Starting phenix.real_space_refine
on Tue Feb 11 00:46:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8swh_40814/02_2025/8swh_40814.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8swh_40814/02_2025/8swh_40814.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8swh_40814/02_2025/8swh_40814.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8swh_40814/02_2025/8swh_40814.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8swh_40814/02_2025/8swh_40814.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8swh_40814/02_2025/8swh_40814.cif"
  }
  resolution = 3.88
  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=   0.007
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      14      5.16       5
     C    2155      2.51       5
     N     560      2.21       5
     O     661      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3390
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1509
          Classifications: {'peptide': 187}
          Link IDs: {'PTRANS': 8, 'TRANS': 178}
          Chain breaks: 5
    Chain: "H"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 967
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 3, 'TRANS': 121}
    Chain: "L"
      Number of atoms: 847
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 847
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 8, 'TRANS': 101}
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.54, per 1000 atoms: 1.63
  Number of scatterers: 3390
  At special positions: 0
  Unit cell: (59.45, 89.175, 89.9, 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      14     16.00
     O     661      8.00
     N     560      7.00
     C    2155      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.06

  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
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
    NAG-ASN
      " NAG A1301 " - " ASN A  17 "
      " NAG A1302 " - " ASN A 149 "
      " NAG B   1 " - " ASN A 122 "
  Time building additional restraints: 0.88
  Conformation dependent library (CDL) restraints added in 393.7 milliseconds
  

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  780

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 11 sheets defined
      4.3% alpha, 40.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 72 through 75
    Processing helix  chain 'A' and resid 96 through 99
    Processing helix  chain 'A' and resid 156 through 159
    Processing helix  chain 'H' and resid 28 through 30
      No H-bonds generated for 'chain 'H' and resid 28 through 30'
    Processing helix  chain 'H' and resid 73 through 75
      No H-bonds generated for 'chain 'H' and resid 73 through 75'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70
    Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85
      removed outlier: 6.692A  pdb=" N   LEU A 141 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85
      removed outlier: 6.191A  pdb=" N   ALA A 243 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ILE A 101 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   ARG A 102 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   PHE A 168 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 206 through 207
    Processing sheet with id=AA5, first strand: chain 'H' and resid 5 through 6
    Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 59
      removed outlier: 6.727A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   GLY H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ILE H  34 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 57 through 59
      removed outlier: 6.727A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   GLY H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ILE H  34 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 23
    Processing sheet with id=AA9, first strand: chain 'L' and resid 19 through 23
    Processing sheet with id=AB1, first strand: chain 'L' and resid 45 through 48
      removed outlier: 6.726A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 45 through 48
      removed outlier: 6.726A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    127 hydrogen bonds defined for protein.
    294 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.95

