Starting phenix.real_space_refine
on Tue Feb 11 15:24:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vq4_32085/02_2025/7vq4_32085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vq4_32085/02_2025/7vq4_32085.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vq4_32085/02_2025/7vq4_32085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vq4_32085/02_2025/7vq4_32085.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vq4_32085/02_2025/7vq4_32085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vq4_32085/02_2025/7vq4_32085.cif"
  }
  resolution = 3.2
  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=   0.000 sd=   0.005
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      34      5.16       5
     C    4070      2.51       5
     N    1052      2.21       5
     O    1150      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6306
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 400, 3153
          Classifications: {'peptide': 400}
          Link IDs: {'PTRANS': 12, 'TRANS': 387}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 400, 3153
          Classifications: {'peptide': 400}
          Link IDs: {'PTRANS': 12, 'TRANS': 387}
          Chain breaks: 1
  Time building chain proxies: 3.99, per 1000 atoms: 0.63
  Number of scatterers: 6306
  At special positions: 0
  Unit cell: (82.134, 84.162, 111.54, 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      34     16.00
     O    1150      8.00
     N    1052      7.00
     C    4070      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: 1.69
  Conformation dependent library (CDL) restraints added in 981.5 milliseconds
  

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1504

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      84.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 18
      removed outlier: 3.624A  pdb=" N   ASP A  18 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 41
      removed outlier: 3.863A  pdb=" N   GLY A  29 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 66
    Processing helix  chain 'A' and resid 69 through 102
      removed outlier: 3.756A  pdb=" N   THR A  73 " --> pdb=" O   SER A  69 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLY A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 125
    Processing helix  chain 'A' and resid 127 through 134
      removed outlier: 3.524A  pdb=" N   LYS A 131 " --> pdb=" O   PHE A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 151
      removed outlier: 3.601A  pdb=" N   SER A 151 " --> pdb=" O   LEU A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 183
    Processing helix  chain 'A' and resid 187 through 214
      removed outlier: 3.694A  pdb=" N   ASP A 191 " --> pdb=" O   TRP A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 241
      removed outlier: 4.615A  pdb=" N   ARG A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   TYR A 236 " --> pdb=" O   ASN A 232 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   VAL A 239 " --> pdb=" O   ARG A 235 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU A 240 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 254
    Processing helix  chain 'A' and resid 267 through 293
      removed outlier: 3.720A  pdb=" N   TYR A 271 " --> pdb=" O   PRO A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 306
      removed outlier: 3.833A  pdb=" N   LYS A 303 " --> pdb=" O   PRO A 299 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU A 306 " --> pdb=" O   ILE A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 330
      removed outlier: 3.738A  pdb=" N   LEU A 310 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLN A 330 " --> pdb=" O   ILE A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 357
      removed outlier: 4.368A  pdb=" N   ILE A 339 " --> pdb=" O   SER A 335 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   SER A 344 " --> pdb=" O   HIS A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 398
    Processing helix  chain 'B' and resid 2 through 18
      removed outlier: 3.624A  pdb=" N   ASP B  18 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 41
      removed outlier: 3.864A  pdb=" N   GLY B  29 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 66
    Processing helix  chain 'B' and resid 69 through 102
      removed outlier: 3.757A  pdb=" N   THR B  73 " --> pdb=" O   SER B  69 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLY B 102 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 125
    Processing helix  chain 'B' and resid 127 through 134
      removed outlier: 3.523A  pdb=" N   LYS B 131 " --> pdb=" O   PHE B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 151
      removed outlier: 3.601A  pdb=" N   SER B 151 " --> pdb=" O   LEU B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 183
    Processing helix  chain 'B' and resid 187 through 214
      removed outlier: 3.693A  pdb=" N   ASP B 191 " --> pdb=" O   TRP B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 241
      removed outlier: 4.615A  pdb=" N   ARG B 235 " --> pdb=" O   LYS B 231 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   TYR B 236 " --> pdb=" O   ASN B 232 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   VAL B 239 " --> pdb=" O   ARG B 235 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU B 240 " --> pdb=" O   TYR B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 254
    Processing helix  chain 'B' and resid 267 through 293
      removed outlier: 3.720A  pdb=" N   TYR B 271 " --> pdb=" O   PRO B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 306
      removed outlier: 3.833A  pdb=" N   LYS B 303 " --> pdb=" O   PRO B 299 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU B 306 " --> pdb=" O   ILE B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 330
      removed outlier: 3.737A  pdb=" N   LEU B 310 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLN B 330 " --> pdb=" O   ILE B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 357
      removed outlier: 4.368A  pdb=" N   ILE B 339 " --> pdb=" O   SER B 335 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   SER B 344 " --> pdb=" O   HIS B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 398

    509 hydrogen bonds defined for protein.
