Starting phenix.real_space_refine
on Sat Apr 26 21:08:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8swh_40814/04_2025/8swh_40814.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8swh_40814/04_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_40814/04_2025/8swh_40814.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8swh_40814/04_2025/8swh_40814.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8swh_40814/04_2025/8swh_40814.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8swh_40814/04_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-5669/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: 6.29, per 1000 atoms: 1.86
  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: 1.10
  Conformation dependent library (CDL) restraints added in 398.2 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: 0.47
  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: 0.90

  Time building geometry restraints manager: 1.13 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:             12.680
  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:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     17.130
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.080
-------------------------------------------------------------------------------
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  : 0.394 
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: 0.1839
  time to fit residues: 42.3636
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  : 0.370 
-------------------------------------------------------------------------------
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 = 33)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.131454 restraints weight = 9303.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.134630 restraints weight = 5372.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.136660 restraints weight = 3681.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6782
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       3.68518 (    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  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ASP cc_start: 0.8131 (t0) cc_final: 0.7762 (t0)
REVERT: A   82 PRO cc_start: 0.8545 (Cg_endo) cc_final: 0.8209 (Cg_exo)
REVERT: A   83 VAL cc_start: 0.8687 (t) cc_final: 0.8326 (m)
REVERT: H   38 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7754 (mtm180)
REVERT: H   48 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7523 (mtp)
REVERT: H   58 ILE cc_start: 0.8649 (mm) cc_final: 0.7949 (pt)
REVERT: H   61 GLN cc_start: 0.8411 (tt0) cc_final: 0.7932 (pm20)
REVERT: H   72 ASP cc_start: 0.8993 (t0) cc_final: 0.8493 (t70)
REVERT: H   96 PHE cc_start: 0.7358 (m-10) cc_final: 0.6375 (m-80)
REVERT: L    4 LEU cc_start: 0.6935 (mp) cc_final: 0.6534 (mp)
REVERT: L   70 ASP cc_start: 0.8794 (t0) cc_final: 0.8456 (t0)
REVERT: L   71 PHE cc_start: 0.7393 (m-80) cc_final: 0.6988 (m-10)
REVERT: L   88 CYS cc_start: 0.4089 (p) cc_final: 0.3403 (p)
REVERT: L   98 PHE cc_start: 0.8306 (m-80) cc_final: 0.8060 (m-80)
  outliers start: 22
  outliers final: 11
  residues processed: 156
  average time/residue: 0.1771
  time to fit residues: 32.5178
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  : 0.361 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4156 r_free = 0.4156 target = 0.147849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.128218 restraints weight = 9470.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.131439 restraints weight = 5537.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.133366 restraints weight = 3870.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6928
moved from start:          0.5560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3480  Z= 0.189
  Angle     :  0.794   6.248   4741  Z= 0.421
  Chirality :  0.051   0.290    539
  Planarity :  0.006   0.061    592
  Dihedral  :  6.764  31.099    559
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 17.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  7.38 %
    Allowed  : 19.40 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.39), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.52 (0.39), residues: 166
  loop : -1.13 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 104 
 HIS   0.004   0.001   HIS A  66 
 PHE   0.019   0.003   PHE A  65 
 TYR   0.024   0.002   TYR A  91 
 ARG   0.008   0.001   ARG A 246 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00931 (    3)