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 775
        1.32 -     1.46: 1087
        1.46 -     1.59: 1577
        1.59 -     1.73: 12
        1.73 -     1.86: 20
  Bond restraints: 3471
  Sorted by residual:
  bond pdb=" CB  TYR A 266 "
       pdb=" CG  TYR A 266 "
    ideal  model  delta    sigma   weight residual
    1.512  1.661 -0.149 2.20e-02 2.07e+03 4.58e+01
  bond pdb=" CD  ARG A 102 "
       pdb=" NE  ARG A 102 "
    ideal  model  delta    sigma   weight residual
    1.458  1.378  0.080 1.40e-02 5.10e+03 3.30e+01
  bond pdb=" CB  ILE L 106 "
       pdb=" CG1 ILE L 106 "
    ideal  model  delta    sigma   weight residual
    1.530  1.639 -0.109 2.00e-02 2.50e+03 2.99e+01
  bond pdb=" CG  PHE A 192 "
       pdb=" CD1 PHE A 192 "
    ideal  model  delta    sigma   weight residual
    1.384  1.493 -0.109 2.10e-02 2.27e+03 2.70e+01
  bond pdb=" CG  PHE A 186 "
       pdb=" CD2 PHE A 186 "
    ideal  model  delta    sigma   weight residual
    1.384  1.490 -0.106 2.10e-02 2.27e+03 2.53e+01
  ... (remaining 3466 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.47: 3983
        2.47 -     4.94: 605
        4.94 -     7.42: 110
        7.42 -     9.89: 18
        9.89 -    12.36: 2
  Bond angle restraints: 4718
  Sorted by residual:
  angle pdb=" C   THR A 250 "
        pdb=" N   PRO A 251 "
        pdb=" CA  PRO A 251 "
      ideal   model   delta    sigma   weight residual
     119.56  128.38   -8.82 1.02e+00 9.61e-01 7.48e+01
  angle pdb=" N   VAL L  13 "
        pdb=" CA  VAL L  13 "
        pdb=" C   VAL L  13 "
      ideal   model   delta    sigma   weight residual
     108.12  120.48  -12.36 1.44e+00 4.82e-01 7.37e+01
  angle pdb=" C   ASP H  52 "
        pdb=" N   PRO H  52A"
        pdb=" CA  PRO H  52A"
      ideal   model   delta    sigma   weight residual
     119.47  128.90   -9.43 1.16e+00 7.43e-01 6.61e+01
  angle pdb=" C   ASN A  81 "
        pdb=" N   PRO A  82 "
        pdb=" CA  PRO A  82 "
      ideal   model   delta    sigma   weight residual
     120.03  127.40   -7.37 9.90e-01 1.02e+00 5.53e+01
  angle pdb=" C   LEU A  24 "
        pdb=" N   PRO A  25 "
        pdb=" CA  PRO A  25 "
      ideal   model   delta    sigma   weight residual
     120.38  127.95   -7.57 1.03e+00 9.43e-01 5.40e+01
  ... (remaining 4713 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.00: 2018
       21.00 -    41.99: 49
       41.99 -    62.98: 8
       62.98 -    83.97: 11
       83.97 -   104.97: 6
  Dihedral angle restraints: 2092
    sinusoidal: 874
      harmonic: 1218
  Sorted by residual:
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  144.41  -51.41     1      1.00e+01 1.00e-02 3.61e+01
  dihedral pdb=" CB  CYS A 131 "
           pdb=" SG  CYS A 131 "
           pdb=" SG  CYS A 166 "
           pdb=" CB  CYS A 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   61.81   31.19     1      1.00e+01 1.00e-02 1.39e+01
  dihedral pdb=" O4  BMA B   3 "
           pdb=" C4  BMA B   3 "
           pdb=" C5  BMA B   3 "
           pdb=" O5  BMA B   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -176.26  104.97     1      3.00e+01 1.11e-03 1.34e+01
  ... (remaining 2089 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 359
       0.096 -    0.191: 119
       0.191 -    0.287: 45
       0.287 -    0.382: 10
       0.382 -    0.478: 6
  Chirality restraints: 539
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.63    0.23 2.00e-02 2.50e+03 1.29e+02
  chirality pdb=" C1  BMA B   3 "
            pdb=" O4  NAG B   2 "
            pdb=" C2  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.56    0.16 2.00e-02 2.50e+03 6.34e+01
  chirality pdb=" C5  BMA B   3 "
            pdb=" C4  BMA B   3 "
            pdb=" C6  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.75    0.48 2.00e-01 2.50e+01 5.71e+00
  ... (remaining 536 not shown)