    1527 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: 1.82

  Time building geometry restraints manager: 1.94 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2008
        1.34 -     1.46: 1045
        1.46 -     1.57: 3321
        1.57 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 6434
  Sorted by residual:
  bond pdb=" CB  TRP B  57 "
       pdb=" CG  TRP B  57 "
    ideal  model  delta    sigma   weight residual
    1.498  1.454  0.044 3.10e-02 1.04e+03 2.05e+00
  bond pdb=" CB  TRP A  57 "
       pdb=" CG  TRP A  57 "
    ideal  model  delta    sigma   weight residual
    1.498  1.454  0.044 3.10e-02 1.04e+03 2.04e+00
  bond pdb=" CB  TRP B 187 "
       pdb=" CG  TRP B 187 "
    ideal  model  delta    sigma   weight residual
    1.498  1.458  0.040 3.10e-02 1.04e+03 1.63e+00
  bond pdb=" CB  TRP A 187 "
       pdb=" CG  TRP A 187 "
    ideal  model  delta    sigma   weight residual
    1.498  1.459  0.039 3.10e-02 1.04e+03 1.62e+00
  bond pdb=" CA  VAL A 186 "
       pdb=" C   VAL A 186 "
    ideal  model  delta    sigma   weight residual
    1.527  1.518  0.009 8.50e-03 1.38e+04 1.14e+00
  ... (remaining 6429 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 8313
        1.50 -     3.01: 299
        3.01 -     4.51: 56
        4.51 -     6.01: 20
        6.01 -     7.52: 4
  Bond angle restraints: 8692
  Sorted by residual:
  angle pdb=" N   VAL B 105 "
        pdb=" CA  VAL B 105 "
        pdb=" C   VAL B 105 "
      ideal   model   delta    sigma   weight residual
     112.17  108.66    3.51 9.50e-01 1.11e+00 1.36e+01
  angle pdb=" N   VAL A 105 "
        pdb=" CA  VAL A 105 "
        pdb=" C   VAL A 105 "
      ideal   model   delta    sigma   weight residual
     112.17  108.67    3.50 9.50e-01 1.11e+00 1.36e+01
  angle pdb=" N   PHE B 134 "
        pdb=" CA  PHE B 134 "
        pdb=" C   PHE B 134 "
      ideal   model   delta    sigma   weight residual
     110.44  114.21   -3.77 1.20e+00 6.94e-01 9.89e+00
  angle pdb=" N   PHE A 134 "
        pdb=" CA  PHE A 134 "
        pdb=" C   PHE A 134 "
      ideal   model   delta    sigma   weight residual
     110.44  114.16   -3.72 1.20e+00 6.94e-01 9.62e+00
  angle pdb=" CA  PRO B 267 "
        pdb=" C   PRO B 267 "
        pdb=" O   PRO B 267 "
      ideal   model   delta    sigma   weight residual
     123.07  119.36    3.71 1.38e+00 5.25e-01 7.22e+00
  ... (remaining 8687 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.03: 3396
       18.03 -    36.05: 366
       36.05 -    54.08: 62
       54.08 -    72.10: 26
       72.10 -    90.13: 6
  Dihedral angle restraints: 3856
    sinusoidal: 1532
      harmonic: 2324
  Sorted by residual:
  dihedral pdb=" CA  CYS A 184 "
           pdb=" C   CYS A 184 "
           pdb=" N   PRO A 185 "
           pdb=" CA  PRO A 185 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.67  -20.33     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" CA  CYS B 184 "
           pdb=" C   CYS B 184 "
           pdb=" N   PRO B 185 "
           pdb=" CA  PRO B 185 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.70  -20.30     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" CA  HIS B 259 "
           pdb=" C   HIS B 259 "
           pdb=" N   GLY B 260 "
           pdb=" CA  GLY B 260 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.77  -17.23     0      5.00e+00 4.00e-02 1.19e+01
  ... (remaining 3853 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 499
       0.030 -    0.060: 357
       0.060 -    0.090: 105
       0.090 -    0.119: 30
       0.119 -    0.149: 5
  Chirality restraints: 996
  Sorted by residual:
  chirality pdb=" CA  PRO B 365 "
            pdb=" N   PRO B 365 "
            pdb=" C   PRO B 365 "
            pdb=" CB  PRO B 365 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.56e-01
  chirality pdb=" CA  PRO A 365 "
            pdb=" N   PRO A 365 "
            pdb=" C   PRO A 365 "
            pdb=" CB  PRO A 365 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.26e-01
  chirality pdb=" CA  ILE A 332 "
            pdb=" N   ILE A 332 "
            pdb=" C   ILE A 332 "
            pdb=" CB  ILE A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.77e-01
  ... (remaining 993 not shown)

  Planarity restraints: 1090
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 364 "    0.033 5.00e-02 4.00e+02   5.02e-02 4.03e+00
        pdb=" N   PRO A 365 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A 365 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 365 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 364 "   -0.033 5.00e-02 4.00e+02   5.01e-02 4.01e+00
        pdb=" N   PRO B 365 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO B 365 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 365 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 127 "    0.025 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO B 128 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B 128 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 128 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1087 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.70: 239