  link_NAG-ASN         : angle       3.14976 (    9)
  link_BETA1-4         : bond        0.00288 (    2)
  link_BETA1-4         : angle       2.62581 (    6)
  hydrogen bonds       : bond        0.04812 (   97)
  hydrogen bonds       : angle       6.10830 (  294)
  SS BOND              : bond        0.00304 (    4)
  SS BOND              : angle       1.12924 (    8)
  covalent geometry    : bond        0.00419 ( 3471)
  covalent geometry    : angle       0.77745 ( 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
  169 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 142
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.8454 (t) cc_final: 0.8176 (m)
REVERT: A  128 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8667 (mm)
REVERT: H   31 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8190 (mt-10)
REVERT: H   58 ILE cc_start: 0.8693 (mm) cc_final: 0.8091 (pt)
REVERT: H   61 GLN cc_start: 0.8362 (tt0) cc_final: 0.7921 (pm20)
REVERT: H   72 ASP cc_start: 0.9127 (t0) cc_final: 0.8803 (t70)
REVERT: L    4 LEU cc_start: 0.7091 (mp) cc_final: 0.6697 (mp)
REVERT: L   70 ASP cc_start: 0.8790 (t0) cc_final: 0.8516 (t0)
REVERT: L   71 PHE cc_start: 0.7608 (m-80) cc_final: 0.7050 (m-10)
REVERT: L   88 CYS cc_start: 0.3317 (p) cc_final: 0.2870 (p)
REVERT: L   98 PHE cc_start: 0.8286 (m-80) cc_final: 0.8086 (m-80)
  outliers start: 27
  outliers final: 20
  residues processed: 153
  average time/residue: 0.1648
  time to fit residues: 30.0147
Evaluate side-chains
  148 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   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
Chi-restraints excluded: chain L residue   97 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4145 r_free = 0.4145 target = 0.147435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.126544 restraints weight = 9832.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.129761 restraints weight = 5821.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.131827 restraints weight = 4098.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6972
moved from start:          0.6062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3480  Z= 0.169
  Angle     :  0.744   8.337   4741  Z= 0.393
  Chirality :  0.051   0.396    539
  Planarity :  0.005   0.038    592
  Dihedral  :  5.836  21.076    559
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 19.12
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.68 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  7.92 %
    Allowed  : 22.13 %
    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: -1.40 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.58 (0.39), residues: 166
  loop : -1.18 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 104 
 HIS   0.004   0.001   HIS A 245 
 PHE   0.017   0.003   PHE A 106 
 TYR   0.018   0.002   TYR A 170 
 ARG   0.007   0.001   ARG L  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00117 (    3)
  link_NAG-ASN         : angle       2.80969 (    9)
  link_BETA1-4         : bond        0.00311 (    2)
  link_BETA1-4         : angle       2.26930 (    6)
  hydrogen bonds       : bond        0.04325 (   97)
  hydrogen bonds       : angle       5.81989 (  294)
  SS BOND              : bond        0.00243 (    4)
  SS BOND              : angle       0.87263 (    8)
  covalent geometry    : bond        0.00382 ( 3471)
  covalent geometry    : angle       0.73060 ( 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
  156 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 127
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.8384 (t) cc_final: 0.8075 (m)
REVERT: A  128 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8646 (mm)
REVERT: A  177 MET cc_start: 0.6110 (OUTLIER) cc_final: 0.5907 (mmp)
REVERT: H   31 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8032 (mt-10)
REVERT: H   58 ILE cc_start: 0.8727 (mm) cc_final: 0.8155 (pt)
REVERT: H   61 GLN cc_start: 0.8372 (tt0) cc_final: 0.7910 (pm20)
REVERT: H   72 ASP cc_start: 0.9212 (t0) cc_final: 0.8841 (t70)
REVERT: H   96 PHE cc_start: 0.7242 (m-80) cc_final: 0.7000 (m-80)
REVERT: L    4 LEU cc_start: 0.7119 (mp) cc_final: 0.6903 (mp)
REVERT: L   34 SER cc_start: 0.7764 (p) cc_final: 0.7527 (p)
REVERT: L   70 ASP cc_start: 0.8730 (t0) cc_final: 0.8448 (t0)
REVERT: L   71 PHE cc_start: 0.7541 (m-80) cc_final: 0.7003 (m-10)
REVERT: L   88 CYS cc_start: 0.3273 (p) cc_final: 0.2758 (p)
REVERT: L   98 PHE cc_start: 0.8233 (m-80) cc_final: 0.7913 (m-80)
