pdb=" CA  GLU B 300 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.35   15.65     0      5.00e+00 4.00e-02 9.79e+00
  ... (remaining 2949 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 516
       0.049 -    0.099: 147
       0.099 -    0.148: 55
       0.148 -    0.197: 25
       0.197 -    0.246: 5
  Chirality restraints: 748
  Sorted by residual:
  chirality pdb=" CA  MET A 203 "
            pdb=" N   MET A 203 "
            pdb=" C   MET A 203 "
            pdb=" CB  MET A 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CA  MET B 203 "
            pdb=" N   MET B 203 "
            pdb=" C   MET B 203 "
            pdb=" CB  MET B 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CA  TYR A  96 "
            pdb=" N   TYR A  96 "
            pdb=" C   TYR A  96 "
            pdb=" CB  TYR A  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.08e+00
  ... (remaining 745 not shown)

  Planarity restraints: 844
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 206 "   -0.008 2.00e-02 2.50e+03   1.31e-02 4.31e+00
        pdb=" CG  TRP B 206 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 206 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 206 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 206 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 206 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 206 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 206 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 206 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 206 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 206 "   -0.008 2.00e-02 2.50e+03   1.31e-02 4.30e+00
        pdb=" CG  TRP A 206 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 206 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 206 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 206 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 206 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 206 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 206 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 206 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 206 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  90 "    0.010 2.00e-02 2.50e+03   1.49e-02 3.89e+00
        pdb=" CG  PHE B  90 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  90 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  90 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  90 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  90 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  90 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 841 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1010
        2.78 -     3.31: 5029
        3.31 -     3.84: 7936
        3.84 -     4.37: 8858
        4.37 -     4.90: 14744
  Nonbonded interactions: 37577
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 230 "
            pdb=" OE1 GLN A 233 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OE1 GLN B 230 "
            pdb=" OE1 GLN B 233 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" NE  ARG A  86 "
            pdb=" CZ  PHE A  90 "
     model   vdw
     2.290 3.420
  nonbonded pdb=" NE  ARG B  86 "
            pdb=" CZ  PHE B  90 "
     model   vdw
     2.290 3.420
  nonbonded pdb=" O   LYS A  49 "
            pdb=" ND1 HIS A  53 "
     model   vdw
     2.303 3.120
  ... (remaining 37572 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.480
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6920
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   0.045   5064  Z= 0.412
  Angle     :  1.070  10.003   6844  Z= 0.679
  Chirality :  0.061   0.246    748
  Planarity :  0.005   0.027    844
  Dihedral  : 15.265  85.051   1820
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  :  0.37 %
    Favored  : 95.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.32), residues: 578
  helix:  0.32 (0.22), residues: 476
  sheet:  None (None), residues: 0
  loop : -0.25 (0.51), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 216 
 TYR   0.011   0.002   TYR A 125 
 PHE   0.034   0.002   PHE B  90 
 TRP   0.032   0.003   TRP A 206 
 HIS   0.013   0.002   HIS B 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00660 ( 5064)
  covalent geometry    : angle       1.07033 ( 6844)
  hydrogen bonds       : bond        0.14573 (  411)
  hydrogen bonds       : angle       6.08636 ( 1233)

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASN cc_start: 0.7987 (t0) cc_final: 0.7583 (p0)
REVERT: A  130 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7155 (mm-30)
REVERT: A  149 PHE cc_start: 0.5286 (OUTLIER) cc_final: 0.4864 (m-80)
REVERT: B  149 PHE cc_start: 0.5172 (OUTLIER) cc_final: 0.4686 (m-80)
  outliers start: 22
  outliers final: 8
  residues processed: 121
  average time/residue: 0.0804
  time to fit residues: 12.1175
Evaluate side-chains
  76 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  149 PHE
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  225 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  78 GLN
B 302 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4771 r_free = 0.4771 target = 0.237362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.207363 restraints weight = 7676.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.193919 restraints weight = 10037.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.196379 restraints weight = 7456.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.197172 restraints weight = 6055.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.198172 restraints weight = 5422.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.4378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5064  Z= 0.155
  Angle     :  0.645   6.617   6844  Z= 0.347
  Chirality :  0.039   0.171    748
  Planarity :  0.004   0.024    844
  Dihedral  :  8.488  58.492    659
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  :  9.14 %
    Favored  : 86.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.94 (0.33), residues: 578
  helix:  1.70 (0.23), residues: 478
  sheet:  None (None), residues: 0
  loop : -0.63 (0.58), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  27 
 TYR   0.012   0.002   TYR A 236 
 PHE   0.015   0.001   PHE B 290 
 TRP   0.016   0.002   TRP A 206 
 HIS   0.005   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 5064)
  covalent geometry    : angle       0.64498 ( 6844)
  hydrogen bonds       : bond        0.05732 (  411)
  hydrogen bonds       : angle       4.45525 ( 1233)