        2.70 -     3.25: 6944
        3.25 -     3.80: 10031
        3.80 -     4.35: 11847
        4.35 -     4.90: 20167
  Nonbonded interactions: 49228
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 295 "
            pdb=" N   PHE A 296 "
     model   vdw
     2.155 3.120
  nonbonded pdb=" OD1 ASP B 295 "
            pdb=" N   PHE B 296 "
     model   vdw
     2.155 3.120
  nonbonded pdb=" O   MET B   1 "
            pdb=" N   ARG B   5 "
     model   vdw
     2.178 3.120
  nonbonded pdb=" OH  TYR A 291 "
            pdb=" OG  SER B 376 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" NH1 ARG A  80 "
            pdb=" OH  TYR A 136 "
     model   vdw
     2.225 3.120
  ... (remaining 49223 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: 0.03
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 individual isotropic
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:             0.620
  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:             0.020
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     17.630
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
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   0.044   6434  Z= 0.439
  Angle     :  0.740   7.518   8692  Z= 0.423
  Chirality :  0.042   0.149    996
  Planarity :  0.004   0.050   1090
  Dihedral  : 16.105  90.127   2352
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  :  8.62 %
    Favored  : 89.08 %
  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: -1.96 (0.27), residues: 792
  helix: -0.72 (0.18), residues: 666
  sheet:  None (None), residues: 0
  loop : -3.76 (0.50), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 255 
 HIS   0.003   0.001   HIS B 266 
 PHE   0.018   0.002   PHE B 153 
 TYR   0.013   0.002   TYR B 291 
 ARG   0.003   0.001   ARG B  13 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 206
  time to evaluate  : 0.747 
Fit side-chains
REVERT: A   40 TYR cc_start: 0.8043 (t80) cc_final: 0.7503 (t80)
REVERT: A  180 SER cc_start: 0.9003 (t) cc_final: 0.8580 (p)
REVERT: A  237 LYS cc_start: 0.8450 (mttt) cc_final: 0.8150 (mtmt)
REVERT: A  306 LEU cc_start: 0.8688 (tp) cc_final: 0.8481 (tp)
REVERT: A  307 GLU cc_start: 0.7515 (pt0) cc_final: 0.7258 (pm20)
REVERT: A  322 LYS cc_start: 0.7820 (tptm) cc_final: 0.7412 (ttpt)
REVERT: B    1 MET cc_start: 0.5033 (OUTLIER) cc_final: 0.4477 (ptp)
REVERT: B   40 TYR cc_start: 0.8064 (t80) cc_final: 0.7540 (t80)
REVERT: B  328 LEU cc_start: 0.9183 (tp) cc_final: 0.8902 (tp)
  outliers start: 16
  outliers final: 7
  residues processed: 216
  average time/residue: 0.2350
  time to fit residues: 63.3003
Evaluate side-chains
  162 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 154
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 THR
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  223 TYR
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  223 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A  24 HIS
A  54 ASN
A 251 ASN
A 259 HIS
A 293 ASN
A 297 GLN
A 340 HIS
A 343 ASN
B  24 HIS
B  54 ASN
B 251 ASN
B 259 HIS
B 280 GLN
B 293 ASN
B 297 GLN
B 330 GLN
B 340 HIS
B 343 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.158101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.129566 restraints weight = 9295.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 2.61
r_work: 0.3589 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6434  Z= 0.199
  Angle     :  0.562   5.791   8692  Z= 0.296
  Chirality :  0.038   0.142    996
  Planarity :  0.004   0.047   1090
  Dihedral  :  5.546  49.915    870
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 15.66 %
    Favored  : 79.45 %
  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:  1.20 (0.30), residues: 792
  helix:  1.55 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -3.20 (0.53), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  57 
 HIS   0.003   0.001   HIS A 259 
 PHE   0.013   0.001   PHE A 145 
 TYR   0.014   0.001   TYR A 291 
 ARG   0.006   0.001   ARG A 265 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 168
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8413 (pp30)
REVERT: A  105 VAL cc_start: 0.6457 (OUTLIER) cc_final: 0.6078 (t)
REVERT: A  159 MET cc_start: 0.7025 (ptt) cc_final: 0.6584 (mtm)
REVERT: A  180 SER cc_start: 0.8991 (t) cc_final: 0.8406 (p)
REVERT: A  193 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.7186 (t-90)
REVERT: A  237 LYS cc_start: 0.8380 (mttt) cc_final: 0.8021 (mtmt)
REVERT: A  263 ARG cc_start: 0.8108 (tpp80) cc_final: 0.7209 (tmt170)
REVERT: A  286 ASP cc_start: 0.8614 (t70) cc_final: 0.8341 (t0)
REVERT: A  321 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7605 (mmt)
