Starting phenix.real_space_refine
on Fri Aug 22 13:40:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8swh_40814/08_2025/8swh_40814.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8swh_40814/08_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_40814/08_2025/8swh_40814.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8swh_40814/08_2025/8swh_40814.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8swh_40814/08_2025/8swh_40814.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8swh_40814/08_2025/8swh_40814.cif"
  }
  resolution = 3.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.26, per 1000 atoms: 0.37
  Number of scatterers: 3390
  At special positions: 0
  Unit cell: (59.45, 89.175, 89.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      14     16.00
     O     661      8.00
     N     560      7.00
     C    2155      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
    NAG-ASN
      " NAG A1301 " - " ASN A  17 "
      " NAG A1302 " - " ASN A 149 "
      " NAG B   1 " - " ASN A 122 "
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 134.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.20
  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: 0.52

  Time building geometry restraints manager: 0.46 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:             13.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     6.070
  Find NCS groups from input model:        0.010
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.730
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.008   0.001   ARG H  83 
 TYR   0.076   0.011   TYR L  87 
 PHE   0.065   0.009   PHE A 192 
 TRP   0.061   0.013   TRP H  47 
 HIS   0.005   0.002   HIS A 146 

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

*********************** 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  : 0.134 
Fit side-chains
   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: 0.7177 (t0)
REVERT: A   83 VAL cc_start: 0.8524 (t) cc_final: 0.8145 (m)
REVERT: A  151 SER cc_start: 0.8094 (p) cc_final: 0.7637 (m)
REVERT: A  153 MET cc_start: 0.8307 (mtt) cc_final: 0.8066 (mtt)
REVERT: A  207 HIS cc_start: 0.7008 (t-170) cc_final: 0.6226 (t-170)
REVERT: A  242 LEU cc_start: 0.7954 (mt) cc_final: 0.7728 (mp)
REVERT: H   31 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7872 (mt-10)
REVERT: L   32 TYR cc_start: 0.5490 (m-80) cc_final: 0.5229 (m-10)
REVERT: L   71 PHE cc_start: 0.7407 (m-80) cc_final: 0.6929 (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: 0.8105 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 197
  average time/residue: 0.0869
  time to fit residues: 20.1024
Evaluate side-chains
  124 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    0.4980
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
A 134 GLN
A 148 ASN
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  62 GLN
L  38 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  93 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.148689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.129330 restraints weight = 9757.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.132860 restraints weight = 5437.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.135085 restraints weight = 3661.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.136454 restraints weight = 2769.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.137362 restraints weight = 2267.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6796
moved from start:          0.4784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   3480  Z= 0.221
  Angle     :  0.882   7.026   4741  Z= 0.469
  Chirality :  0.053   0.400    539
  Planarity :  0.006   0.048    592
  Dihedral  :  9.414  61.233    559
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 17.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 18.58 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.01 (0.39), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.23 (0.38), residues: 169
  loop : -0.98 (0.38), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 190 
 TYR   0.019   0.002   TYR A  91 
 PHE   0.020   0.003   PHE A 133 
 TRP   0.016   0.002   TRP A 104 
 HIS   0.004   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 3471)
  covalent geometry    : angle       0.85816 ( 4718)
  SS BOND              : bond        0.00612 (    4)
  SS BOND              : angle       1.84273 (    8)
  hydrogen bonds       : bond        0.05431 (   97)
  hydrogen bonds       : angle       6.46981 (  294)
  link_BETA1-4         : bond        0.00232 (    2)
  link_BETA1-4         : angle       3.37451 (    6)
  link_NAG-ASN         : bond        0.00521 (    3)
  link_NAG-ASN         : angle       3.58338 (    9)