  Planarity restraints: 595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 149 "    0.055 2.00e-02 2.50e+03   5.87e-02 4.31e+01
        pdb=" CG  ASN A 149 "   -0.021 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 149 "   -0.011 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 149 "   -0.093 2.00e-02 2.50e+03
        pdb=" C1  NAG A1302 "    0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  87 "    0.054 2.00e-02 2.50e+03   3.92e-02 3.08e+01
        pdb=" CG  TYR L  87 "    0.001 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  87 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  87 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  87 "   -0.027 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  87 "   -0.037 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  87 "   -0.027 2.00e-02 2.50e+03
        pdb=" OH  TYR L  87 "    0.076 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 192 "    0.065 2.00e-02 2.50e+03   3.97e-02 2.76e+01
        pdb=" CG  PHE A 192 "   -0.056 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 192 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 192 "   -0.033 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 192 "    0.012 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 192 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 192 "    0.037 2.00e-02 2.50e+03
  ... (remaining 592 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 1291
        2.88 -     3.39: 3037
        3.39 -     3.89: 5703
        3.89 -     4.40: 6762
        4.40 -     4.90: 10627
  Nonbonded interactions: 27420
  Sorted by model distance:
  nonbonded pdb=" O   THR A 108 "
            pdb=" OG1 THR A 236 "
     model   vdw
     2.378 3.040
  nonbonded pdb=" N   GLN H  62 "
            pdb=" O   GLN H  62 "
     model   vdw
     2.445 2.496
  nonbonded pdb=" N   ASP L  60 "
            pdb=" OD1 ASP L  60 "
     model   vdw
     2.454 3.120
  nonbonded pdb=" N   ASP A 253 "
            pdb=" OD1 ASP A 253 "
     model   vdw
     2.454 3.120
  nonbonded pdb=" N   THR H  99 "
            pdb=" O   THR H  99 "
     model   vdw
     2.458 2.496
  ... (remaining 27415 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.870
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6715
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      :  0.021   0.149   3471  Z= 1.384
  Angle     :  1.931  12.361   4718  Z= 1.293
  Chirality :  0.119   0.478    539
  Planarity :  0.010   0.044    592
  Dihedral  : 12.946 104.968   1300
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 1.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.82 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet:  0.14 (0.38), residues: 164
  loop : -0.20 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.013   TRP H  47 
 HIS   0.005   0.002   HIS A 146 
 PHE   0.065   0.009   PHE A 192 
 TYR   0.076   0.011   TYR L  87 
 ARG   0.008   0.001   ARG H  83 

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 196
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ASP cc_start: 0.7643 (t0) cc_final: 0.7294 (t0)
REVERT: A   83 VAL cc_start: 0.8524 (t) cc_final: 0.8118 (m)
REVERT: A  151 SER cc_start: 0.8094 (p) cc_final: 0.7643 (m)
REVERT: A  153 MET cc_start: 0.8307 (mtt) cc_final: 0.8072 (mtt)
REVERT: A  242 LEU cc_start: 0.7954 (mt) cc_final: 0.7715 (mp)
REVERT: H   31 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7868 (mt-10)
REVERT: L   32 TYR cc_start: 0.5490 (m-80) cc_final: 0.5233 (m-10)
REVERT: L   71 PHE cc_start: 0.7407 (m-80) cc_final: 0.6922 (m-10)
REVERT: L   85 LEU cc_start: 0.8763 (mt) cc_final: 0.8341 (mt)
REVERT: L   87 TYR cc_start: 0.8386 (m-80) cc_final: 0.8109 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 197
  average time/residue: 0.1782
  time to fit residues: 41.0169
Evaluate side-chains
  126 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 16 optimal weight:    0.1980
   chunk 32 optimal weight:    0.1980
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 23 optimal weight:    0.4980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
A 134 GLN
A 148 ASN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  62 GLN
L  17 GLN
L  38 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  93 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.150619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.131439 restraints weight = 9303.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.134591 restraints weight = 5370.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.136631 restraints weight = 3694.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6783
moved from start:          0.4579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   3471  Z= 0.288
  Angle     :  0.838   5.760   4718  Z= 0.453
  Chirality :  0.052   0.312    539
  Planarity :  0.006   0.049    592
  Dihedral  :  9.355  61.328    559
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 17.49 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -1.01 (0.39), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.37 (0.38), residues: 166
  loop : -0.85 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 104 
 HIS   0.004   0.001   HIS A 146 
 PHE   0.022   0.003   PHE A 133 
 TYR   0.020   0.002   TYR H  27 
 ARG   0.010   0.001   ARG A 237 