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 HIS cc_start: 0.8568 (m90) cc_final: 0.8295 (m-70)
REVERT: A   52 LYS cc_start: 0.9184 (tmtt) cc_final: 0.8821 (tppt)
REVERT: A  111 ASN cc_start: 0.8210 (t0) cc_final: 0.7474 (p0)
REVERT: A  149 PHE cc_start: 0.6013 (OUTLIER) cc_final: 0.5288 (m-80)
REVERT: A  234 TYR cc_start: 0.7573 (t80) cc_final: 0.7368 (t80)
REVERT: B   27 ARG cc_start: 0.8434 (ptt90) cc_final: 0.8096 (ptt90)
REVERT: B   91 PHE cc_start: 0.8023 (m-10) cc_final: 0.7791 (m-80)
REVERT: B  149 PHE cc_start: 0.5930 (OUTLIER) cc_final: 0.5337 (m-80)
REVERT: B  203 MET cc_start: 0.7974 (mmm) cc_final: 0.7642 (tpp)
  outliers start: 22
  outliers final: 11
  residues processed: 99
  average time/residue: 0.0703
  time to fit residues: 8.8449
Evaluate side-chains
  84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  123 PHE
Chi-restraints excluded: chain A residue  149 PHE
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  225 PHE
Chi-restraints excluded: chain B residue  303 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 4 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  40 GLN
** B  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  78 GLN
B 193 HIS
B 302 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.205002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.173219 restraints weight = 7915.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.156480 restraints weight = 11001.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.157554 restraints weight = 10448.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.158016 restraints weight = 9249.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.158245 restraints weight = 8393.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.4296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.3673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5064  Z= 0.152
  Angle     :  0.642  11.007   6844  Z= 0.338
  Chirality :  0.038   0.152    748
  Planarity :  0.004   0.025    844
  Dihedral  :  6.607  54.476    650
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 15.67 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.34 (0.34), residues: 578
  helix:  1.98 (0.23), residues: 484
  sheet:  None (None), residues: 0
  loop : -0.68 (0.61), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  63 
 TYR   0.020   0.001   TYR A  29 
 PHE   0.030   0.001   PHE A  91 
 TRP   0.011   0.001   TRP A 206 
 HIS   0.005   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5064)
  covalent geometry    : angle       0.64206 ( 6844)
  hydrogen bonds       : bond        0.05391 (  411)
  hydrogen bonds       : angle       4.22545 ( 1233)

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASN cc_start: 0.8326 (t0) cc_final: 0.7344 (p0)
REVERT: A  142 LEU cc_start: 0.8063 (tp) cc_final: 0.7835 (tp)
REVERT: A  149 PHE cc_start: 0.6521 (OUTLIER) cc_final: 0.5700 (m-80)
REVERT: B   93 MET cc_start: 0.9030 (pmm) cc_final: 0.8802 (pmm)
REVERT: B  149 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.5492 (m-80)
REVERT: B  203 MET cc_start: 0.7852 (mmm) cc_final: 0.7439 (tpp)
  outliers start: 21
  outliers final: 12
  residues processed: 94
  average time/residue: 0.0700
  time to fit residues: 8.3975
Evaluate side-chains
  90 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  149 PHE
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  225 PHE
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain B residue  305 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 29 optimal weight:   20.0000
   chunk 49 optimal weight:    1.9990
   chunk 52 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 HIS
** B  50 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 = 0.4604 r_free = 0.4604 target = 0.219746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.183123 restraints weight = 7350.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.174023 restraints weight = 9229.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.175645 restraints weight = 6994.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.175905 restraints weight = 5573.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.176297 restraints weight = 5128.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.4223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5064  Z= 0.146
  Angle     :  0.628  12.337   6844  Z= 0.328
  Chirality :  0.038   0.159    748
  Planarity :  0.003   0.023    844
  Dihedral  :  6.122  54.190    648
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 17.91 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.65 (0.34), residues: 578
  helix:  2.20 (0.23), residues: 486
  sheet:  None (None), residues: 0
  loop : -0.68 (0.62), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  63 
 TYR   0.015   0.001   TYR A 235 
 PHE   0.029   0.001   PHE B  91 
 TRP   0.013   0.001   TRP A 206 
 HIS   0.007   0.001   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 5064)
  covalent geometry    : angle       0.62830 ( 6844)
  hydrogen bonds       : bond        0.05182 (  411)
  hydrogen bonds       : angle       4.08044 ( 1233)