REVERT: L  105 ASP cc_start: 0.6988 (t0) cc_final: 0.6481 (t70)
  outliers start: 29
  outliers final: 16
  residues processed: 142
  average time/residue: 0.1473
  time to fit residues: 25.4011
Evaluate side-chains
  143 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
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   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   13 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   27 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0020
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7592

-------------------------------------------------------------------------------
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**
L  37 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.146782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.125609 restraints weight = 9714.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.128603 restraints weight = 5973.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.130587 restraints weight = 4287.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6995
moved from start:          0.6516

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= 0.170
  Angle     :  0.741   7.449   4741  Z= 0.388
  Chirality :  0.051   0.348    539
  Planarity :  0.005   0.037    592
  Dihedral  :  5.612  19.891    559
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 20.02
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.67 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  6.83 %
    Allowed  : 22.95 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.67 (0.39), residues: 167
  loop : -1.36 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  64 
 HIS   0.003   0.001   HIS A  66 
 PHE   0.023   0.003   PHE A 106 
 TYR   0.020   0.002   TYR A  91 
 ARG   0.006   0.001   ARG H  66 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00296 (    3)
  link_NAG-ASN         : angle       2.96928 (    9)
  link_BETA1-4         : bond        0.00284 (    2)
  link_BETA1-4         : angle       1.92027 (    6)
  hydrogen bonds       : bond        0.04252 (   97)
  hydrogen bonds       : angle       5.68145 (  294)
  SS BOND              : bond        0.00290 (    4)
  SS BOND              : angle       0.78781 (    8)
  covalent geometry    : bond        0.00391 ( 3471)
  covalent geometry    : angle       0.72732 ( 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
  147 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8685 (mm)
REVERT: A  153 MET cc_start: 0.8045 (mmm) cc_final: 0.7823 (mmm)
REVERT: A  158 ARG cc_start: 0.7723 (mmt180) cc_final: 0.6827 (mmp-170)
REVERT: A  239 GLN cc_start: 0.8331 (mt0) cc_final: 0.8046 (mt0)
REVERT: H   31 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8008 (mt-10)
REVERT: H   61 GLN cc_start: 0.8488 (tt0) cc_final: 0.7969 (pm20)
REVERT: H   72 ASP cc_start: 0.9237 (t0) cc_final: 0.8900 (t70)
REVERT: H  105 GLN cc_start: 0.8273 (pm20) cc_final: 0.7737 (pm20)
REVERT: L    4 LEU cc_start: 0.7412 (mp) cc_final: 0.7031 (mp)
REVERT: L   34 SER cc_start: 0.7744 (p) cc_final: 0.7526 (p)
REVERT: L   70 ASP cc_start: 0.8776 (t0) cc_final: 0.8496 (t0)
REVERT: L   71 PHE cc_start: 0.7614 (m-80) cc_final: 0.7037 (m-10)
REVERT: L   88 CYS cc_start: 0.3098 (p) cc_final: 0.2753 (p)
REVERT: L  105 ASP cc_start: 0.6898 (t0) cc_final: 0.6325 (t70)
  outliers start: 25
  outliers final: 19
  residues processed: 137
  average time/residue: 0.1507
  time to fit residues: 24.8483
Evaluate side-chains
  137 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
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 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  108 THR
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   97 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0030
   chunk 24 optimal weight:    0.2980
   chunk 17 optimal weight:    0.4980
   overall best weight:    0.4590

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.147531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.125872 restraints weight = 9747.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.129170 restraints weight = 5638.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.131238 restraints weight = 3964.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6977
moved from start:          0.6812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3480  Z= 0.147
  Angle     :  0.750   8.289   4741  Z= 0.385
  Chirality :  0.051   0.374    539