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 146
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ASP cc_start: 0.8132 (t0) cc_final: 0.7763 (t0)
REVERT: A   82 PRO cc_start: 0.8546 (Cg_endo) cc_final: 0.8210 (Cg_exo)
REVERT: A   83 VAL cc_start: 0.8688 (t) cc_final: 0.8327 (m)
REVERT: H   38 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7753 (mtm180)
REVERT: H   48 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7522 (mtp)
REVERT: H   58 ILE cc_start: 0.8648 (mm) cc_final: 0.7949 (pt)
REVERT: H   61 GLN cc_start: 0.8411 (tt0) cc_final: 0.7931 (pm20)
REVERT: H   72 ASP cc_start: 0.8993 (t0) cc_final: 0.8492 (t70)
REVERT: H   96 PHE cc_start: 0.7359 (m-10) cc_final: 0.6375 (m-80)
REVERT: L    4 LEU cc_start: 0.6934 (mp) cc_final: 0.6533 (mp)
REVERT: L   70 ASP cc_start: 0.8793 (t0) cc_final: 0.8455 (t0)
REVERT: L   71 PHE cc_start: 0.7392 (m-80) cc_final: 0.6987 (m-10)
REVERT: L   88 CYS cc_start: 0.4088 (p) cc_final: 0.3403 (p)
REVERT: L   98 PHE cc_start: 0.8307 (m-80) cc_final: 0.8061 (m-80)
  outliers start: 22
  outliers final: 11
  residues processed: 156
  average time/residue: 0.1760
  time to fit residues: 32.2893
Evaluate side-chains
  134 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   48 MET
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  100 MET
Chi-restraints excluded: chain H residue  108 THR
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   97 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0970
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.148766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.129236 restraints weight = 9595.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.132532 restraints weight = 5509.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.134563 restraints weight = 3815.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6903
moved from start:          0.5506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3471  Z= 0.251
  Angle     :  0.768   5.678   4718  Z= 0.414
  Chirality :  0.051   0.355    539
  Planarity :  0.006   0.055    592
  Dihedral  :  6.875  33.609    559
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 17.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  7.10 %
    Allowed  : 19.67 %
    Favored  : 73.22 %
  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: -1.30 (0.39), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.52 (0.39), residues: 166
  loop : -1.10 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 104 
 HIS   0.004   0.001   HIS A 207 
 PHE   0.020   0.003   PHE A  65 
 TYR   0.023   0.002   TYR A  91 
 ARG   0.006   0.001   ARG A 246 

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.8437 (t) cc_final: 0.8158 (m)
REVERT: A  128 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8661 (mm)
REVERT: H   31 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8140 (mt-10)
REVERT: H   58 ILE cc_start: 0.8681 (mm) cc_final: 0.8081 (pt)
REVERT: H   61 GLN cc_start: 0.8331 (tt0) cc_final: 0.7905 (pm20)
REVERT: H   72 ASP cc_start: 0.9107 (t0) cc_final: 0.8788 (t70)
REVERT: L    4 LEU cc_start: 0.7102 (mp) cc_final: 0.6713 (mp)
REVERT: L   70 ASP cc_start: 0.8777 (t0) cc_final: 0.8510 (t0)
REVERT: L   71 PHE cc_start: 0.7549 (m-80) cc_final: 0.7002 (m-10)
REVERT: L   88 CYS cc_start: 0.3294 (p) cc_final: 0.2843 (p)
  outliers start: 26
  outliers final: 19
  residues processed: 151
  average time/residue: 0.1523
  time to fit residues: 27.5895
Evaluate side-chains
  145 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue  100 MET
Chi-restraints excluded: chain H residue  108 THR
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   97 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 28 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 39 optimal weight:    0.1980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 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 = 0.4119 r_free = 0.4119 target = 0.145074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.124592 restraints weight = 9912.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.127587 restraints weight = 6037.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.129488 restraints weight = 4327.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7034
moved from start:          0.6117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3471  Z= 0.304
  Angle     :  0.767   8.957   4718  Z= 0.410
  Chirality :  0.051   0.336    539
  Planarity :  0.005   0.037    592
  Dihedral  :  6.058  20.661    559
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 20.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  9.29 %
    Allowed  : 20.49 %
    Favored  : 70.22 %
  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: -1.50 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.55 (0.39), residues: 165
  loop : -1.32 (0.38), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  64 
 HIS   0.014   0.003   HIS A 207 
 PHE   0.024   0.003   PHE A 168 
 TYR   0.019   0.002   TYR A 170 
 ARG   0.009   0.001   ARG A 190 