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 83
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASN cc_start: 0.8263 (t0) cc_final: 0.7130 (p0)
REVERT: A  142 LEU cc_start: 0.8064 (tp) cc_final: 0.7860 (tp)
REVERT: A  149 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.5672 (m-80)
REVERT: B   90 PHE cc_start: 0.8256 (m-80) cc_final: 0.7919 (m-80)
REVERT: B   91 PHE cc_start: 0.7796 (m-80) cc_final: 0.7531 (t80)
REVERT: B  111 ASN cc_start: 0.8108 (t0) cc_final: 0.6874 (p0)
REVERT: B  149 PHE cc_start: 0.6365 (OUTLIER) cc_final: 0.5678 (m-80)
REVERT: B  290 PHE cc_start: 0.6490 (t80) cc_final: 0.6152 (t80)
  outliers start: 24
  outliers final: 13
  residues processed: 100
  average time/residue: 0.0603
  time to fit residues: 8.1350
Evaluate side-chains
  90 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  149 PHE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  138 ILE
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain B residue  305 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  78 GLN
** B 279 HIS ** 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 = 0.4553 r_free = 0.4553 target = 0.215132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.179090 restraints weight = 7380.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.176919 restraints weight = 12808.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.177448 restraints weight = 11669.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.177401 restraints weight = 8755.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.177786 restraints weight = 7386.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.4166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          0.4605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5064  Z= 0.176
  Angle     :  0.688  11.621   6844  Z= 0.352
  Chirality :  0.040   0.183    748
  Planarity :  0.004   0.027    844
  Dihedral  :  5.348  53.200    643
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 20.71 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.41 (0.34), residues: 578
  helix:  1.97 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -0.66 (0.65), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 174 
 TYR   0.021   0.002   TYR A 234 
 PHE   0.022   0.001   PHE B  91 
 TRP   0.012   0.001   TRP A 206 
 HIS   0.010   0.002   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 5064)
  covalent geometry    : angle       0.68792 ( 6844)
  hydrogen bonds       : bond        0.05533 (  411)
  hydrogen bonds       : angle       4.18791 ( 1233)

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASN cc_start: 0.8212 (t0) cc_final: 0.7053 (p0)
REVERT: A  142 LEU cc_start: 0.8067 (tp) cc_final: 0.7835 (tp)
REVERT: A  149 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.5639 (m-80)
REVERT: B  111 ASN cc_start: 0.8180 (t0) cc_final: 0.6983 (p0)
REVERT: B  149 PHE cc_start: 0.6357 (OUTLIER) cc_final: 0.5728 (m-80)
REVERT: B  203 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7613 (tpp)
REVERT: B  290 PHE cc_start: 0.6478 (t80) cc_final: 0.6125 (t80)
  outliers start: 26
  outliers final: 18
  residues processed: 93
  average time/residue: 0.0534
  time to fit residues: 6.8047
Evaluate side-chains
  95 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  149 PHE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain B residue   78 GLN
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  138 ILE
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain B residue  305 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 35 optimal weight:    0.0370
   chunk 15 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 52 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.8860