*********************** 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
  171 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.8815 (t) cc_final: 0.8594 (m)
REVERT: A  150 LYS cc_start: 0.9115 (mtpt) cc_final: 0.8910 (tttp)
REVERT: H   31 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7862 (mt-10)
REVERT: H   38 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7737 (mtm180)
REVERT: H   48 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7645 (mtp)
REVERT: H   58 ILE cc_start: 0.8691 (mm) cc_final: 0.8017 (pt)
REVERT: H   61 GLN cc_start: 0.8318 (tt0) cc_final: 0.7900 (pm20)
REVERT: H   72 ASP cc_start: 0.9095 (t0) cc_final: 0.8672 (t70)
REVERT: H   96 PHE cc_start: 0.7504 (m-10) cc_final: 0.6460 (m-80)
REVERT: L    4 LEU cc_start: 0.6970 (mp) cc_final: 0.6552 (mp)
REVERT: L   70 ASP cc_start: 0.8644 (t70) cc_final: 0.8265 (t0)
REVERT: L   71 PHE cc_start: 0.7388 (m-80) cc_final: 0.6973 (m-10)
REVERT: L   88 CYS cc_start: 0.4089 (p) cc_final: 0.3477 (p)
REVERT: L   98 PHE cc_start: 0.8280 (m-80) cc_final: 0.8058 (m-80)
  outliers start: 21
  outliers final: 12
  residues processed: 160
  average time/residue: 0.0835
  time to fit residues: 15.6908
Evaluate side-chains
  141 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  247 SER
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 H residue  109 VAL
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 25 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4141 r_free = 0.4141 target = 0.146573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.126751 restraints weight = 9767.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.130136 restraints weight = 5548.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.132233 restraints weight = 3812.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.133523 restraints weight = 2931.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.134312 restraints weight = 2441.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6906
moved from start:          0.5694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   3480  Z= 0.208
  Angle     :  0.814   8.035   4741  Z= 0.431
  Chirality :  0.051   0.346    539
  Planarity :  0.006   0.050    592
  Dihedral  :  7.021  32.563    559
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 19.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  8.47 %
    Allowed  : 21.31 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.41 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.47 (0.38), residues: 172
  loop : -1.29 (0.39), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  54 
 TYR   0.025   0.002   TYR A  91 
 PHE   0.021   0.003   PHE A 106 
 TRP   0.016   0.002   TRP A 104 
 HIS   0.004   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 3471)
  covalent geometry    : angle       0.79894 ( 4718)
  SS BOND              : bond        0.00399 (    4)
  SS BOND              : angle       1.21630 (    8)
  hydrogen bonds       : bond        0.04930 (   97)
  hydrogen bonds       : angle       6.19279 (  294)
  link_BETA1-4         : bond        0.00409 (    2)
  link_BETA1-4         : angle       2.58629 (    6)
  link_NAG-ASN         : bond        0.00382 (    3)
  link_NAG-ASN         : angle       2.90691 (    9)

*********************** 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
  170 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 139
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLN cc_start: 0.5531 (OUTLIER) cc_final: 0.5240 (mp10)
REVERT: A  128 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8634 (mm)
REVERT: H   31 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7795 (mt-10)
REVERT: H   58 ILE cc_start: 0.8692 (mm) cc_final: 0.8089 (pt)
REVERT: H   61 GLN cc_start: 0.8330 (tt0) cc_final: 0.7909 (pm20)
REVERT: H   72 ASP cc_start: 0.9163 (t0) cc_final: 0.8787 (t70)
REVERT: H   81 GLU cc_start: 0.8307 (pp20) cc_final: 0.8098 (pp20)
REVERT: L    4 LEU cc_start: 0.7048 (mp) cc_final: 0.6601 (mp)
REVERT: L   54 ARG cc_start: 0.7952 (mtp85) cc_final: 0.7224 (ttm-80)
REVERT: L   70 ASP cc_start: 0.8698 (t70) cc_final: 0.8366 (t0)
REVERT: L   71 PHE cc_start: 0.7598 (m-80) cc_final: 0.7081 (m-10)
REVERT: L   88 CYS cc_start: 0.3442 (p) cc_final: 0.2980 (p)
  outliers start: 31
  outliers final: 22
  residues processed: 151
  average time/residue: 0.0770
  time to fit residues: 13.9355
Evaluate side-chains
  154 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLN
Chi-restraints excluded: chain A residue   66 HIS
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   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   77 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    0.2980
   chunk 18 optimal weight:    0.2980
   chunk 34 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 4 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0370
   chunk 29 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.4058

-------------------------------------------------------------------------------
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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   3 GLN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.149264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.128622 restraints weight = 9483.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.132120 restraints weight = 5382.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.134154 restraints weight = 3682.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.135607 restraints weight = 2843.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.136390 restraints weight = 2365.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6842
moved from start:          0.6171

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     :  0.747   9.518   4741  Z= 0.388
  Chirality :  0.050   0.288    539
  Planarity :  0.005   0.037    592
  Dihedral  :  5.728  21.865    559
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.17 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  7.10 %
    Allowed  : 21.86 %
    Favored  : 71.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.54 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.67 (0.39), residues: 167
  loop : -1.27 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  54 
 TYR   0.019   0.002   TYR A 170 
 PHE   0.021   0.003   PHE A 106 
 TRP   0.017   0.002   TRP A 104 
 HIS   0.003   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 3471)
  covalent geometry    : angle       0.73487 ( 4718)
  SS BOND              : bond        0.00270 (    4)
  SS BOND              : angle       0.84225 (    8)
  hydrogen bonds       : bond        0.04360 (   97)
  hydrogen bonds       : angle       5.72853 (  294)
  link_BETA1-4         : bond        0.00359 (    2)
  link_BETA1-4         : angle       2.21988 (    6)
  link_NAG-ASN         : bond        0.00404 (    3)
  link_NAG-ASN         : angle       2.67829 (    9)