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 123
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.8464 (t) cc_final: 0.8222 (m)
REVERT: A  128 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8697 (mm)
REVERT: A  239 GLN cc_start: 0.8426 (mt0) cc_final: 0.8170 (mt0)
REVERT: H   31 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8039 (mt-10)
REVERT: H   58 ILE cc_start: 0.8703 (mm) cc_final: 0.8111 (pt)
REVERT: H   61 GLN cc_start: 0.8454 (tt0) cc_final: 0.7962 (pm20)
REVERT: H   72 ASP cc_start: 0.9236 (t0) cc_final: 0.8902 (t70)
REVERT: H   96 PHE cc_start: 0.7372 (m-80) cc_final: 0.7160 (m-80)
REVERT: H  100 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8366 (mtt)
REVERT: L   54 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7542 (ttm-80)
REVERT: L   70 ASP cc_start: 0.8829 (t0) cc_final: 0.8540 (t0)
REVERT: L   71 PHE cc_start: 0.7693 (m-80) cc_final: 0.7091 (m-10)
REVERT: L   87 TYR cc_start: 0.8482 (m-80) cc_final: 0.8188 (m-10)
REVERT: L   88 CYS cc_start: 0.3288 (p) cc_final: 0.2824 (p)
REVERT: L  105 ASP cc_start: 0.7096 (t0) cc_final: 0.6564 (t70)
  outliers start: 34
  outliers final: 22
  residues processed: 143
  average time/residue: 0.1474
  time to fit residues: 25.5376
Evaluate side-chains
  143 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 HIS
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  100 MET
Chi-restraints excluded: chain H residue  102 VAL
Chi-restraints excluded: chain H residue  108 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue   97 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 105 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 = 0.4121 r_free = 0.4121 target = 0.145212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.123979 restraints weight = 9788.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.127109 restraints weight = 5984.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.129079 restraints weight = 4282.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.6583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3471  Z= 0.270
  Angle     :  0.762  13.527   4718  Z= 0.394
  Chirality :  0.050   0.354    539
  Planarity :  0.005   0.039    592
  Dihedral  :  5.811  19.054    559
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 19.42
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.93 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  8.47 %
    Allowed  : 21.86 %
    Favored  : 69.67 %
  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: -1.70 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.60 (0.40), residues: 166
  loop : -1.55 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  64 
 HIS   0.002   0.001   HIS A 245 
 PHE   0.018   0.003   PHE A 168 
 TYR   0.021   0.002   TYR A  91 
 ARG   0.004   0.001   ARG H  66 

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.8494 (t) cc_final: 0.8272 (m)
REVERT: A  128 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8728 (mm)
REVERT: A  158 ARG cc_start: 0.7708 (mmt180) cc_final: 0.6891 (mmp-170)
REVERT: A  239 GLN cc_start: 0.8431 (mt0) cc_final: 0.8147 (mt0)
REVERT: H   48 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8587 (ptm)
REVERT: H   61 GLN cc_start: 0.8543 (tt0) cc_final: 0.7892 (pm20)
REVERT: H   72 ASP cc_start: 0.9261 (t0) cc_final: 0.8979 (t70)
REVERT: H  100 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8273 (mtt)
REVERT: H  105 GLN cc_start: 0.8304 (pm20) cc_final: 0.8047 (pm20)
REVERT: L   34 SER cc_start: 0.7857 (p) cc_final: 0.7616 (p)
REVERT: L   70 ASP cc_start: 0.8803 (t0) cc_final: 0.8534 (t0)
REVERT: L   71 PHE cc_start: 0.7741 (m-80) cc_final: 0.7130 (m-10)
REVERT: L   87 TYR cc_start: 0.8523 (m-80) cc_final: 0.8191 (m-10)
REVERT: L  105 ASP cc_start: 0.6966 (t0) cc_final: 0.6377 (t70)
  outliers start: 31
  outliers final: 21
  residues processed: 139
  average time/residue: 0.1522
  time to fit residues: 25.7667
Evaluate side-chains
  139 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 HIS
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   48 MET
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue  100 MET
Chi-restraints excluded: chain H residue  102 VAL
Chi-restraints excluded: chain H residue  108 THR
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   46 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 31 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H   3 GLN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.145982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.125895 restraints weight = 9629.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.128778 restraints weight = 5619.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.130008 restraints weight = 3831.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.6904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3471  Z= 0.258
  Angle     :  0.770  10.758   4718  Z= 0.395
  Chirality :  0.053   0.438    539
  Planarity :  0.005   0.050    592
  Dihedral  :  5.659  18.889    559
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 19.87
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.65 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  7.10 %
    Allowed  : 24.86 %
    Favored  : 68.03 %
  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: -1.78 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.70 (0.41), residues: 167
  loop : -1.57 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  64 
 HIS   0.003   0.001   HIS A 245 
 PHE   0.020   0.003   PHE A 106 
 TYR   0.021   0.002   TYR L  49 
 ARG   0.011   0.001   ARG H  38 