REVERT: A  322 LYS cc_start: 0.7670 (tptm) cc_final: 0.7046 (ttpt)
REVERT: A  368 MET cc_start: 0.8135 (mmm) cc_final: 0.7894 (mmm)
REVERT: B    1 MET cc_start: 0.4655 (ttt) cc_final: 0.4259 (tpp)
REVERT: B    9 ARG cc_start: 0.6220 (mtt-85) cc_final: 0.5436 (ptp90)
REVERT: B  154 ARG cc_start: 0.7481 (mtp-110) cc_final: 0.7233 (mtm110)
REVERT: B  193 HIS cc_start: 0.7719 (OUTLIER) cc_final: 0.7296 (t-90)
REVERT: B  201 ASP cc_start: 0.8314 (t0) cc_final: 0.8007 (t0)
REVERT: B  237 LYS cc_start: 0.8255 (mtmt) cc_final: 0.7955 (mtmt)
REVERT: B  328 LEU cc_start: 0.9060 (tp) cc_final: 0.8642 (tp)
REVERT: B  377 MET cc_start: 0.8628 (mmt) cc_final: 0.8291 (mmm)
  outliers start: 34
  outliers final: 19
  residues processed: 186
  average time/residue: 0.1821
  time to fit residues: 44.3226
Evaluate side-chains
  172 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 149
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 THR
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  223 TYR
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  117 GLN
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  193 HIS
Chi-restraints excluded: chain B residue  223 TYR
Chi-restraints excluded: chain B residue  342 SER
Chi-restraints excluded: chain B residue  363 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0770
   chunk 66 optimal weight:    0.9980
   chunk 38 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.7338

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.160813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.132371 restraints weight = 9737.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3784 rms_B_bonded: 2.52
r_work: 0.3675 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6434  Z= 0.174
  Angle     :  0.523   6.210   8692  Z= 0.273
  Chirality :  0.036   0.170    996
  Planarity :  0.004   0.047   1090
  Dihedral  :  4.415  34.201    866
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 18.10 %
    Favored  : 77.16 %
  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:  2.25 (0.30), residues: 792
  helix:  2.25 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -2.66 (0.56), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 129 
 HIS   0.003   0.001   HIS B  95 
 PHE   0.011   0.001   PHE B 141 
 TYR   0.011   0.001   TYR B 236 
 ARG   0.004   0.000   ARG B   5 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 171
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8408 (pp30)
REVERT: A  105 VAL cc_start: 0.6438 (OUTLIER) cc_final: 0.6127 (t)
REVERT: A  159 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6617 (mtm)
REVERT: A  180 SER cc_start: 0.9017 (t) cc_final: 0.8484 (p)
REVERT: A  193 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.6786 (t-90)
REVERT: A  201 ASP cc_start: 0.8272 (t0) cc_final: 0.8006 (t0)
REVERT: A  237 LYS cc_start: 0.8483 (mttt) cc_final: 0.8125 (mtmt)
REVERT: A  322 LYS cc_start: 0.7589 (tptm) cc_final: 0.6883 (ttpt)
REVERT: A  372 MET cc_start: 0.8621 (mmt) cc_final: 0.8326 (mmt)
REVERT: A  377 MET cc_start: 0.8487 (mmt) cc_final: 0.8225 (mmm)
REVERT: B    1 MET cc_start: 0.5089 (ttt) cc_final: 0.4546 (tpp)
REVERT: B   90 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7536 (mp)
REVERT: B  154 ARG cc_start: 0.7489 (mtp-110) cc_final: 0.7251 (mtm110)
REVERT: B  193 HIS cc_start: 0.7669 (OUTLIER) cc_final: 0.7065 (t-90)
REVERT: B  286 ASP cc_start: 0.8615 (t70) cc_final: 0.8407 (t0)
REVERT: B  328 LEU cc_start: 0.8975 (tp) cc_final: 0.8575 (tp)
  outliers start: 33
  outliers final: 20
  residues processed: 190
  average time/residue: 0.1822
  time to fit residues: 45.4509
Evaluate side-chains
  169 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 144
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  223 TYR
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  117 GLN
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  193 HIS
Chi-restraints excluded: chain B residue  223 TYR
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  388 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 74 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 28 optimal weight:    0.1980
   chunk 15 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 266 HIS
A 330 GLN
B 345 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.161053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.132568 restraints weight = 9827.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 2.54
r_work: 0.3676 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6434  Z= 0.173
  Angle     :  0.549   7.035   8692  Z= 0.280
  Chirality :  0.037   0.221    996
  Planarity :  0.004   0.048   1090
  Dihedral  :  4.110  22.738    864
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 19.40 %
    Favored  : 75.14 %
  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:  2.66 (0.31), residues: 792
