Starting phenix.real_space_refine
on Thu Mar  6 04:31:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f73_31484/03_2025/7f73_31484.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f73_31484/03_2025/7f73_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f73_31484/03_2025/7f73_31484.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f73_31484/03_2025/7f73_31484.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f73_31484/03_2025/7f73_31484.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f73_31484/03_2025/7f73_31484.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.64, per 1000 atoms: 0.74
  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: 1.24
  Conformation dependent library (CDL) restraints added in 612.1 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: 0.42
  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: 1.37

  Time building geometry restraints manager: 1.45 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: 0.02
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:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     16.320
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.470
-------------------------------------------------------------------------------
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= 0.415
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.032   0.003   TRP A 206 
 HIS   0.013   0.002   HIS B 192 
 PHE   0.034   0.002   PHE B  90 
 TYR   0.011   0.002   TYR A 125 
 ARG   0.003   0.001   ARG B 216 

*********************** 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  : 0.509 
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: 0.7986 (t0) cc_final: 0.7583 (p0)
REVERT: A  130 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7155 (mm-30)
REVERT: A  149 PHE cc_start: 0.5287 (OUTLIER) cc_final: 0.4865 (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: 0.2044
  time to fit residues: 30.3928
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  : 0.572 
-------------------------------------------------------------------------------
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 48 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   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  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 302 GLN
B  78 GLN
** B  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 193 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4813 r_free = 0.4813 target = 0.241236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.210285 restraints weight = 7536.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.207849 restraints weight = 9948.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.202258 restraints weight = 6136.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.4400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7019
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5064  Z= 0.207
  Angle     :  0.643   7.231   6844  Z= 0.346
  Chirality :  0.039   0.165    748
  Planarity :  0.004   0.023    844
  Dihedral  :  8.489  57.460    659
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 10.26 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.33), residues: 578
  helix:  1.68 (0.23), residues: 478
  sheet:  None (None), residues: 0
  loop : -0.63 (0.58), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 206 
 HIS   0.005   0.001   HIS A 192 
 PHE   0.016   0.001   PHE B 290 
 TYR   0.013   0.002   TYR A 236 
 ARG   0.003   0.000   ARG B  27 

*********************** 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
  104 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.507 
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: 0.7478 (p0)
REVERT: A  142 LEU cc_start: 0.7916 (tp) cc_final: 0.7696 (tp)
REVERT: A  149 PHE cc_start: 0.5990 (OUTLIER) cc_final: 0.5379 (m-80)
REVERT: A  224 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7535 (mt)
REVERT: A  234 TYR cc_start: 0.7613 (t80) cc_final: 0.7297 (t80)
REVERT: B   27 ARG cc_start: 0.8165 (ptt90) cc_final: 0.7947 (ptt90)
REVERT: B  149 PHE cc_start: 0.6057 (OUTLIER) cc_final: 0.5521 (m-80)
REVERT: B  203 MET cc_start: 0.8006 (mmm) cc_final: 0.7627 (tpp)
  outliers start: 22
  outliers final: 11
  residues processed: 97
  average time/residue: 0.1727
  time to fit residues: 21.2989
Evaluate side-chains
  86 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
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  224 ILE
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 25 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 43 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 HIS
A 302 GLN
B  40 GLN
B  50 GLN
B  78 GLN
B 192 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.218036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.182384 restraints weight = 7341.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.179803 restraints weight = 12834.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.181149 restraints weight = 11674.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.4202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7017
moved from start:          0.3741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5064  Z= 0.225
  Angle     :  0.674  10.772   6844  Z= 0.356
  Chirality :  0.039   0.153    748
  Planarity :  0.004   0.024    844
  Dihedral  :  6.773  53.341    652
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 16.42 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.34), residues: 578
  helix:  1.91 (0.23), residues: 486
  sheet:  None (None), residues: 0
  loop : -0.60 (0.63), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  12 
 HIS   0.008   0.001   HIS A  13 
 PHE   0.030   0.002   PHE A  91 
 TYR   0.020   0.001   TYR A  29 
 ARG   0.004   0.001   ARG B  63 