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.8398 (t) cc_final: 0.8022 (m)
REVERT: A  128 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8667 (mm)
REVERT: A  158 ARG cc_start: 0.7727 (mmt180) cc_final: 0.6683 (mmp-170)
REVERT: A  239 GLN cc_start: 0.8414 (mt0) cc_final: 0.8086 (mt0)
REVERT: H   31 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8214 (mt-10)
REVERT: H   48 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8494 (ptm)
REVERT: H   61 GLN cc_start: 0.8492 (tt0) cc_final: 0.7932 (pm20)
REVERT: H   72 ASP cc_start: 0.9301 (t0) cc_final: 0.8935 (t70)
REVERT: H  105 GLN cc_start: 0.8178 (pm20) cc_final: 0.7889 (pm20)
REVERT: L   70 ASP cc_start: 0.8809 (t0) cc_final: 0.8577 (t0)
REVERT: L   71 PHE cc_start: 0.7740 (m-80) cc_final: 0.7106 (m-10)
REVERT: L   87 TYR cc_start: 0.8380 (m-80) cc_final: 0.7919 (m-10)
REVERT: L  105 ASP cc_start: 0.6768 (t0) cc_final: 0.6109 (t70)
  outliers start: 26
  outliers final: 17
  residues processed: 140
  average time/residue: 0.1717
  time to fit residues: 28.5696
Evaluate side-chains
  136 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 HIS
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  215 ASP
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   48 MET
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue  108 THR
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 39 optimal weight:    0.0170
   chunk 38 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 16 optimal weight:    0.2980
   chunk 21 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 105 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 = 0.4148 r_free = 0.4148 target = 0.146853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.126990 restraints weight = 9448.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.129854 restraints weight = 5522.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.130983 restraints weight = 3668.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.7116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3471  Z= 0.237
  Angle     :  0.762   8.722   4718  Z= 0.391
  Chirality :  0.051   0.263    539
  Planarity :  0.006   0.069    592
  Dihedral  :  5.498  18.156    559
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 20.47
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.65 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 25.14 %
    Favored  : 68.85 %
  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: -1.89 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.74 (0.41), residues: 166
  loop : -1.66 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 104 
 HIS   0.003   0.001   HIS A 146 
 PHE   0.020   0.002   PHE A 106 
 TYR   0.021   0.002   TYR H  27 
 ARG   0.008   0.001   ARG A 246 