*********************** 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
  166 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8667 (mm)
REVERT: A  158 ARG cc_start: 0.7401 (mmt180) cc_final: 0.6517 (mmp-170)
REVERT: H   58 ILE cc_start: 0.8747 (mm) cc_final: 0.8171 (pt)
REVERT: H   61 GLN cc_start: 0.8286 (tt0) cc_final: 0.7868 (pm20)
REVERT: H   72 ASP cc_start: 0.9188 (t0) cc_final: 0.8790 (t70)
REVERT: H   81 GLU cc_start: 0.8397 (pp20) cc_final: 0.8158 (pp20)
REVERT: L    4 LEU cc_start: 0.7063 (mp) cc_final: 0.6672 (mp)
REVERT: L   70 ASP cc_start: 0.8578 (t70) cc_final: 0.8242 (t0)
REVERT: L   71 PHE cc_start: 0.7459 (m-80) cc_final: 0.6988 (m-10)
REVERT: L   87 TYR cc_start: 0.8490 (m-80) cc_final: 0.8221 (m-10)
REVERT: L   88 CYS cc_start: 0.3210 (p) cc_final: 0.2762 (p)
REVERT: L  105 ASP cc_start: 0.6837 (t0) cc_final: 0.6400 (t70)
  outliers start: 26
  outliers final: 15
  residues processed: 149
  average time/residue: 0.0699
  time to fit residues: 12.5221
Evaluate side-chains
  141 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
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  128 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   29 LEU
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue  102 VAL
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 17 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0060
   chunk 36 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 207 HIS
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   3 GLN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 105 GLN
L  27 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.147667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.127054 restraints weight = 9513.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.130319 restraints weight = 5520.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.132395 restraints weight = 3839.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.133700 restraints weight = 2971.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.134471 restraints weight = 2485.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.6513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3480  Z= 0.160
  Angle     :  0.758   8.595   4741  Z= 0.390
  Chirality :  0.051   0.355    539
  Planarity :  0.005   0.037    592
  Dihedral  :  5.537  19.980    559
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 18.37
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.16 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  8.47 %
    Allowed  : 24.04 %
    Favored  : 67.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.73 (0.39), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.79 (0.39), residues: 167
  loop : -1.41 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 190 
 TYR   0.018   0.001   TYR A  91 
 PHE   0.022   0.002   PHE A 106 
 TRP   0.013   0.002   TRP A 104 
 HIS   0.010   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 3471)
  covalent geometry    : angle       0.74384 ( 4718)
  SS BOND              : bond        0.00280 (    4)
  SS BOND              : angle       0.77085 (    8)
  hydrogen bonds       : bond        0.04402 (   97)
  hydrogen bonds       : angle       5.58548 (  294)
  link_BETA1-4         : bond        0.00332 (    2)
  link_BETA1-4         : angle       2.02269 (    6)
  link_NAG-ASN         : bond        0.00218 (    3)
  link_NAG-ASN         : angle       3.09823 (    9)

