Starting phenix.real_space_refine
on Fri May  9 18:39:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8swh_40814/05_2025/8swh_40814.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8swh_40814/05_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_40814/05_2025/8swh_40814.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8swh_40814/05_2025/8swh_40814.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8swh_40814/05_2025/8swh_40814.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8swh_40814/05_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-5687/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: 3.98, per 1000 atoms: 1.17
  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: 0.98
  Conformation dependent library (CDL) restraints added in 404.0 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: 0.55
  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: 0.88

  Time building geometry restraints manager: 1.14 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:             7.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.450
  Find NCS groups from input model:        0.030
  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:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.900
-------------------------------------------------------------------------------
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      :  0.022   0.149   3480  Z= 1.106
  Angle     :  1.938  12.361   4741  Z= 1.292
  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 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.07864 (    3)
  link_NAG-ASN         : angle       2.13446 (    9)
  link_BETA1-4         : bond        0.06719 (    2)
  link_BETA1-4         : angle       4.86255 (    6)
  hydrogen bonds       : bond        0.14107 (   97)
  hydrogen bonds       : angle       8.05148 (  294)
  SS BOND              : bond        0.01680 (    4)
  SS BOND              : angle       1.58437 (    8)
  covalent geometry    : bond        0.02134 ( 3471)
  covalent geometry    : angle       1.93121 ( 4718)

*********************** 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  : 0.383 
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: 0.1811
  time to fit residues: 41.8034
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  : 0.353 
-------------------------------------------------------------------------------
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   3480  Z= 0.195
  Angle     :  0.865   7.936   4741  Z= 0.459
  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 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00284 (    3)
  link_NAG-ASN         : angle       3.68517 (    9)
  link_BETA1-4         : bond        0.00340 (    2)
  link_BETA1-4         : angle       3.34699 (    6)
  hydrogen bonds       : bond        0.05330 (   97)
  hydrogen bonds       : angle       6.46296 (  294)
  SS BOND              : bond        0.00128 (    4)
  SS BOND              : angle       2.23182 (    8)
  covalent geometry    : bond        0.00444 ( 3471)
  covalent geometry    : angle       0.83839 ( 4718)

*********************** 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  : 0.398 
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: 0.1797
  time to fit residues: 32.9479
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:    3.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.4147 r_free = 0.4147 target = 0.147098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.127314 restraints weight = 9680.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.130528 restraints weight = 5569.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.132605 restraints weight = 3882.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6951
moved from start:          0.5645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3480  Z= 0.194
  Angle     :  0.795   5.821   4741  Z= 0.423
  Chirality :  0.052   0.365    539
  Planarity :  0.006   0.061    592
  Dihedral  :  6.581  26.688    559
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 17.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  7.38 %
    Allowed  : 19.13 %
    Favored  : 73.50 %
  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: -1.35 (0.39), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.47 (0.39), residues: 167
  loop : -1.21 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 258 
 HIS   0.006   0.001   HIS A  66 
 PHE   0.019   0.003   PHE A 168 
 TYR   0.026   0.002   TYR A  91 
 ARG   0.009   0.001   ARG A 246 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00595 (    3)
  link_NAG-ASN         : angle       2.95049 (    9)
  link_BETA1-4         : bond        0.00395 (    2)
  link_BETA1-4         : angle       2.44279 (    6)
  hydrogen bonds       : bond        0.04769 (   97)
  hydrogen bonds       : angle       6.06879 (  294)
  SS BOND              : bond        0.00307 (    4)
  SS BOND              : angle       1.12298 (    8)
  covalent geometry    : bond        0.00431 ( 3471)
  covalent geometry    : angle       0.77986 ( 4718)