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.8388 (t) cc_final: 0.8168 (m)
REVERT: A  128 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8572 (mm)
REVERT: A  158 ARG cc_start: 0.7718 (mmt180) cc_final: 0.6768 (mmp-170)
REVERT: H   72 ASP cc_start: 0.9262 (t0) cc_final: 0.8835 (t70)
REVERT: H   81 GLU cc_start: 0.8494 (pp20) cc_final: 0.8132 (pp20)
REVERT: H  100 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.7664 (mmt)
REVERT: H  105 GLN cc_start: 0.8170 (pm20) cc_final: 0.7907 (pm20)
REVERT: L   70 ASP cc_start: 0.8741 (t0) cc_final: 0.8520 (t0)
REVERT: L   71 PHE cc_start: 0.7659 (m-80) cc_final: 0.7032 (m-10)
REVERT: L   87 TYR cc_start: 0.8257 (m-80) cc_final: 0.7969 (m-10)
REVERT: L  105 ASP cc_start: 0.6672 (t0) cc_final: 0.6004 (t70)
  outliers start: 22
  outliers final: 14
  residues processed: 135
  average time/residue: 0.1629
  time to fit residues: 26.3529
Evaluate side-chains
  127 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 HIS
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue  100 MET
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   46 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 234 ASN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.144591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.124345 restraints weight = 9503.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.127463 restraints weight = 5405.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.128475 restraints weight = 3600.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
moved from start:          0.7387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3471  Z= 0.291
  Angle     :  0.795   9.231   4718  Z= 0.410
  Chirality :  0.053   0.397    539
  Planarity :  0.006   0.061    592
  Dihedral  :  5.641  19.132    559
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 22.88
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.14 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 26.78 %
    Favored  : 67.21 %
  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: -2.00 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.74 (0.41), residues: 161
  loop : -1.79 (0.37), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  64 
 HIS   0.004   0.001   HIS A 245 
 PHE   0.020   0.003   PHE A 106 
 TYR   0.019   0.002   TYR A  91 
 ARG   0.007   0.001   ARG A 246 

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.8611 (t) cc_final: 0.8141 (m)
REVERT: A  128 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8717 (mm)
REVERT: A  158 ARG cc_start: 0.7693 (mmt180) cc_final: 0.6907 (mmp-170)
REVERT: A  239 GLN cc_start: 0.8535 (mt0) cc_final: 0.8211 (mt0)
REVERT: H   51 PHE cc_start: 0.8030 (t80) cc_final: 0.7798 (t80)
REVERT: H   72 ASP cc_start: 0.9220 (t0) cc_final: 0.8845 (t70)
REVERT: H  100 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.7709 (mmt)
REVERT: H  105 GLN cc_start: 0.8324 (pm20) cc_final: 0.8085 (pm20)
REVERT: L   70 ASP cc_start: 0.8909 (t0) cc_final: 0.8638 (t0)
REVERT: L   71 PHE cc_start: 0.7892 (m-80) cc_final: 0.7277 (m-10)
REVERT: L  105 ASP cc_start: 0.6780 (t0) cc_final: 0.6077 (t70)
  outliers start: 22
  outliers final: 15
  residues processed: 133
  average time/residue: 0.1681
  time to fit residues: 26.9739
Evaluate side-chains
  130 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  215 ASP
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue  100 MET
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 134 GLN
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.144880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.122876 restraints weight = 9651.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.126233 restraints weight = 5692.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.128407 restraints weight = 3985.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
moved from start:          0.7737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   3471  Z= 0.309
  Angle     :  0.852  10.099   4718  Z= 0.438
  Chirality :  0.052   0.300    539
  Planarity :  0.007   0.076    592
  Dihedral  :  5.770  20.154    559
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 23.18
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.64 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 27.60 %
    Favored  : 66.12 %
  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: -2.11 (0.39), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.93 (0.40), residues: 165
  loop : -1.79 (0.37), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 104 
 HIS   0.003   0.001   HIS A 245 
 PHE   0.023   0.003   PHE A 133 
 TYR   0.023   0.002   TYR H  27 
 ARG   0.013   0.002   ARG H  83 