  helix:  2.49 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -2.30 (0.58), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 129 
 HIS   0.003   0.001   HIS B 259 
 PHE   0.012   0.001   PHE B 141 
 TYR   0.014   0.001   TYR A 236 
 ARG   0.007   0.000   ARG B 265 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 150
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8390 (pp30)
REVERT: A  159 MET cc_start: 0.7078 (ptt) cc_final: 0.6620 (mtm)
REVERT: A  180 SER cc_start: 0.9060 (t) cc_final: 0.8519 (p)
REVERT: A  193 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.6778 (t-90)
REVERT: A  201 ASP cc_start: 0.8287 (t0) cc_final: 0.8003 (t0)
REVERT: A  237 LYS cc_start: 0.8466 (mttt) cc_final: 0.8132 (mtmt)
REVERT: A  321 MET cc_start: 0.7806 (mmt) cc_final: 0.7582 (mmt)
REVERT: A  322 LYS cc_start: 0.7485 (tptm) cc_final: 0.6761 (ttpt)
REVERT: A  328 LEU cc_start: 0.8339 (tp) cc_final: 0.7980 (tp)
REVERT: B    1 MET cc_start: 0.5302 (ttt) cc_final: 0.4788 (tpp)
REVERT: B    9 ARG cc_start: 0.6157 (mtt-85) cc_final: 0.5530 (ptp90)
REVERT: B  154 ARG cc_start: 0.7586 (mtp-110) cc_final: 0.7277 (mtm110)
REVERT: B  193 HIS cc_start: 0.7735 (OUTLIER) cc_final: 0.7070 (t-90)
REVERT: B  328 LEU cc_start: 0.8919 (tp) cc_final: 0.8540 (tp)
REVERT: B  405 MET cc_start: 0.2750 (mpp) cc_final: 0.2278 (mmp)
  outliers start: 38
  outliers final: 25
  residues processed: 171
  average time/residue: 0.1823
  time to fit residues: 40.8944
Evaluate side-chains
  171 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  223 TYR
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  117 GLN
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  193 HIS
Chi-restraints excluded: chain B residue  223 TYR
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  384 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 31 optimal weight:    7.9990
   chunk 58 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 21 optimal weight:    0.1980
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B 345 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.157782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.129693 restraints weight = 9514.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 2.55
r_work: 0.3606 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.3659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6434  Z= 0.188
  Angle     :  0.552   7.180   8692  Z= 0.284
  Chirality :  0.037   0.213    996
  Planarity :  0.004   0.048   1090
  Dihedral  :  3.968  20.826    862
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 19.25 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.84 (0.31), residues: 792
  helix:  2.58 (0.20), residues: 660
  sheet:  None (None), residues: 0
  loop : -2.02 (0.59), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 129 
 HIS   0.003   0.001   HIS B 259 
 PHE   0.010   0.001   PHE B 141 
 TYR   0.013   0.001   TYR B 236 
 ARG   0.005   0.000   ARG B 235 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 155
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8405 (pp30)
REVERT: A  159 MET cc_start: 0.7101 (ptt) cc_final: 0.6681 (mtm)
REVERT: A  193 HIS cc_start: 0.7714 (OUTLIER) cc_final: 0.6947 (t-90)
REVERT: A  201 ASP cc_start: 0.8335 (t0) cc_final: 0.8023 (t0)
REVERT: A  322 LYS cc_start: 0.7505 (tptm) cc_final: 0.6712 (ttpt)
REVERT: A  331 MET cc_start: 0.8180 (tpp) cc_final: 0.7862 (tpp)
REVERT: B    1 MET cc_start: 0.5595 (ttt) cc_final: 0.5267 (tpp)
REVERT: B    2 GLU cc_start: 0.6063 (mp0) cc_final: 0.5812 (mp0)
REVERT: B  154 ARG cc_start: 0.7583 (mtp-110) cc_final: 0.7257 (mtm110)
REVERT: B  193 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7175 (t-90)
REVERT: B  284 ARG cc_start: 0.8082 (mpt90) cc_final: 0.7862 (mpt90)
REVERT: B  307 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7434 (pm20)
REVERT: B  328 LEU cc_start: 0.8898 (tp) cc_final: 0.8472 (tp)
REVERT: B  331 MET cc_start: 0.8148 (mmm) cc_final: 0.7870 (mmm)
  outliers start: 40
  outliers final: 27
  residues processed: 174
  average time/residue: 0.1744
  time to fit residues: 40.3061
Evaluate side-chains
  174 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 144
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  223 TYR
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  117 GLN
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  193 HIS
Chi-restraints excluded: chain B residue  223 TYR
Chi-restraints excluded: chain B residue  307 GLU
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  384 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0570
   chunk 16 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0370
   chunk 29 optimal weight:    1.9990
   chunk 62 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   chunk 76 optimal weight:    7.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