*********************** 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
  110 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 86
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASN cc_start: 0.8314 (t0) cc_final: 0.7340 (p0)
REVERT: A  142 LEU cc_start: 0.8028 (tp) cc_final: 0.7761 (tp)
REVERT: A  149 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.5572 (m-80)
REVERT: A  203 MET cc_start: 0.7694 (tpp) cc_final: 0.7363 (tpp)
REVERT: A  224 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7475 (mt)
REVERT: B  111 ASN cc_start: 0.8141 (t0) cc_final: 0.6913 (p0)
REVERT: B  149 PHE cc_start: 0.6388 (OUTLIER) cc_final: 0.5651 (m-80)
REVERT: B  203 MET cc_start: 0.7885 (mmm) cc_final: 0.7399 (tpp)
  outliers start: 24
  outliers final: 13
  residues processed: 101
  average time/residue: 0.1952
  time to fit residues: 25.7329
Evaluate side-chains
  94 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
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  224 ILE
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  287 VAL
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 57 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 27 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 0 optimal weight:   20.0000
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 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 = 0.4612 r_free = 0.4612 target = 0.221094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.184817 restraints weight = 7383.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.174782 restraints weight = 9114.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.176109 restraints weight = 6702.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.4334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5064  Z= 0.175
  Angle     :  0.657  12.518   6844  Z= 0.335
  Chirality :  0.038   0.182    748
  Planarity :  0.003   0.024    844
  Dihedral  :  6.248  54.456    650
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 17.54 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.56 (0.34), residues: 578
  helix:  2.15 (0.23), residues: 484
  sheet:  None (None), residues: 0
  loop : -0.71 (0.60), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  12 
 HIS   0.005   0.001   HIS B 279 
 PHE   0.009   0.001   PHE A 270 
 TYR   0.014   0.001   TYR A 235 
 ARG   0.005   0.000   ARG A  63 

*********************** 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
  103 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 1.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASN cc_start: 0.8292 (t0) cc_final: 0.7164 (p0)
REVERT: A  142 LEU cc_start: 0.7999 (tp) cc_final: 0.7786 (tp)
REVERT: A  149 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.5671 (m-80)
REVERT: A  224 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7260 (mt)
REVERT: B   27 ARG cc_start: 0.8272 (ptt90) cc_final: 0.8041 (ptt90)
REVERT: B  111 ASN cc_start: 0.8096 (t0) cc_final: 0.6885 (p0)
REVERT: B  149 PHE cc_start: 0.6342 (OUTLIER) cc_final: 0.5645 (m-80)
REVERT: B  203 MET cc_start: 0.7753 (mmm) cc_final: 0.7331 (tpp)
  outliers start: 24
  outliers final: 14
  residues processed: 96
  average time/residue: 0.2606
  time to fit residues: 33.4647
Evaluate side-chains
  87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
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  224 ILE
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  145 VAL
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  303 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 10 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 29 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   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**
B  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.218978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.181770 restraints weight = 7369.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.170854 restraints weight = 9806.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.173269 restraints weight = 7156.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.4104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7171
moved from start:          0.4594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5064  Z= 0.192
  Angle     :  0.666  10.105   6844  Z= 0.343
  Chirality :  0.039   0.185    748
  Planarity :  0.003   0.024    844
  Dihedral  :  5.803  55.072    646
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 19.40 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.47 (0.34), residues: 578
  helix:  2.00 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -0.60 (0.65), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 206 
 HIS   0.006   0.001   HIS B  53 
 PHE   0.009   0.001   PHE A 270 
 TYR   0.021   0.001   TYR A 234 
 ARG   0.003   0.000   ARG A  63 