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8609 (mm)
REVERT: A  158 ARG cc_start: 0.7788 (mmt180) cc_final: 0.6965 (mmp-170)
REVERT: H   23 LYS cc_start: 0.8674 (mtpp) cc_final: 0.8468 (mmmt)
REVERT: H   31 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8284 (tt0)
REVERT: H   51 PHE cc_start: 0.8066 (t80) cc_final: 0.7831 (t80)
REVERT: H   72 ASP cc_start: 0.9249 (t0) cc_final: 0.8895 (t70)
REVERT: H   81 GLU cc_start: 0.8476 (pp20) cc_final: 0.8096 (pp20)
REVERT: H  100 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.7700 (mmt)
REVERT: H  105 GLN cc_start: 0.8348 (pm20) cc_final: 0.8105 (pm20)
REVERT: L   70 ASP cc_start: 0.8799 (t0) cc_final: 0.8511 (t0)
REVERT: L   71 PHE cc_start: 0.7888 (m-80) cc_final: 0.7328 (m-10)
REVERT: L  105 ASP cc_start: 0.6555 (t0) cc_final: 0.5885 (t70)
  outliers start: 23
  outliers final: 17
  residues processed: 134
  average time/residue: 0.1689
  time to fit residues: 26.8593
Evaluate side-chains
  131 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  215 ASP
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  100 MET
Chi-restraints excluded: chain H residue  108 THR
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   27 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    0.0170
   chunk 28 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  30 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.146731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.124858 restraints weight = 9446.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.128089 restraints weight = 5711.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.130049 restraints weight = 4074.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.7924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   3471  Z= 0.268
  Angle     :  0.829  10.670   4718  Z= 0.423
  Chirality :  0.051   0.260    539
  Planarity :  0.007   0.059    592
  Dihedral  :  5.590  18.637    559
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 20.47
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.37 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 29.78 %
    Favored  : 64.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.15 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.71 (0.41), residues: 157
  loop : -1.99 (0.36), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 104 
 HIS   0.004   0.001   HIS A  66 
 PHE   0.031   0.003   PHE A  65 
 TYR   0.018   0.002   TYR H  27 
 ARG   0.011   0.002   ARG H  83 

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8638 (mm)
REVERT: A  158 ARG cc_start: 0.7888 (mmt180) cc_final: 0.7449 (mmp-170)
REVERT: H   31 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8330 (tt0)
REVERT: H   38 ARG cc_start: 0.7881 (mtp85) cc_final: 0.7544 (mtp85)
REVERT: H   51 PHE cc_start: 0.8058 (t80) cc_final: 0.7842 (t80)
REVERT: H   72 ASP cc_start: 0.9277 (t0) cc_final: 0.8954 (t70)
REVERT: H  105 GLN cc_start: 0.8329 (pm20) cc_final: 0.8075 (pm20)
REVERT: L   70 ASP cc_start: 0.8762 (t0) cc_final: 0.8490 (t0)
REVERT: L   71 PHE cc_start: 0.7875 (m-80) cc_final: 0.7314 (m-10)
REVERT: L  105 ASP cc_start: 0.6357 (t0) cc_final: 0.5685 (t70)
  outliers start: 20
  outliers final: 18
  residues processed: 135
  average time/residue: 0.1607
  time to fit residues: 25.9943
Evaluate side-chains
  132 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  215 ASP
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0060
   chunk 38 optimal weight:    0.0970
   chunk 9 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0970
   chunk 8 optimal weight:    4.9990
   overall best weight:    0.3392

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

Flipped N/Q/H residues before XYZ refinement:
A 239 GLN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  61 GLN
H 105 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.149200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.127675 restraints weight = 9528.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.130823 restraints weight = 5830.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.132866 restraints weight = 4162.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6951
moved from start:          0.8095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   3471  Z= 0.234
  Angle     :  0.808  11.656   4718  Z= 0.412
  Chirality :  0.051   0.229    539
  Planarity :  0.006   0.067    592
  Dihedral  :  5.349  28.213    559
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 18.67
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.13 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 30.60 %
    Favored  : 65.03 %
  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: -2.07 (0.41), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.61 (0.43), residues: 155
  loop : -1.96 (0.37), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 104 
 HIS   0.002   0.001   HIS A  66 
 PHE   0.021   0.002   PHE H  63 
 TYR   0.015   0.001   TYR L  32 
 ARG   0.011   0.001   ARG H  83 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2090.95 seconds
wall clock time: 38 minutes 2.16 seconds (2282.16 seconds total)