  Planarity :  0.006   0.061    592
  Dihedral  :  5.439  18.473    559
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 17.76
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.91 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 26.23 %
    Favored  : 68.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.64 (0.40), residues: 169
  loop : -1.37 (0.38), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 104 
 HIS   0.002   0.001   HIS A 245 
 PHE   0.020   0.002   PHE A 106 
 TYR   0.029   0.002   TYR H  27 
 ARG   0.013   0.001   ARG L  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00283 (    3)
  link_NAG-ASN         : angle       3.47476 (    9)
  link_BETA1-4         : bond        0.00390 (    2)
  link_BETA1-4         : angle       1.72384 (    6)
  hydrogen bonds       : bond        0.04106 (   97)
  hydrogen bonds       : angle       5.62315 (  294)
  SS BOND              : bond        0.00202 (    4)
  SS BOND              : angle       0.57000 (    8)
  covalent geometry    : bond        0.00337 ( 3471)
  covalent geometry    : angle       0.73318 ( 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
  151 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8645 (mm)
REVERT: A  153 MET cc_start: 0.8058 (mmm) cc_final: 0.7813 (mmm)
REVERT: A  158 ARG cc_start: 0.7661 (mmt180) cc_final: 0.6922 (mmp-170)
REVERT: A  160 TYR cc_start: 0.8465 (p90) cc_final: 0.8188 (p90)
REVERT: A  239 GLN cc_start: 0.8323 (mt0) cc_final: 0.7900 (mt0)
REVERT: H   31 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7866 (mt-10)
REVERT: H   61 GLN cc_start: 0.8545 (tt0) cc_final: 0.7885 (pm20)
REVERT: H   72 ASP cc_start: 0.9232 (t0) cc_final: 0.8835 (t70)
REVERT: H  105 GLN cc_start: 0.8294 (pm20) cc_final: 0.7796 (pm20)
REVERT: L   34 SER cc_start: 0.7759 (p) cc_final: 0.7425 (p)
REVERT: L   70 ASP cc_start: 0.8784 (t0) cc_final: 0.8526 (t0)
REVERT: L   71 PHE cc_start: 0.7698 (m-80) cc_final: 0.7085 (m-10)
REVERT: L   89 THR cc_start: 0.9217 (t) cc_final: 0.8871 (t)
REVERT: L  105 ASP cc_start: 0.6597 (t0) cc_final: 0.5886 (t70)
  outliers start: 21
  outliers final: 16
  residues processed: 139
  average time/residue: 0.1515
  time to fit residues: 25.4113
Evaluate side-chains
  137 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
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   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 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:    0.0570
   chunk 25 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 HIS ** 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 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 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 = 0.4152 r_free = 0.4152 target = 0.146348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.125038 restraints weight = 9623.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.128220 restraints weight = 5754.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.130213 restraints weight = 4061.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6994
moved from start:          0.7034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3480  Z= 0.161
  Angle     :  0.764  10.056   4741  Z= 0.394
  Chirality :  0.050   0.267    539
  Planarity :  0.006   0.041    592
  Dihedral  :  5.379  20.400    559
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 20.02
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.90 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 27.32 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.58 (0.40), residues: 165
  loop : -1.43 (0.37), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 104 
 HIS   0.003   0.001   HIS A 146 
 PHE   0.021   0.003   PHE A 106 
 TYR   0.030   0.002   TYR H  27 
 ARG   0.013   0.001   ARG A 246 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00091 (    3)
  link_NAG-ASN         : angle       2.25427 (    9)
  link_BETA1-4         : bond        0.00338 (    2)
  link_BETA1-4         : angle       1.65050 (    6)
  hydrogen bonds       : bond        0.04068 (   97)
  hydrogen bonds       : angle       5.64311 (  294)
  SS BOND              : bond        0.00331 (    4)
  SS BOND              : angle       0.84339 (    8)
  covalent geometry    : bond        0.00371 ( 3471)
  covalent geometry    : angle       0.75675 ( 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
  142 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8613 (mm)