B 345 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.157589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.130016 restraints weight = 9520.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3710 rms_B_bonded: 2.54
r_work: 0.3600 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.3818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6434  Z= 0.193
  Angle     :  0.583   9.063   8692  Z= 0.291
  Chirality :  0.037   0.206    996
  Planarity :  0.004   0.048   1090
  Dihedral  :  4.006  21.866    862
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 20.40 %
    Favored  : 74.71 %
  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:  2.87 (0.31), residues: 792
  helix:  2.56 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.99 (0.58), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 129 
 HIS   0.004   0.001   HIS B 259 
 PHE   0.012   0.001   PHE B 145 
 TYR   0.012   0.001   TYR A 236 
 ARG   0.007   0.000   ARG B 265 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 151
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8399 (pp30)
REVERT: A  159 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6626 (mtm)
REVERT: A  193 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.6901 (t-90)
REVERT: A  201 ASP cc_start: 0.8355 (t0) cc_final: 0.8065 (t0)
REVERT: A  237 LYS cc_start: 0.8448 (mttt) cc_final: 0.8187 (mmmt)
REVERT: A  322 LYS cc_start: 0.7429 (tptm) cc_final: 0.6593 (ttpt)
REVERT: A  405 MET cc_start: 0.2979 (mpp) cc_final: 0.2280 (mmp)
REVERT: B  154 ARG cc_start: 0.7605 (mtp-110) cc_final: 0.7259 (mtm110)
REVERT: B  193 HIS cc_start: 0.7847 (OUTLIER) cc_final: 0.7119 (t-90)
REVERT: B  405 MET cc_start: 0.3151 (mpp) cc_final: 0.2744 (mpp)
  outliers start: 34
  outliers final: 28
  residues processed: 171
  average time/residue: 0.1757
  time to fit residues: 39.8491
Evaluate side-chains
  172 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 141
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  223 TYR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  117 GLN
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  193 HIS
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  223 TYR
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  384 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 55 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 67 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 70 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 361 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.156615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.129260 restraints weight = 9446.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 2.49
r_work: 0.3616 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.3952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6434  Z= 0.195
  Angle     :  0.599  13.585   8692  Z= 0.295
  Chirality :  0.037   0.203    996
  Planarity :  0.003   0.049   1090
  Dihedral  :  3.981  22.615    862
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 20.26 %
    Favored  : 73.71 %
  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:  2.94 (0.31), residues: 792
  helix:  2.59 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.87 (0.59), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 129 
 HIS   0.003   0.001   HIS B 259 
 PHE   0.009   0.001   PHE B 141 
 TYR   0.012   0.001   TYR A 236 
 ARG   0.006   0.000   ARG B 265 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 148
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 ASN cc_start: 0.8483 (m-40) cc_final: 0.8180 (m-40)
REVERT: A   95 HIS cc_start: 0.8238 (OUTLIER) cc_final: 0.7205 (t-90)
REVERT: A   96 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8395 (pp30)
REVERT: A  159 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6575 (mtm)
REVERT: A  193 HIS cc_start: 0.7592 (OUTLIER) cc_final: 0.6923 (t-90)
REVERT: A  201 ASP cc_start: 0.8333 (t0) cc_final: 0.8062 (t0)
REVERT: A  322 LYS cc_start: 0.7522 (tptm) cc_final: 0.6660 (ttpt)
REVERT: A  328 LEU cc_start: 0.8331 (tp) cc_final: 0.7979 (tp)
REVERT: A  405 MET cc_start: 0.2856 (mpp) cc_final: 0.2175 (mmp)
REVERT: B  106 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6400 (tt0)
REVERT: B  154 ARG cc_start: 0.7578 (mtp-110) cc_final: 0.7247 (mtm110)
REVERT: B  193 HIS cc_start: 0.7804 (OUTLIER) cc_final: 0.7125 (t-90)
  outliers start: 42
  outliers final: 32
  residues processed: 172
  average time/residue: 0.1722
  time to fit residues: 39.4452
Evaluate side-chains
  176 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 139
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   84 THR
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  223 TYR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  106 GLU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  117 GLN
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  193 HIS
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  223 TYR
Chi-restraints excluded: chain B residue  307 GLU