*********************** 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
  98 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASN cc_start: 0.8213 (t0) cc_final: 0.7027 (p0)
REVERT: A  142 LEU cc_start: 0.8055 (tp) cc_final: 0.7848 (tp)
REVERT: A  149 PHE cc_start: 0.6640 (OUTLIER) cc_final: 0.5689 (m-80)
REVERT: B   27 ARG cc_start: 0.8252 (ptt90) cc_final: 0.7983 (ptt90)
REVERT: B  111 ASN cc_start: 0.8170 (t0) cc_final: 0.6894 (p0)
REVERT: B  140 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7461 (mp)
REVERT: B  149 PHE cc_start: 0.6380 (OUTLIER) cc_final: 0.5698 (m-80)
  outliers start: 22
  outliers final: 16
  residues processed: 94
  average time/residue: 0.2349
  time to fit residues: 29.9961
Evaluate side-chains
  89 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
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  140 LEU
Chi-restraints excluded: chain A residue  149 PHE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain B residue   78 GLN
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  140 LEU
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  303 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 38 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 49 optimal weight:    0.6980
   overall best weight:    1.2986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.213928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.182247 restraints weight = 7397.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.179901 restraints weight = 12427.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.178998 restraints weight = 11335.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.4153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
moved from start:          0.4864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5064  Z= 0.251
  Angle     :  0.737   9.701   6844  Z= 0.386
  Chirality :  0.042   0.211    748
  Planarity :  0.004   0.027    844
  Dihedral  :  5.602  54.709    645
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 21.27 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.34), residues: 578
  helix:  1.90 (0.22), residues: 494
  sheet:  None (None), residues: 0
  loop : -0.76 (0.62), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  12 
 HIS   0.010   0.002   HIS B  13 
 PHE   0.018   0.002   PHE A 290 
 TYR   0.023   0.002   TYR A  29 
 ARG   0.005   0.001   ARG A  86 

*********************** 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
  97 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 71
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASN cc_start: 0.8202 (t0) cc_final: 0.6957 (p0)
REVERT: A  149 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.5403 (m-80)
REVERT: B  111 ASN cc_start: 0.8212 (t0) cc_final: 0.6976 (p0)
REVERT: B  149 PHE cc_start: 0.6198 (OUTLIER) cc_final: 0.5600 (m-80)
REVERT: B  203 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7642 (tpp)
  outliers start: 26
  outliers final: 17
  residues processed: 90
  average time/residue: 0.2217
  time to fit residues: 26.3135
Evaluate side-chains
  88 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
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  224 ILE
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   78 GLN
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 57 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 18 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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  78 GLN
B  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.217246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.182026 restraints weight = 7489.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.168824 restraints weight = 10378.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.171224 restraints weight = 7817.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.4059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
moved from start:          0.5138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5064  Z= 0.201
  Angle     :  0.718  11.106   6844  Z= 0.380
  Chirality :  0.041   0.244    748
  Planarity :  0.004   0.025    844
  Dihedral  :  5.484  55.431    645
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 22.95 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.34), residues: 578
  helix:  1.97 (0.23), residues: 494
  sheet:  None (None), residues: 0
  loop : -0.81 (0.63), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 206 
 HIS   0.010   0.002   HIS B  13 
 PHE   0.015   0.001   PHE A 290 
 TYR   0.035   0.001   TYR A  29 
 ARG   0.003   0.000   ARG B 174 

*********************** 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: 24
    poor density    : 74
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 TYR cc_start: 0.7210 (t80) cc_final: 0.6890 (t80)
REVERT: A  111 ASN cc_start: 0.8159 (t0) cc_final: 0.6876 (p0)
REVERT: A  149 PHE cc_start: 0.6675 (OUTLIER) cc_final: 0.5594 (m-80)
REVERT: A  234 TYR cc_start: 0.7733 (t80) cc_final: 0.7298 (t80)
REVERT: B   27 ARG cc_start: 0.8162 (ptt90) cc_final: 0.7715 (mtm-85)
REVERT: B   90 PHE cc_start: 0.8323 (m-80) cc_final: 0.8094 (m-80)
REVERT: B  111 ASN cc_start: 0.8205 (t0) cc_final: 0.7005 (p0)
REVERT: B  140 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7424 (mp)
REVERT: B  149 PHE cc_start: 0.6539 (OUTLIER) cc_final: 0.5757 (m-80)
REVERT: B  203 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7458 (tpp)
REVERT: B  277 CYS cc_start: 0.6640 (m) cc_final: 0.6201 (t)
  outliers start: 24
  outliers final: 18
  residues processed: 91
  average time/residue: 0.1614
  time to fit residues: 19.5297
Evaluate side-chains
  91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
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  140 LEU
Chi-restraints excluded: chain A residue  149 PHE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  224 ILE
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 B residue   78 GLN
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  140 LEU
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  303 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 52 optimal weight:    0.3980
   chunk 8 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0170
   chunk 18 optimal weight:    0.3980
   chunk 54 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 30 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.4818