REVERT: A  153 MET cc_start: 0.8048 (mmm) cc_final: 0.7838 (mmm)
REVERT: A  158 ARG cc_start: 0.7620 (mmt180) cc_final: 0.6875 (mmp-170)
REVERT: A  160 TYR cc_start: 0.8470 (p90) cc_final: 0.8216 (p90)
REVERT: A  239 GLN cc_start: 0.8227 (mt0) cc_final: 0.7912 (mt0)
REVERT: H   31 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7989 (mt-10)
REVERT: H   61 GLN cc_start: 0.8585 (tt0) cc_final: 0.7933 (pm20)
REVERT: H   72 ASP cc_start: 0.9265 (t0) cc_final: 0.8900 (t70)
REVERT: H   81 GLU cc_start: 0.8361 (pp20) cc_final: 0.8085 (pp20)
REVERT: H  105 GLN cc_start: 0.8298 (pm20) cc_final: 0.8037 (pm20)
REVERT: L   34 SER cc_start: 0.7654 (p) cc_final: 0.7452 (p)
REVERT: L   36 LEU cc_start: 0.9085 (mp) cc_final: 0.8803 (mt)
REVERT: L   70 ASP cc_start: 0.8788 (t0) cc_final: 0.8556 (t0)
REVERT: L   71 PHE cc_start: 0.7675 (m-80) cc_final: 0.7058 (m-10)
REVERT: L  105 ASP cc_start: 0.6466 (t0) cc_final: 0.5800 (t70)
  outliers start: 22
  outliers final: 15
  residues processed: 133
  average time/residue: 0.1495
  time to fit residues: 24.2308
Evaluate side-chains
  135 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
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 A residue  245 HIS
Chi-restraints excluded: chain A residue  247 SER
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 L residue   13 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   81 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0070
   chunk 31 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0570
   chunk 35 optimal weight:    0.0020
   chunk 33 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0770
   overall best weight:    0.1482

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  62 GLN
** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.149134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.127736 restraints weight = 9138.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.131090 restraints weight = 5479.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.133182 restraints weight = 3866.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.7336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3480  Z= 0.146
  Angle     :  0.797   9.816   4741  Z= 0.406
  Chirality :  0.051   0.317    539
  Planarity :  0.006   0.057    592
  Dihedral  :  5.190  19.914    559
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 18.67
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.40 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 28.96 %
    Favored  : 67.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.67 (0.42), residues: 162
  loop : -1.55 (0.37), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 104 
 HIS   0.001   0.000   HIS A 245 
 PHE   0.021   0.002   PHE A 106 
 TYR   0.029   0.001   TYR H  27 
 ARG   0.007   0.001   ARG H  66 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00124 (    3)
  link_NAG-ASN         : angle       4.49530 (    9)
  link_BETA1-4         : bond        0.00596 (    2)
  link_BETA1-4         : angle       1.56394 (    6)
  hydrogen bonds       : bond        0.03937 (   97)
  hydrogen bonds       : angle       5.52078 (  294)
  SS BOND              : bond        0.00259 (    4)
  SS BOND              : angle       0.79299 (    8)
  covalent geometry    : bond        0.00329 ( 3471)
  covalent geometry    : angle       0.77170 ( 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: 14
    poor density    : 126
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8550 (mm)
REVERT: A  153 MET cc_start: 0.8115 (mmm) cc_final: 0.7863 (mmm)
REVERT: A  158 ARG cc_start: 0.7509 (mmt180) cc_final: 0.6881 (mmp-170)
REVERT: A  160 TYR cc_start: 0.8416 (p90) cc_final: 0.8192 (p90)
REVERT: H   31 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7973 (mt-10)
REVERT: H   46 GLU cc_start: 0.8310 (pt0) cc_final: 0.7747 (pm20)
REVERT: H   61 GLN cc_start: 0.8472 (tt0) cc_final: 0.7848 (pm20)
REVERT: H   72 ASP cc_start: 0.9232 (t0) cc_final: 0.8844 (t70)
REVERT: H   81 GLU cc_start: 0.8395 (pp20) cc_final: 0.8033 (pp20)
REVERT: H   86 ASP cc_start: 0.8628 (m-30) cc_final: 0.8318 (m-30)
REVERT: H  100 MET cc_start: 0.8323 (mtt) cc_final: 0.7964 (mtt)
REVERT: H  105 GLN cc_start: 0.8279 (pm20) cc_final: 0.8062 (pm20)
REVERT: L   34 SER cc_start: 0.7627 (p) cc_final: 0.7342 (p)
REVERT: L   36 LEU cc_start: 0.9045 (mp) cc_final: 0.8768 (mt)
REVERT: L   70 ASP cc_start: 0.8677 (t0) cc_final: 0.8445 (t0)
REVERT: L   71 PHE cc_start: 0.7519 (m-80) cc_final: 0.7045 (m-10)