*********************** 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
  167 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 140
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.8440 (t) cc_final: 0.8164 (m)
REVERT: A  128 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8608 (mm)
REVERT: H   31 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8054 (mt-10)
REVERT: H   58 ILE cc_start: 0.8692 (mm) cc_final: 0.8095 (pt)
REVERT: H   61 GLN cc_start: 0.8364 (tt0) cc_final: 0.7918 (pm20)
REVERT: H   72 ASP cc_start: 0.9149 (t0) cc_final: 0.8826 (t70)
REVERT: L    4 LEU cc_start: 0.7133 (mp) cc_final: 0.6733 (mp)
REVERT: L   70 ASP cc_start: 0.8794 (t0) cc_final: 0.8513 (t0)
REVERT: L   71 PHE cc_start: 0.7611 (m-80) cc_final: 0.7039 (m-10)
REVERT: L   88 CYS cc_start: 0.3202 (p) cc_final: 0.2747 (p)
REVERT: L   98 PHE cc_start: 0.8305 (m-80) cc_final: 0.8102 (m-80)
  outliers start: 27
  outliers final: 20
  residues processed: 150
  average time/residue: 0.1680
  time to fit residues: 29.9014
Evaluate side-chains
  147 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 HIS
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   29 LEU
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
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:    0.7980
   chunk 8 optimal weight:    0.3980
   chunk 28 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.4131 r_free = 0.4131 target = 0.145919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.125047 restraints weight = 9639.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.128165 restraints weight = 5686.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.130161 restraints weight = 4039.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.6116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3480  Z= 0.180
  Angle     :  0.760   8.864   4741  Z= 0.398
  Chirality :  0.051   0.377    539
  Planarity :  0.005   0.037    592
  Dihedral  :  5.810  20.851    559
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 18.82
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.68 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  8.47 %
    Allowed  : 21.04 %
    Favored  : 70.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.60 (0.39), residues: 166
  loop : -1.25 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  64 
 HIS   0.005   0.001   HIS A 207 
 PHE   0.018   0.003   PHE A 106 
 TYR   0.018   0.002   TYR A 170 
 ARG   0.005   0.001   ARG A 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00582 (    3)
  link_NAG-ASN         : angle       2.91320 (    9)
  link_BETA1-4         : bond        0.00200 (    2)
  link_BETA1-4         : angle       2.16011 (    6)
  hydrogen bonds       : bond        0.04346 (   97)
  hydrogen bonds       : angle       5.76122 (  294)
  SS BOND              : bond        0.00241 (    4)
  SS BOND              : angle       0.86297 (    8)
  covalent geometry    : bond        0.00409 ( 3471)
  covalent geometry    : angle       0.74677 ( 4718)