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.218836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.183517 restraints weight = 7695.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.170071 restraints weight = 10392.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.171278 restraints weight = 8072.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.171890 restraints weight = 6757.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.172288 restraints weight = 6459.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.4825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5064  Z= 0.150
  Angle     :  0.657  10.118   6844  Z= 0.343
  Chirality :  0.040   0.200    748
  Planarity :  0.003   0.025    844
  Dihedral  :  5.231  54.098    643
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 23.13 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.46 (0.34), residues: 578
  helix:  2.04 (0.22), residues: 496
  sheet:  None (None), residues: 0
  loop : -0.86 (0.63), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  63 
 TYR   0.024   0.001   TYR A  29 
 PHE   0.033   0.001   PHE A  90 
 TRP   0.011   0.001   TRP A  12 
 HIS   0.017   0.002   HIS B 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 5064)
  covalent geometry    : angle       0.65748 ( 6844)
  hydrogen bonds       : bond        0.05107 (  411)
  hydrogen bonds       : angle       4.10615 ( 1233)

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASN cc_start: 0.8161 (t0) cc_final: 0.6929 (p0)
REVERT: A  142 LEU cc_start: 0.8056 (tp) cc_final: 0.7837 (tp)
REVERT: A  149 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.5644 (m-80)
REVERT: B   90 PHE cc_start: 0.8375 (m-80) cc_final: 0.8006 (m-80)
REVERT: B  111 ASN cc_start: 0.8144 (t0) cc_final: 0.6992 (p0)
REVERT: B  149 PHE cc_start: 0.6559 (OUTLIER) cc_final: 0.5799 (m-80)
REVERT: B  203 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7495 (tpp)
  outliers start: 22
  outliers final: 16
  residues processed: 93
  average time/residue: 0.0527
  time to fit residues: 6.6998
Evaluate side-chains
  90 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  149 PHE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain B residue   78 GLN
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  138 ILE
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  270 PHE
Chi-restraints excluded: chain B residue  303 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 29 optimal weight:    0.2980
   chunk 28 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  20 GLN
A  78 GLN
** B  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  78 GLN
B  82 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.222152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.181896 restraints weight = 7451.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.179305 restraints weight = 10305.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.182291 restraints weight = 8914.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.181700 restraints weight = 6574.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.181598 restraints weight = 5899.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.4136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.5152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5064  Z= 0.149
  Angle     :  0.667  11.179   6844  Z= 0.348
  Chirality :  0.040   0.218    748
  Planarity :  0.003   0.025    844
  Dihedral  :  5.192  54.702    643
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 22.39 %
    Favored  : 72.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.53 (0.34), residues: 578
  helix:  2.10 (0.22), residues: 494
  sheet:  None (None), residues: 0
  loop : -0.88 (0.62), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 174 
 TYR   0.015   0.001   TYR A  29 
 PHE   0.010   0.001   PHE B 270 
 TRP   0.011   0.001   TRP A  12 
 HIS   0.015   0.002   HIS B 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 5064)
  covalent geometry    : angle       0.66709 ( 6844)
  hydrogen bonds       : bond        0.05068 (  411)
  hydrogen bonds       : angle       4.07922 ( 1233)

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 71
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 TYR cc_start: 0.6660 (t80) cc_final: 0.6333 (t80)
REVERT: A  111 ASN cc_start: 0.8167 (t0) cc_final: 0.6887 (p0)
REVERT: A  142 LEU cc_start: 0.8078 (tp) cc_final: 0.7818 (tp)
REVERT: A  149 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.5723 (m-80)
REVERT: B  111 ASN cc_start: 0.8197 (t0) cc_final: 0.7013 (p0)
REVERT: B  149 PHE cc_start: 0.6495 (OUTLIER) cc_final: 0.5737 (m-80)
REVERT: B  203 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7550 (tpp)
  outliers start: 27
  outliers final: 19
  residues processed: 88
  average time/residue: 0.0482
  time to fit residues: 5.9315
Evaluate side-chains
  88 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  149 PHE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain B residue   78 GLN
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  138 ILE
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  270 PHE
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  303 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 11 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 41 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 57 optimal weight:    0.4980
   chunk 10 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 55 optimal weight:    0.1980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.220365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.186165 restraints weight = 7583.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 73)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.173240 restraints weight = 9668.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.174524 restraints weight = 7379.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.176393 restraints weight = 6323.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.176721 restraints weight = 5629.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.4123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.5329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5064  Z= 0.140
  Angle     :  0.676  11.778   6844  Z= 0.355
  Chirality :  0.040   0.215    748
  Planarity :  0.003   0.026    844
  Dihedral  :  5.165  56.703    643
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 24.81 %
    Favored  : 71.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.55 (0.34), residues: 578
  helix:  2.10 (0.22), residues: 496
  sheet:  None (None), residues: 0
  loop : -0.91 (0.64), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  63 
 TYR   0.036   0.001   TYR A  29 
 PHE   0.033   0.001   PHE A  90 
 TRP   0.009   0.001   TRP A  12 
 HIS   0.012   0.002   HIS B 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 5064)
  covalent geometry    : angle       0.67586 ( 6844)
  hydrogen bonds       : bond        0.04846 (  411)
  hydrogen bonds       : angle       4.02248 ( 1233)