REVERT: L  105 ASP cc_start: 0.5891 (t0) cc_final: 0.5283 (t70)
  outliers start: 14
  outliers final: 10
  residues processed: 133
  average time/residue: 0.1547
  time to fit residues: 25.2426
Evaluate side-chains
  129 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    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  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0070
   chunk 32 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 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 = 0.4145 r_free = 0.4145 target = 0.146639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.124556 restraints weight = 9331.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.127969 restraints weight = 5431.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.130247 restraints weight = 3797.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6988
moved from start:          0.7596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3480  Z= 0.171
  Angle     :  0.813  10.241   4741  Z= 0.414
  Chirality :  0.050   0.272    539
  Planarity :  0.006   0.047    592
  Dihedral  :  5.260  20.314    559
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 20.32
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.90 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 29.51 %
    Favored  : 66.39 %
  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: -0.65 (0.41), residues: 164
  loop : -1.60 (0.37), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  64 
 HIS   0.002   0.001   HIS A 245 
 PHE   0.020   0.003   PHE A 106 
 TYR   0.024   0.002   TYR H 100H
 ARG   0.006   0.001   ARG H  66 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00204 (    3)
  link_NAG-ASN         : angle       3.08215 (    9)
  link_BETA1-4         : bond        0.00326 (    2)
  link_BETA1-4         : angle       1.63550 (    6)
  hydrogen bonds       : bond        0.04027 (   97)
  hydrogen bonds       : angle       5.52158 (  294)
  SS BOND              : bond        0.00358 (    4)
  SS BOND              : angle       0.80182 (    8)
  covalent geometry    : bond        0.00403 ( 3471)
  covalent geometry    : angle       0.80129 ( 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
  135 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLN cc_start: 0.5909 (mp10) cc_final: 0.5646 (mp10)
REVERT: A  128 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8538 (mm)
REVERT: A  153 MET cc_start: 0.8017 (mmm) cc_final: 0.7745 (mmm)
REVERT: A  158 ARG cc_start: 0.7659 (mmt180) cc_final: 0.6961 (mmp-170)
REVERT: A  160 TYR cc_start: 0.8434 (p90) cc_final: 0.8225 (p90)
REVERT: A  239 GLN cc_start: 0.8192 (mt0) cc_final: 0.7852 (mt0)
REVERT: H   31 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8030 (mt-10)
REVERT: H   72 ASP cc_start: 0.9247 (t0) cc_final: 0.8910 (t70)
REVERT: H   81 GLU cc_start: 0.8425 (pp20) cc_final: 0.8082 (pp20)
REVERT: H  105 GLN cc_start: 0.8318 (pm20) cc_final: 0.8092 (pm20)
REVERT: L   36 LEU cc_start: 0.9084 (mp) cc_final: 0.8808 (mt)
REVERT: L   70 ASP cc_start: 0.8673 (t0) cc_final: 0.8424 (t0)
REVERT: L   71 PHE cc_start: 0.7616 (m-80) cc_final: 0.7092 (m-10)
REVERT: L   77 ARG cc_start: 0.8103 (ppt170) cc_final: 0.7377 (ppt170)
REVERT: L  105 ASP cc_start: 0.5928 (t0) cc_final: 0.5296 (t70)
  outliers start: 15
  outliers final: 12
  residues processed: 129
  average time/residue: 0.1716
  time to fit residues: 26.9245
Evaluate side-chains
  131 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
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   11 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   29 LEU
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   81 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 34 optimal weight:    0.3980
   chunk 26 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 5 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 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 = 0.147152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.125726 restraints weight = 9391.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.129032 restraints weight = 5489.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.131215 restraints weight = 3832.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.7780

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= 0.161
  Angle     :  0.790  10.482   4741  Z= 0.401
  Chirality :  0.050   0.255    539
  Planarity :  0.006   0.065    592