*********************** 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
  160 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.8427 (t) cc_final: 0.8145 (m)
REVERT: A  128 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8739 (mm)
REVERT: A  177 MET cc_start: 0.6170 (OUTLIER) cc_final: 0.5907 (mmp)
REVERT: H   31 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8017 (mt-10)
REVERT: H   61 GLN cc_start: 0.8461 (tt0) cc_final: 0.7946 (pm20)
REVERT: H   72 ASP cc_start: 0.9221 (t0) cc_final: 0.8919 (t70)
REVERT: L   34 SER cc_start: 0.7783 (p) cc_final: 0.7561 (p)
REVERT: L   70 ASP cc_start: 0.8802 (t0) cc_final: 0.8508 (t0)
REVERT: L   71 PHE cc_start: 0.7655 (m-80) cc_final: 0.7081 (m-10)
REVERT: L   87 TYR cc_start: 0.8460 (m-80) cc_final: 0.8196 (m-10)
REVERT: L   88 CYS cc_start: 0.3269 (p) cc_final: 0.2808 (p)
REVERT: L   98 PHE cc_start: 0.8290 (m-80) cc_final: 0.7965 (m-80)
REVERT: L  105 ASP cc_start: 0.7143 (t0) cc_final: 0.6613 (t70)
  outliers start: 31
  outliers final: 20
  residues processed: 145
  average time/residue: 0.1414
  time to fit residues: 24.9253
Evaluate side-chains
  143 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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  177 MET
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   29 LEU
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  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   97 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   chunk 33 optimal weight:    0.4980
   chunk 13 optimal weight:    0.5980
   chunk 3 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.4144 r_free = 0.4144 target = 0.146949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.125872 restraints weight = 9687.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.128866 restraints weight = 6042.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.130876 restraints weight = 4291.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6990
moved from start:          0.6533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3480  Z= 0.161
  Angle     :  0.744   8.244   4741  Z= 0.387
  Chirality :  0.051   0.394    539
  Planarity :  0.005   0.037    592
  Dihedral  :  5.579  18.976    559
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 19.12
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.42 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  6.83 %
    Allowed  : 23.22 %
    Favored  : 69.95 %
  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: -1.73 (0.39), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.75 (0.39), residues: 167
  loop : -1.45 (0.37), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 104 
 HIS   0.002   0.001   HIS A 245 
 PHE   0.017   0.003   PHE A 106 
 TYR   0.020   0.002   TYR A  91 
 ARG   0.008   0.001   ARG L  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00191 (    3)
  link_NAG-ASN         : angle       3.11843 (    9)
  link_BETA1-4         : bond        0.00370 (    2)
  link_BETA1-4         : angle       1.87459 (    6)
  hydrogen bonds       : bond        0.04303 (   97)
  hydrogen bonds       : angle       5.67950 (  294)
  SS BOND              : bond        0.00239 (    4)
  SS BOND              : angle       0.72363 (    8)
  covalent geometry    : bond        0.00367 ( 3471)
  covalent geometry    : angle       0.72923 ( 4718)

*********************** 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
  152 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 0.402 
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: 0.8872 (OUTLIER) cc_final: 0.8611 (mm)
REVERT: A  158 ARG cc_start: 0.7712 (mmt180) cc_final: 0.6858 (mmp-170)
REVERT: A  160 TYR cc_start: 0.8395 (p90) cc_final: 0.8127 (p90)
REVERT: H   31 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8092 (mt-10)
REVERT: H   61 GLN cc_start: 0.8452 (tt0) cc_final: 0.7837 (pm20)
REVERT: H   72 ASP cc_start: 0.9262 (t0) cc_final: 0.8841 (t70)
REVERT: H   86 ASP cc_start: 0.8839 (m-30) cc_final: 0.8628 (m-30)
REVERT: H  105 GLN cc_start: 0.8266 (pm20) cc_final: 0.7728 (pm20)
REVERT: L   34 SER cc_start: 0.7737 (p) cc_final: 0.7509 (p)
REVERT: L   70 ASP cc_start: 0.8755 (t0) cc_final: 0.8474 (t0)
REVERT: L   71 PHE cc_start: 0.7672 (m-80) cc_final: 0.7121 (m-10)
REVERT: L   87 TYR cc_start: 0.8432 (m-80) cc_final: 0.8105 (m-10)
REVERT: L  105 ASP cc_start: 0.6781 (t0) cc_final: 0.6243 (t70)
  outliers start: 25
  outliers final: 18
  residues processed: 140
  average time/residue: 0.1586
  time to fit residues: 26.6162
Evaluate side-chains
  140 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
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   29 LEU
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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 32 optimal weight:    0.3980
   chunk 29 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0030
   chunk 17 optimal weight:    7.9990
   overall best weight:    0.4390