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

Flipped N/Q/H residues before XYZ refinement:
A  78 GLN
** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.220865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.187215 restraints weight = 7632.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.173140 restraints weight = 10213.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.175146 restraints weight = 8448.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.5356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5064  Z= 0.170
  Angle     :  0.704  13.766   6844  Z= 0.365
  Chirality :  0.041   0.270    748
  Planarity :  0.003   0.025    844
  Dihedral  :  5.403  56.662    645
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 23.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.34), residues: 578
  helix:  2.04 (0.22), residues: 496
  sheet:  None (None), residues: 0
  loop : -0.77 (0.65), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 206 
 HIS   0.013   0.002   HIS B 279 
 PHE   0.015   0.001   PHE B 290 
 TYR   0.030   0.001   TYR A  29 
 ARG   0.004   0.000   ARG A 174 

*********************** 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
  101 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 72
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 HIS cc_start: 0.8064 (m90) cc_final: 0.7487 (p-80)
REVERT: A   55 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8832 (pttp)
REVERT: A   96 TYR cc_start: 0.7271 (t80) cc_final: 0.7000 (t80)
REVERT: A  111 ASN cc_start: 0.8066 (t0) cc_final: 0.6771 (p0)
REVERT: A  149 PHE cc_start: 0.6624 (OUTLIER) cc_final: 0.5650 (m-80)
REVERT: A  234 TYR cc_start: 0.7713 (t80) cc_final: 0.7360 (t80)
REVERT: B   27 ARG cc_start: 0.8177 (ptt90) cc_final: 0.7726 (mtm-85)
REVERT: B  111 ASN cc_start: 0.8130 (t0) cc_final: 0.6953 (p0)
REVERT: B  140 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7200 (mp)
REVERT: B  149 PHE cc_start: 0.6405 (OUTLIER) cc_final: 0.5516 (m-80)
REVERT: B  277 CYS cc_start: 0.6681 (m) cc_final: 0.6237 (t)
REVERT: B  290 PHE cc_start: 0.6538 (OUTLIER) cc_final: 0.5870 (t80)
  outliers start: 29
  outliers final: 18
  residues processed: 92
  average time/residue: 0.1709
  time to fit residues: 21.0737
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  : 0.548 
-------------------------------------------------------------------------------
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  224 ILE
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  321 THR
Chi-restraints excluded: chain B residue   78 GLN
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  140 LEU
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  290 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 44 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 33 optimal weight:    8.9990
   chunk 10 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.214778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 117)---------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.181054 restraints weight = 7351.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 71)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.167984 restraints weight = 9757.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.169734 restraints weight = 7681.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.4030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.5400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5064  Z= 0.208
  Angle     :  0.735  14.205   6844  Z= 0.391
  Chirality :  0.042   0.286    748
  Planarity :  0.004   0.035    844
  Dihedral  :  5.467  56.950    645
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 22.95 %
    Favored  : 71.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.34), residues: 578
  helix:  2.06 (0.22), residues: 494
  sheet:  None (None), residues: 0
  loop : -0.88 (0.64), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  12 
 HIS   0.014   0.002   HIS B 279 
 PHE   0.046   0.002   PHE B  91 
 TYR   0.009   0.001   TYR A  29 
 ARG   0.003   0.000   ARG A 174 

*********************** 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
  97 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 68
  time to evaluate  : 0.593 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 HIS cc_start: 0.8042 (m90) cc_final: 0.7510 (p-80)
REVERT: A   96 TYR cc_start: 0.7090 (t80) cc_final: 0.6878 (t80)
REVERT: A  111 ASN cc_start: 0.8114 (t0) cc_final: 0.6774 (p0)
REVERT: A  149 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.5584 (m-80)
REVERT: A  234 TYR cc_start: 0.7755 (t80) cc_final: 0.7440 (t80)
REVERT: A  290 PHE cc_start: 0.6542 (OUTLIER) cc_final: 0.5855 (t80)
REVERT: B   27 ARG cc_start: 0.8146 (ptt90) cc_final: 0.7651 (mtm-85)
REVERT: B  111 ASN cc_start: 0.8200 (t0) cc_final: 0.6951 (p0)
REVERT: B  140 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7336 (mp)
REVERT: B  149 PHE cc_start: 0.6502 (OUTLIER) cc_final: 0.5618 (m-80)
  outliers start: 29
  outliers final: 21
  residues processed: 88
  average time/residue: 0.1477
  time to fit residues: 17.7684
Evaluate side-chains
  90 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
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  224 ILE
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  290 PHE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  317 ASN
Chi-restraints excluded: chain A residue  321 THR
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  140 LEU
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 16 optimal weight:    0.0270
   chunk 17 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 30 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   chunk 35 optimal weight:    7.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.6238