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  401 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0770
   chunk 59 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.7540

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

Flipped N/Q/H residues before XYZ refinement:
** B 345 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 = 0.4029 r_free = 0.4029 target = 0.157986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.130866 restraints weight = 9459.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 2.49
r_work: 0.3634 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.4207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6434  Z= 0.179
  Angle     :  0.602  14.044   8692  Z= 0.296
  Chirality :  0.037   0.193    996
  Planarity :  0.003   0.046   1090
  Dihedral  :  3.955  24.021    862
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 22.41 %
    Favored  : 72.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.04 (0.31), residues: 792
  helix:  2.64 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.78 (0.60), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 129 
 HIS   0.003   0.001   HIS B 259 
 PHE   0.014   0.001   PHE B 145 
 TYR   0.013   0.001   TYR A 236 
 ARG   0.006   0.000   ARG B 265 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 144
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7151 (t-90)
REVERT: A   96 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8386 (pp30)
REVERT: A  159 MET cc_start: 0.6999 (ptt) cc_final: 0.6537 (mtm)
REVERT: A  193 HIS cc_start: 0.7616 (OUTLIER) cc_final: 0.6885 (t-90)
REVERT: A  201 ASP cc_start: 0.8332 (t0) cc_final: 0.8018 (t0)
REVERT: A  237 LYS cc_start: 0.8441 (mttt) cc_final: 0.8172 (mmmt)
REVERT: A  322 LYS cc_start: 0.7464 (tptm) cc_final: 0.6612 (ttpt)
REVERT: A  328 LEU cc_start: 0.8264 (tp) cc_final: 0.7957 (tp)
REVERT: A  405 MET cc_start: 0.2818 (mpp) cc_final: 0.2187 (mmp)
REVERT: B  154 ARG cc_start: 0.7524 (mtp-110) cc_final: 0.7195 (mtm110)
REVERT: B  193 HIS cc_start: 0.7708 (OUTLIER) cc_final: 0.6981 (t-90)
REVERT: B  405 MET cc_start: 0.2688 (mpp) cc_final: 0.2154 (mpp)
  outliers start: 36
  outliers final: 29
  residues processed: 168
  average time/residue: 0.1513
  time to fit residues: 34.7987
Evaluate side-chains
  172 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 140
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 ILE
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  223 TYR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  117 GLN
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  193 HIS
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  223 TYR
Chi-restraints excluded: chain B residue  307 GLU
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  384 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 55 optimal weight:    7.9990
   chunk 70 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 75 optimal weight:    9.9990
   chunk 58 optimal weight:    0.0870
   overall best weight:    1.3762

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

Flipped N/Q/H residues before XYZ refinement:
** B 345 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 = 0.4010 r_free = 0.4010 target = 0.156070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.128658 restraints weight = 9504.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3711 rms_B_bonded: 2.48
r_work: 0.3603 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.4120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6434  Z= 0.218
  Angle     :  0.638  14.202   8692  Z= 0.313
  Chirality :  0.038   0.196    996
  Planarity :  0.004   0.046   1090
  Dihedral  :  4.020  23.369    862
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 22.84 %
    Favored  : 71.84 %
  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:  2.98 (0.31), residues: 792
  helix:  2.59 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.76 (0.60), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 259 
 PHE   0.011   0.001   PHE A 206 
 TYR   0.012   0.001   TYR A 236 
 ARG   0.005   0.000   ARG A   9 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 146
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 HIS cc_start: 0.8249 (OUTLIER) cc_final: 0.7251 (t-90)
REVERT: A   96 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8436 (pp30)
REVERT: A  159 MET cc_start: 0.7047 (ptt) cc_final: 0.6556 (mtm)
REVERT: A  193 HIS cc_start: 0.7664 (OUTLIER) cc_final: 0.6993 (t-90)
REVERT: A  201 ASP cc_start: 0.8351 (t0) cc_final: 0.8067 (t0)
REVERT: A  322 LYS cc_start: 0.7528 (tptm) cc_final: 0.6711 (ttpt)
REVERT: A  328 LEU cc_start: 0.8406 (tp) cc_final: 0.8126 (tp)
REVERT: A  405 MET cc_start: 0.2784 (mpp) cc_final: 0.2160 (mmp)
REVERT: B  154 ARG cc_start: 0.7545 (mtp-110) cc_final: 0.7222 (mtm110)
REVERT: B  193 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7293 (t-90)