-------------------------------------------------------------------------------
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 ** 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 = 0.4170 r_free = 0.4170 target = 0.148463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.126914 restraints weight = 9748.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.130197 restraints weight = 5763.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.132268 restraints weight = 4053.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6960
moved from start:          0.6833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3480  Z= 0.145
  Angle     :  0.763   9.232   4741  Z= 0.391
  Chirality :  0.051   0.371    539
  Planarity :  0.005   0.049    592
  Dihedral  :  5.413  17.917    559
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 17.16
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.67 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 25.14 %
    Favored  : 69.40 %
  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: -1.76 (0.39), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.74 (0.40), residues: 167
  loop : -1.50 (0.37), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 104 
 HIS   0.003   0.001   HIS A 245 
 PHE   0.017   0.002   PHE H  96 
 TYR   0.024   0.001   TYR A 170 
 ARG   0.006   0.001   ARG H  66 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00192 (    3)
  link_NAG-ASN         : angle       3.75486 (    9)
  link_BETA1-4         : bond        0.00334 (    2)
  link_BETA1-4         : angle       1.62517 (    6)
  hydrogen bonds       : bond        0.04194 (   97)
  hydrogen bonds       : angle       5.59233 (  294)
  SS BOND              : bond        0.00182 (    4)
  SS BOND              : angle       1.57670 (    8)
  covalent geometry    : bond        0.00330 ( 3471)
  covalent geometry    : angle       0.74223 ( 4718)

*********************** 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
  150 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8543 (mm)
REVERT: A  158 ARG cc_start: 0.7649 (mmt180) cc_final: 0.6681 (mmp-170)
REVERT: A  160 TYR cc_start: 0.8441 (p90) cc_final: 0.8178 (p90)
REVERT: A  239 GLN cc_start: 0.8287 (mt0) cc_final: 0.8071 (mt0)
REVERT: H   27 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.8227 (m-10)
REVERT: H   31 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8194 (mt-10)
REVERT: H   61 GLN cc_start: 0.8427 (tt0) cc_final: 0.7832 (pm20)
REVERT: H   72 ASP cc_start: 0.9229 (t0) cc_final: 0.8833 (t70)
REVERT: H  105 GLN cc_start: 0.8293 (pm20) cc_final: 0.8046 (pm20)
REVERT: L   70 ASP cc_start: 0.8770 (t0) cc_final: 0.8540 (t0)
REVERT: L   71 PHE cc_start: 0.7680 (m-80) cc_final: 0.7087 (m-10)
REVERT: L   87 TYR cc_start: 0.8317 (m-80) cc_final: 0.8068 (m-10)
REVERT: L  105 ASP cc_start: 0.6516 (t0) cc_final: 0.5900 (t70)
  outliers start: 20
  outliers final: 15
  residues processed: 140
  average time/residue: 0.1629
  time to fit residues: 27.5180
Evaluate side-chains
  135 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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  110 LEU
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    3 GLN
Chi-restraints excluded: chain H residue   27 TYR
Chi-restraints excluded: chain H residue   29 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 38 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0060
   chunk 3 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0970
   chunk 21 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 6 optimal weight:    0.3980
   overall best weight:    0.4194

-------------------------------------------------------------------------------
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**
** 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 = 0.4151 r_free = 0.4151 target = 0.146927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.126252 restraints weight = 9574.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.129274 restraints weight = 5900.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.131243 restraints weight = 4243.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.7075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3480  Z= 0.144
  Angle     :  0.745   9.169   4741  Z= 0.384
  Chirality :  0.050   0.248    539
  Planarity :  0.005   0.039    592
  Dihedral  :  5.290  19.401    559
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 18.97
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.40 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 27.05 %
    Favored  : 66.94 %
  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: -0.77 (0.40), residues: 167
  loop : -1.49 (0.37), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 258 
 HIS   0.002   0.001   HIS A 146 
 PHE   0.021   0.002   PHE A 106 
 TYR   0.013   0.001   TYR A  91 
 ARG   0.018   0.001   ARG A 246 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00044 (    3)
  link_NAG-ASN         : angle       2.29342 (    9)
  link_BETA1-4         : bond        0.00469 (    2)
  link_BETA1-4         : angle       1.60480 (    6)
  hydrogen bonds       : bond        0.04170 (   97)
  hydrogen bonds       : angle       5.55699 (  294)
  SS BOND              : bond        0.00196 (    4)
  SS BOND              : angle       0.74950 (    8)
  covalent geometry    : bond        0.00328 ( 3471)
  covalent geometry    : angle       0.73692 ( 4718)