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 PHE cc_start: 0.8618 (t80) cc_final: 0.8365 (t80)
REVERT: A   96 TYR cc_start: 0.7005 (t80) cc_final: 0.6763 (t80)
REVERT: A  111 ASN cc_start: 0.8066 (t0) cc_final: 0.6761 (p0)
REVERT: A  142 LEU cc_start: 0.7978 (tp) cc_final: 0.7694 (tp)
REVERT: A  149 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.5766 (m-80)
REVERT: A  234 TYR cc_start: 0.7694 (t80) cc_final: 0.7395 (t80)
REVERT: B   63 ARG cc_start: 0.7650 (mmm160) cc_final: 0.7437 (mmm-85)
REVERT: B   90 PHE cc_start: 0.8329 (m-80) cc_final: 0.8006 (m-80)
REVERT: B  111 ASN cc_start: 0.8193 (t0) cc_final: 0.6950 (p0)
REVERT: B  149 PHE cc_start: 0.6443 (OUTLIER) cc_final: 0.5553 (m-80)
REVERT: B  203 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7517 (tpp)
  outliers start: 21
  outliers final: 12
  residues processed: 79
  average time/residue: 0.0535
  time to fit residues: 5.8579
Evaluate side-chains
  79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  149 PHE
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  270 PHE
Chi-restraints excluded: chain B residue  303 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 18 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 37 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  87 GLN
** B  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  78 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.214658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.179765 restraints weight = 7334.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.167571 restraints weight = 10323.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.169896 restraints weight = 7881.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.170669 restraints weight = 6519.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.171713 restraints weight = 5878.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.5453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5064  Z= 0.151
  Angle     :  0.701  15.450   6844  Z= 0.365
  Chirality :  0.041   0.252    748
  Planarity :  0.003   0.027    844
  Dihedral  :  5.204  57.700    643
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 24.44 %
    Favored  : 71.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.46 (0.33), residues: 578
  helix:  2.06 (0.22), residues: 494
  sheet:  None (None), residues: 0
  loop : -1.01 (0.62), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 174 
 TYR   0.016   0.001   TYR A  29 
 PHE   0.045   0.001   PHE A  91 
 TRP   0.010   0.001   TRP A  12 
 HIS   0.011   0.002   HIS B 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 5064)
  covalent geometry    : angle       0.70094 ( 6844)
  hydrogen bonds       : bond        0.05026 (  411)
  hydrogen bonds       : angle       4.05779 ( 1233)

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 TYR cc_start: 0.7009 (t80) cc_final: 0.6713 (t80)
REVERT: A  111 ASN cc_start: 0.8151 (t0) cc_final: 0.6747 (p0)
REVERT: A  123 PHE cc_start: 0.7626 (t80) cc_final: 0.7125 (t80)
REVERT: A  149 PHE cc_start: 0.6588 (OUTLIER) cc_final: 0.5775 (m-80)
REVERT: A  234 TYR cc_start: 0.7767 (t80) cc_final: 0.7459 (t80)
REVERT: B   90 PHE cc_start: 0.8240 (m-80) cc_final: 0.8032 (m-80)
REVERT: B  111 ASN cc_start: 0.8205 (t0) cc_final: 0.6920 (p0)
REVERT: B  149 PHE cc_start: 0.6495 (OUTLIER) cc_final: 0.5564 (m-80)
REVERT: B  203 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7466 (tpp)
  outliers start: 22
  outliers final: 18
  residues processed: 79
  average time/residue: 0.0469
  time to fit residues: 5.2898
Evaluate side-chains
  84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 63
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  149 PHE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  317 ASN
Chi-restraints excluded: chain B residue   78 GLN
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  270 PHE
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  303 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 50 optimal weight:    0.2980
   chunk 9 optimal weight:    0.0670
   chunk 47 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 22 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0570
   overall best weight:    0.3836