-------------------------------------------------------------------------------
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  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.216947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.183261 restraints weight = 7364.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.171884 restraints weight = 9929.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.173116 restraints weight = 7880.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.4067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.5555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5064  Z= 0.187
  Angle     :  0.779  17.691   6844  Z= 0.392
  Chirality :  0.041   0.213    748
  Planarity :  0.004   0.035    844
  Dihedral  :  5.480  58.500    645
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 24.07 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.31 (0.34), residues: 578
  helix:  1.97 (0.22), residues: 502
  sheet:  None (None), residues: 0
  loop : -1.46 (0.63), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 206 
 HIS   0.010   0.002   HIS B 279 
 PHE   0.014   0.001   PHE A 290 
 TYR   0.034   0.001   TYR B 234 
 ARG   0.004   0.000   ARG A 174 

********************** 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
  92 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 67
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 HIS cc_start: 0.8049 (m90) cc_final: 0.7537 (p90)
REVERT: A   19 PHE cc_start: 0.8598 (t80) cc_final: 0.8379 (t80)
REVERT: A   90 PHE cc_start: 0.8233 (m-80) cc_final: 0.7947 (m-80)
REVERT: A   96 TYR cc_start: 0.7212 (t80) cc_final: 0.7006 (t80)
REVERT: A  111 ASN cc_start: 0.8095 (t0) cc_final: 0.6747 (p0)
REVERT: A  123 PHE cc_start: 0.7650 (t80) cc_final: 0.7246 (t80)
REVERT: A  149 PHE cc_start: 0.6567 (OUTLIER) cc_final: 0.5541 (m-80)
REVERT: A  234 TYR cc_start: 0.7787 (t80) cc_final: 0.7497 (t80)
REVERT: B   27 ARG cc_start: 0.8163 (ptt90) cc_final: 0.7662 (mtm-85)
REVERT: B  111 ASN cc_start: 0.8168 (t0) cc_final: 0.6944 (p0)
REVERT: B  140 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7360 (mp)
REVERT: B  149 PHE cc_start: 0.6468 (OUTLIER) cc_final: 0.5484 (m-80)
REVERT: B  277 CYS cc_start: 0.6743 (m) cc_final: 0.6198 (t)
  outliers start: 25
  outliers final: 22
  residues processed: 87
  average time/residue: 0.1392
  time to fit residues: 16.4661
Evaluate side-chains
  92 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 67
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLN
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  224 ILE
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 A residue  321 THR
Chi-restraints excluded: chain B residue   29 TYR
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  140 LEU
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 46 optimal weight:    0.5980
   chunk 29 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0770
   chunk 23 optimal weight:    0.1980
   chunk 53 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.4538

-------------------------------------------------------------------------------
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
** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 161 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.220089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.186638 restraints weight = 7410.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.184197 restraints weight = 12966.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.184661 restraints weight = 11055.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.5677

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= 0.178
  Angle     :  0.758  18.767   6844  Z= 0.389
  Chirality :  0.041   0.256    748
  Planarity :  0.003   0.026    844
  Dihedral  :  5.414  59.253    645
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 23.88 %
    Favored  : 71.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.47 (0.34), residues: 578
  helix:  2.07 (0.22), residues: 504
  sheet:  None (None), residues: 0
  loop : -1.50 (0.65), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  12 
 HIS   0.010   0.002   HIS B  13 
 PHE   0.014   0.001   PHE A 290 
 TYR   0.027   0.001   TYR B 234 
 ARG   0.003   0.000   ARG A 174 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2020.66 seconds
wall clock time: 37 minutes 4.51 seconds (2224.51 seconds total)