*********************** 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
  148 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8551 (mm)
REVERT: A  158 ARG cc_start: 0.7631 (mmt180) cc_final: 0.6886 (mmp-170)
REVERT: A  160 TYR cc_start: 0.8379 (p90) cc_final: 0.8153 (p90)
REVERT: H   31 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8102 (mt-10)
REVERT: H   61 GLN cc_start: 0.8427 (tt0) cc_final: 0.7855 (pm20)
REVERT: H   72 ASP cc_start: 0.9232 (t0) cc_final: 0.8857 (t70)
REVERT: H  105 GLN cc_start: 0.8273 (pm20) cc_final: 0.8017 (pm20)
REVERT: L    5 THR cc_start: 0.7562 (p) cc_final: 0.7302 (p)
REVERT: L   70 ASP cc_start: 0.8717 (t0) cc_final: 0.8474 (t0)
REVERT: L   71 PHE cc_start: 0.7597 (m-80) cc_final: 0.7048 (m-10)
REVERT: L   87 TYR cc_start: 0.8146 (m-80) cc_final: 0.7828 (m-10)
REVERT: L  105 ASP cc_start: 0.6296 (t0) cc_final: 0.5652 (t70)
  outliers start: 22
  outliers final: 15
  residues processed: 136
  average time/residue: 0.1529
  time to fit residues: 25.0070
Evaluate side-chains
  134 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
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  110 LEU
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue   81 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
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:    0.0470
   chunk 31 optimal weight:    6.9990
   chunk 11 optimal weight:    0.5980
   chunk 26 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 36 optimal weight:    0.3980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8082

-------------------------------------------------------------------------------
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**
** 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**
** L   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 = 0.4123 r_free = 0.4123 target = 0.144945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.123978 restraints weight = 9477.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.127103 restraints weight = 5603.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.129087 restraints weight = 3958.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7025
moved from start:          0.7225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3480  Z= 0.172
  Angle     :  0.761  11.061   4741  Z= 0.392
  Chirality :  0.050   0.250    539
  Planarity :  0.005   0.053    592
  Dihedral  :  5.406  19.717    559
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 20.77
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.65 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 28.42 %
    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: -1.86 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.75 (0.42), residues: 162
  loop : -1.61 (0.37), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A  64 
 HIS   0.004   0.001   HIS A 245 
 PHE   0.021   0.003   PHE A 106 
 TYR   0.018   0.002   TYR A  91 
 ARG   0.006   0.001   ARG H  66 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00117 (    3)
  link_NAG-ASN         : angle       1.95110 (    9)
  link_BETA1-4         : bond        0.00318 (    2)
  link_BETA1-4         : angle       1.66399 (    6)
  hydrogen bonds       : bond        0.04164 (   97)
  hydrogen bonds       : angle       5.53050 (  294)
  SS BOND              : bond        0.00215 (    4)
  SS BOND              : angle       0.85904 (    8)
  covalent geometry    : bond        0.00403 ( 3471)
  covalent geometry    : angle       0.75469 ( 4718)

*********************** 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
  140 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.376 
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: 0.8831 (OUTLIER) cc_final: 0.8554 (mm)
REVERT: A  158 ARG cc_start: 0.7688 (mmt180) cc_final: 0.6821 (mmp-170)
REVERT: A  239 GLN cc_start: 0.8287 (mt0) cc_final: 0.8060 (mt0)
REVERT: H   31 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8120 (mt-10)
REVERT: H   72 ASP cc_start: 0.9243 (t0) cc_final: 0.8879 (t70)
REVERT: H  100 MET cc_start: 0.8372 (mtt) cc_final: 0.8158 (mmt)
REVERT: H  105 GLN cc_start: 0.8339 (pm20) cc_final: 0.8099 (pm20)
REVERT: L   36 LEU cc_start: 0.9067 (mp) cc_final: 0.8713 (mt)
REVERT: L   70 ASP cc_start: 0.8671 (t0) cc_final: 0.8453 (t0)
REVERT: L   71 PHE cc_start: 0.7626 (m-80) cc_final: 0.7085 (m-10)
REVERT: L  105 ASP cc_start: 0.6190 (t0) cc_final: 0.5569 (t70)
  outliers start: 20
  outliers final: 14
  residues processed: 131
  average time/residue: 0.1453
  time to fit residues: 23.0203
Evaluate side-chains
  132 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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  234 ASN
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue   29 LEU
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   81 GLU
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   27 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0170
   chunk 13 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.7218