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 161 ASN
B  40 GLN
** B  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  78 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.219461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 100)---------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.185245 restraints weight = 7404.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.174991 restraints weight = 9858.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.177391 restraints weight = 8155.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.177113 restraints weight = 6042.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.177454 restraints weight = 6061.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.4108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.5535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5064  Z= 0.135
  Angle     :  0.707  18.289   6844  Z= 0.362
  Chirality :  0.039   0.189    748
  Planarity :  0.003   0.029    844
  Dihedral  :  5.173  59.936    643
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 25.00 %
    Favored  : 71.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.59 (0.34), residues: 578
  helix:  2.17 (0.22), residues: 496
  sheet:  None (None), residues: 0
  loop : -1.15 (0.62), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  86 
 TYR   0.032   0.001   TYR B 234 
 PHE   0.067   0.002   PHE A  91 
 TRP   0.010   0.001   TRP A  12 
 HIS   0.010   0.002   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 5064)
  covalent geometry    : angle       0.70698 ( 6844)
  hydrogen bonds       : bond        0.04604 (  411)
  hydrogen bonds       : angle       3.89707 ( 1233)

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

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

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1156 Ramachandran restraints generated.
    578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 PHE cc_start: 0.8273 (m-80) cc_final: 0.7954 (m-80)
REVERT: A   96 TYR cc_start: 0.7113 (t80) cc_final: 0.6852 (t80)
REVERT: A  111 ASN cc_start: 0.8169 (t0) cc_final: 0.6773 (p0)
REVERT: A  123 PHE cc_start: 0.7555 (t80) cc_final: 0.7170 (t80)
REVERT: A  149 PHE cc_start: 0.6490 (OUTLIER) cc_final: 0.5698 (m-80)
REVERT: A  234 TYR cc_start: 0.7748 (t80) cc_final: 0.7497 (t80)
REVERT: B   90 PHE cc_start: 0.8372 (m-80) cc_final: 0.8131 (m-80)
REVERT: B  111 ASN cc_start: 0.8127 (t0) cc_final: 0.6833 (p0)
REVERT: B  149 PHE cc_start: 0.6427 (OUTLIER) cc_final: 0.5521 (m-80)
REVERT: B  277 CYS cc_start: 0.6623 (m) cc_final: 0.6159 (t)
  outliers start: 19
  outliers final: 15
  residues processed: 83
  average time/residue: 0.0484
  time to fit residues: 5.6687
Evaluate side-chains
  82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  149 PHE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  317 ASN
Chi-restraints excluded: chain B residue   78 GLN
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  270 PHE
Chi-restraints excluded: chain B residue  303 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0770
   chunk 24 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 6 optimal weight:    0.4980
   chunk 53 optimal weight:    1.9990
   chunk 30 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.6340

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

Flipped N/Q/H residues before XYZ refinement:
** A  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  40 GLN
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 161 ASN
** B  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  78 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.218437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 116)---------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.182512 restraints weight = 7513.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.171579 restraints weight = 10158.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.174000 restraints weight = 7538.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.175141 restraints weight = 6189.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.176481 restraints weight = 5510.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.4120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
moved from start:          0.5686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5064  Z= 0.141
  Angle     :  0.714  14.575   6844  Z= 0.362
  Chirality :  0.039   0.189    748
  Planarity :  0.003   0.031    844
  Dihedral  :  5.181  58.940    643
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 23.88 %
    Favored  : 71.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.56 (0.33), residues: 578
  helix:  2.22 (0.22), residues: 490
  sheet:  None (None), residues: 0
  loop : -1.41 (0.60), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 174 
 TYR   0.029   0.001   TYR B 234 
 PHE   0.012   0.001   PHE A  90 
 TRP   0.011   0.001   TRP A  12 
 HIS   0.012   0.002   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 5064)
  covalent geometry    : angle       0.71393 ( 6844)
  hydrogen bonds       : bond        0.04733 (  411)
  hydrogen bonds       : angle       3.91581 ( 1233)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 929.97 seconds
wall clock time: 16 minutes 43.67 seconds (1003.67 seconds total)