  Dihedral  :  5.308  20.379    559
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 20.47
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.13 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 30.60 %
    Favored  : 65.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.50 (0.42), residues: 160
  loop : -1.81 (0.36), residues: 246

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   0.020   0.003   PHE A 106 
 TYR   0.019   0.002   TYR H 100H
 ARG   0.009   0.001   ARG H  66 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00176 (    3)
  link_NAG-ASN         : angle       2.63742 (    9)
  link_BETA1-4         : bond        0.00398 (    2)
  link_BETA1-4         : angle       1.54413 (    6)
  hydrogen bonds       : bond        0.03961 (   97)
  hydrogen bonds       : angle       5.52862 (  294)
  SS BOND              : bond        0.00278 (    4)
  SS BOND              : angle       0.87769 (    8)
  covalent geometry    : bond        0.00382 ( 3471)
  covalent geometry    : angle       0.78060 ( 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
  134 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 HIS cc_start: 0.7818 (t70) cc_final: 0.7466 (t70)
REVERT: A  153 MET cc_start: 0.8045 (mmm) cc_final: 0.7802 (mmm)
REVERT: A  158 ARG cc_start: 0.7669 (mmt180) cc_final: 0.6990 (mmp-170)
REVERT: A  239 GLN cc_start: 0.8215 (mt0) cc_final: 0.7860 (mt0)
REVERT: H   31 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8033 (mt-10)
REVERT: H   72 ASP cc_start: 0.9243 (t0) cc_final: 0.8931 (t70)
REVERT: H   81 GLU cc_start: 0.8381 (pp20) cc_final: 0.8038 (pp20)
REVERT: H  105 GLN cc_start: 0.8290 (pm20) cc_final: 0.8047 (pm20)
REVERT: L   36 LEU cc_start: 0.9135 (mp) cc_final: 0.8879 (mt)
REVERT: L   70 ASP cc_start: 0.8613 (t0) cc_final: 0.8412 (t0)
REVERT: L   71 PHE cc_start: 0.7570 (m-80) cc_final: 0.7050 (m-10)
REVERT: L   77 ARG cc_start: 0.8135 (ppt170) cc_final: 0.7561 (ppt170)
REVERT: L  105 ASP cc_start: 0.5843 (t0) cc_final: 0.5197 (t70)
  outliers start: 14
  outliers final: 12
  residues processed: 129
  average time/residue: 0.1547
  time to fit residues: 24.0466
Evaluate side-chains
  124 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
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  119 ILE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  234 ASN
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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0980
   chunk 14 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 28 optimal weight:    0.1980
   chunk 3 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  30 ASN
L  37 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.148875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.127244 restraints weight = 9550.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.130597 restraints weight = 5581.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.132662 restraints weight = 3909.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6932
moved from start:          0.7932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085   3480  Z= 0.160
  Angle     :  0.810  10.266   4741  Z= 0.411
  Chirality :  0.050   0.306    539
  Planarity :  0.005   0.058    592
  Dihedral  :  5.216  20.182    559
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 19.72
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.13 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 31.42 %
    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: -1.91 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.53 (0.42), residues: 160
  loop : -1.84 (0.36), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 104 
 HIS   0.001   0.000   HIS A 245 
 PHE   0.021   0.003   PHE A 106 
 TYR   0.018   0.002   TYR H 100H
 ARG   0.008   0.001   ARG H  66 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00144 (    3)
  link_NAG-ASN         : angle       2.22057 (    9)
  link_BETA1-4         : bond        0.00401 (    2)
  link_BETA1-4         : angle       1.44823 (    6)
  hydrogen bonds       : bond        0.04420 (   97)
  hydrogen bonds       : angle       5.54615 (  294)
  SS BOND              : bond        0.00271 (    4)
  SS BOND              : angle       0.84930 (    8)
  covalent geometry    : bond        0.00398 ( 3471)
  covalent geometry    : angle       0.80399 ( 4718)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2210.11 seconds
wall clock time: 39 minutes 0.97 seconds (2340.97 seconds total)