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  61 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.145603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.124591 restraints weight = 9595.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.127742 restraints weight = 5779.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.129831 restraints weight = 4058.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7020
moved from start:          0.7410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   3480  Z= 0.169
  Angle     :  0.800  10.412   4741  Z= 0.403
  Chirality :  0.051   0.342    539
  Planarity :  0.005   0.045    592
  Dihedral  :  5.444  19.720    559
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 19.57
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.64 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 29.23 %
    Favored  : 65.85 %
  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: -1.95 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.75 (0.42), residues: 162
  loop : -1.73 (0.36), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  64 
 HIS   0.002   0.001   HIS A 245 
 PHE   0.029   0.003   PHE H  51 
 TYR   0.014   0.001   TYR A  91 
 ARG   0.007   0.001   ARG H  66 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00191 (    3)
  link_NAG-ASN         : angle       4.85978 (    9)
  link_BETA1-4         : bond        0.00367 (    2)
  link_BETA1-4         : angle       1.59498 (    6)
  hydrogen bonds       : bond        0.04255 (   97)
  hydrogen bonds       : angle       5.57816 (  294)
  SS BOND              : bond        0.00274 (    4)
  SS BOND              : angle       0.87633 (    8)
  covalent geometry    : bond        0.00397 ( 3471)
  covalent geometry    : angle       0.77081 ( 4718)

*********************** 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
  140 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8637 (mm)
REVERT: A  158 ARG cc_start: 0.7701 (mmt180) cc_final: 0.6775 (mmp-170)
REVERT: A  239 GLN cc_start: 0.8317 (mt0) cc_final: 0.7839 (mt0)
REVERT: H   31 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8182 (mt-10)
REVERT: H   72 ASP cc_start: 0.9246 (t0) cc_final: 0.8887 (t70)
REVERT: H   86 ASP cc_start: 0.8640 (m-30) cc_final: 0.8327 (m-30)
REVERT: H  105 GLN cc_start: 0.8326 (pm20) cc_final: 0.8085 (pm20)
REVERT: L   36 LEU cc_start: 0.9057 (mp) cc_final: 0.8802 (mt)
REVERT: L   54 ARG cc_start: 0.7448 (mtp180) cc_final: 0.7181 (ttm170)
REVERT: L   70 ASP cc_start: 0.8719 (t0) cc_final: 0.8499 (t0)
REVERT: L   71 PHE cc_start: 0.7677 (m-80) cc_final: 0.7123 (m-10)
REVERT: L  105 ASP cc_start: 0.5964 (t0) cc_final: 0.5293 (t70)
  outliers start: 18
  outliers final: 12
  residues processed: 132
  average time/residue: 0.1546
  time to fit residues: 24.7216
Evaluate side-chains
  127 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
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  247 SER
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   20 VAL
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 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0770
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  61 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.146004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.124575 restraints weight = 9422.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.127793 restraints weight = 5646.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.129851 restraints weight = 4013.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.7594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   3480  Z= 0.170
  Angle     :  0.822  10.145   4741  Z= 0.421
  Chirality :  0.052   0.306    539
  Planarity :  0.005   0.049    592
  Dihedral  :  5.526  24.980    559
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 19.57
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.37 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 30.87 %
    Favored  : 65.30 %
  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: -2.03 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.80 (0.41), residues: 165
  loop : -1.80 (0.36), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 104 
 HIS   0.019   0.002   HIS A  66 
 PHE   0.025   0.003   PHE H  63 
 TYR   0.025   0.002   TYR H 100H
 ARG   0.008   0.001   ARG H  66 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00241 (    3)
  link_NAG-ASN         : angle       3.57891 (    9)
  link_BETA1-4         : bond        0.00323 (    2)
  link_BETA1-4         : angle       1.54374 (    6)
  hydrogen bonds       : bond        0.04210 (   97)
  hydrogen bonds       : angle       5.55102 (  294)
  SS BOND              : bond        0.00420 (    4)
  SS BOND              : angle       0.94953 (    8)
  covalent geometry    : bond        0.00401 ( 3471)
  covalent geometry    : angle       0.80605 ( 4718)