REVERT: B  405 MET cc_start: 0.2560 (mpp) cc_final: 0.2007 (mpp)
  outliers start: 37
  outliers final: 33
  residues processed: 174
  average time/residue: 0.1637
  time to fit residues: 38.2710
Evaluate side-chains
  176 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 140
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 ILE
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  223 TYR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  117 GLN
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  148 ILE
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  193 HIS
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  223 TYR
Chi-restraints excluded: chain B residue  292 ILE
Chi-restraints excluded: chain B residue  307 GLU
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  401 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** B 345 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 = 0.4017 r_free = 0.4017 target = 0.156733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.129451 restraints weight = 9550.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 2.50
r_work: 0.3617 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.4229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6434  Z= 0.195
  Angle     :  0.624  14.381   8692  Z= 0.303
  Chirality :  0.037   0.200    996
  Planarity :  0.004   0.047   1090
  Dihedral  :  4.001  24.581    862
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 22.41 %
    Favored  : 72.27 %
  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:  3.02 (0.31), residues: 792
  helix:  2.62 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.73 (0.60), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 129 
 HIS   0.004   0.001   HIS B 259 
 PHE   0.017   0.001   PHE B 145 
 TYR   0.012   0.001   TYR A 236 
 ARG   0.007   0.000   ARG B 265 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 140
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.7159 (t-90)
REVERT: A   96 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8427 (pp30)
REVERT: A  159 MET cc_start: 0.7039 (ptt) cc_final: 0.6557 (mtm)
REVERT: A  193 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.6869 (t-90)
REVERT: A  201 ASP cc_start: 0.8348 (t0) cc_final: 0.8069 (t0)
REVERT: A  322 LYS cc_start: 0.7514 (tptm) cc_final: 0.6683 (ttpt)
REVERT: A  328 LEU cc_start: 0.8454 (tp) cc_final: 0.8172 (tp)
REVERT: A  405 MET cc_start: 0.2737 (mpp) cc_final: 0.2152 (mmp)
REVERT: B    1 MET cc_start: 0.6334 (tpp) cc_final: 0.5814 (tmm)
REVERT: B  154 ARG cc_start: 0.7515 (mtp-110) cc_final: 0.7197 (mtm110)
REVERT: B  193 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.7202 (t-90)
REVERT: B  405 MET cc_start: 0.2870 (mpp) cc_final: 0.2372 (mpp)
  outliers start: 37
  outliers final: 32
  residues processed: 166
  average time/residue: 0.1558
  time to fit residues: 35.1806
Evaluate side-chains
  172 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 137
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 ILE
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  223 TYR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  117 GLN
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  148 ILE
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  193 HIS
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  223 TYR
Chi-restraints excluded: chain B residue  292 ILE
Chi-restraints excluded: chain B residue  307 GLU
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  401 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0050
   chunk 0 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 43 optimal weight:    0.4980
   overall best weight:    0.8798

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

Flipped N/Q/H residues before XYZ refinement:
** B 345 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 = 0.4024 r_free = 0.4024 target = 0.157564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.130405 restraints weight = 9641.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 2.51
r_work: 0.3629 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.4365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6434  Z= 0.189
  Angle     :  0.624  14.531   8692  Z= 0.303
  Chirality :  0.037   0.200    996
  Planarity :  0.003   0.045   1090
  Dihedral  :  3.989  25.519    862
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 22.70 %
    Favored  : 71.98 %
  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:  3.11 (0.31), residues: 792
  helix:  2.68 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.69 (0.61), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 129 
 HIS   0.003   0.001   HIS B 259 
 PHE   0.009   0.001   PHE A 206 
 TYR   0.013   0.001   TYR A 236 
 ARG   0.007   0.000   ARG B 265 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2840.17 seconds
wall clock time: 51 minutes 21.54 seconds (3081.54 seconds total)