********************** 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
  133 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 HIS cc_start: 0.7658 (t70) cc_final: 0.7280 (t70)
REVERT: A  158 ARG cc_start: 0.7726 (mmt180) cc_final: 0.6755 (mmp-170)
REVERT: A  239 GLN cc_start: 0.8277 (mt0) cc_final: 0.7836 (mt0)
REVERT: H   31 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8156 (mt-10)
REVERT: H   72 ASP cc_start: 0.9256 (t0) cc_final: 0.8876 (t70)
REVERT: H  100 MET cc_start: 0.8392 (mtt) cc_final: 0.8128 (mmt)
REVERT: H  105 GLN cc_start: 0.8336 (pm20) cc_final: 0.8100 (pm20)
REVERT: L   36 LEU cc_start: 0.9114 (mp) cc_final: 0.8863 (mt)
REVERT: L   54 ARG cc_start: 0.7398 (mtp180) cc_final: 0.7170 (ttm170)
REVERT: L   70 ASP cc_start: 0.8706 (t0) cc_final: 0.8500 (t0)
REVERT: L   71 PHE cc_start: 0.7728 (m-80) cc_final: 0.7147 (m-10)
REVERT: L  105 ASP cc_start: 0.5792 (t0) cc_final: 0.5172 (t70)
  outliers start: 14
  outliers final: 13
  residues processed: 127
  average time/residue: 0.1522
  time to fit residues: 23.1408
Evaluate side-chains
  130 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
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  208 THR
Chi-restraints excluded: chain A residue  215 ASP
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue   29 LEU
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   97 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 115 GLN ** 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**
L  30 ASN

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 = 0.144653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.122824 restraints weight = 9695.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.126099 restraints weight = 5714.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.128082 restraints weight = 4034.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
moved from start:          0.7857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.103   3480  Z= 0.206
  Angle     :  0.847  10.841   4741  Z= 0.433
  Chirality :  0.053   0.291    539
  Planarity :  0.006   0.071    592
  Dihedral  :  5.836  27.669    559
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 20.92
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.62 %
    Favored  : 91.13 %
  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: -2.32 (0.39), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.87 (0.41), residues: 164
  loop : -2.10 (0.36), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 104 
 HIS   0.003   0.001   HIS A 245 
 PHE   0.022   0.004   PHE A 133 
 TYR   0.022   0.002   TYR H 100H
 ARG   0.010   0.001   ARG H  83 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00197 (    3)
  link_NAG-ASN         : angle       2.91251 (    9)
  link_BETA1-4         : bond        0.00342 (    2)
  link_BETA1-4         : angle       1.67317 (    6)
  hydrogen bonds       : bond        0.04977 (   97)
  hydrogen bonds       : angle       5.77049 (  294)
  SS BOND              : bond        0.00346 (    4)
  SS BOND              : angle       1.04342 (    8)
  covalent geometry    : bond        0.00514 ( 3471)
  covalent geometry    : angle       0.83588 ( 4718)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2208.69 seconds
wall clock time: 39 minutes 15.20 seconds (2355.20 seconds total)