*********************** 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
  165 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 134
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8648 (mm)
REVERT: A  153 MET cc_start: 0.8076 (mmm) cc_final: 0.7843 (mmm)
REVERT: A  158 ARG cc_start: 0.7460 (mmt180) cc_final: 0.6580 (mmp-170)
REVERT: H   31 GLU cc_start: 0.8555 (mt-10) cc_final: 0.7940 (mt-10)
REVERT: H   48 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8573 (ptm)
REVERT: H   61 GLN cc_start: 0.8360 (tt0) cc_final: 0.7878 (pm20)
REVERT: H   72 ASP cc_start: 0.9207 (t0) cc_final: 0.8785 (t70)
REVERT: H   81 GLU cc_start: 0.8495 (pp20) cc_final: 0.8288 (pp20)
REVERT: H  105 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7840 (pm20)
REVERT: L    4 LEU cc_start: 0.7103 (mp) cc_final: 0.6887 (mp)
REVERT: L   70 ASP cc_start: 0.8628 (t70) cc_final: 0.8350 (t0)
REVERT: L   71 PHE cc_start: 0.7578 (m-80) cc_final: 0.7102 (m-10)
REVERT: L   88 CYS cc_start: 0.3185 (p) cc_final: 0.2630 (p)
REVERT: L  105 ASP cc_start: 0.6715 (t0) cc_final: 0.6209 (t70)
  outliers start: 31
  outliers final: 18
  residues processed: 147
  average time/residue: 0.0781
  time to fit residues: 13.6911
Evaluate side-chains
  147 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   29 LEU
Chi-restraints excluded: chain H residue   32 LEU
Chi-restraints excluded: chain H residue   48 MET
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue  102 VAL
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain H residue  108 THR
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   27 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 7 optimal weight:    0.4980
   chunk 12 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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**
** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 207 HIS
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.147560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.126880 restraints weight = 9615.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.130095 restraints weight = 5747.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.132145 restraints weight = 4047.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.133391 restraints weight = 3157.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.134308 restraints weight = 2675.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.6753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3480  Z= 0.161
  Angle     :  0.760  10.383   4741  Z= 0.391
  Chirality :  0.052   0.415    539
  Planarity :  0.005   0.044    592
  Dihedral  :  5.435  19.096    559
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 17.91
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.16 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  7.65 %
    Allowed  : 24.59 %
    Favored  : 67.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.84 (0.39), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.84 (0.38), residues: 169
  loop : -1.52 (0.38), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 246 
 TYR   0.024   0.002   TYR A 170 
 PHE   0.022   0.003   PHE A 106 
 TRP   0.012   0.001   TRP A  64 
 HIS   0.002   0.001   HIS A 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 3471)
  covalent geometry    : angle       0.74456 ( 4718)
  SS BOND              : bond        0.00286 (    4)
  SS BOND              : angle       0.72222 (    8)
  hydrogen bonds       : bond        0.04180 (   97)
  hydrogen bonds       : angle       5.60907 (  294)
  link_BETA1-4         : bond        0.00358 (    2)
  link_BETA1-4         : angle       1.86894 (    6)
  link_NAG-ASN         : bond        0.00167 (    3)
  link_NAG-ASN         : angle       3.30096 (    9)

*********************** 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
  157 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 129
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8549 (mm)
REVERT: A  153 MET cc_start: 0.8074 (mmm) cc_final: 0.7836 (mmm)
REVERT: A  158 ARG cc_start: 0.7481 (mmt180) cc_final: 0.6685 (mmp-170)
REVERT: A  160 TYR cc_start: 0.8409 (p90) cc_final: 0.8144 (p90)
REVERT: H   31 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8003 (mt-10)
REVERT: H   48 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8284 (ptm)
REVERT: H   61 GLN cc_start: 0.8417 (tt0) cc_final: 0.7824 (pm20)
REVERT: H   72 ASP cc_start: 0.9210 (t0) cc_final: 0.8831 (t70)
REVERT: H   81 GLU cc_start: 0.8568 (pp20) cc_final: 0.8317 (pp20)
REVERT: L    4 LEU cc_start: 0.7388 (mp) cc_final: 0.6909 (mp)
REVERT: L   36 LEU cc_start: 0.9036 (mp) cc_final: 0.8602 (mt)
REVERT: L   70 ASP cc_start: 0.8577 (t70) cc_final: 0.8306 (t0)
REVERT: L   71 PHE cc_start: 0.7587 (m-80) cc_final: 0.7086 (m-10)
REVERT: L   88 CYS cc_start: 0.3103 (p) cc_final: 0.2747 (p)
REVERT: L  105 ASP cc_start: 0.6573 (t0) cc_final: 0.5995 (t70)
  outliers start: 28
  outliers final: 19
  residues processed: 140
  average time/residue: 0.0808
  time to fit residues: 13.4706
Evaluate side-chains
  146 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   27 TYR
Chi-restraints excluded: chain H residue   29 LEU
Chi-restraints excluded: chain H residue   32 LEU
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   48 MET
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain 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   77 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    0.4980
   chunk 18 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 10 optimal weight:    0.3980
   chunk 1 optimal weight:    0.1980
   chunk 22 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.4982

-------------------------------------------------------------------------------
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**
A 148 ASN
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.146980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.125865 restraints weight = 9587.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.129190 restraints weight = 5525.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.131288 restraints weight = 3853.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.132667 restraints weight = 2988.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.133528 restraints weight = 2494.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6915
moved from start:          0.7029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3480  Z= 0.153
  Angle     :  0.753   9.273   4741  Z= 0.392
  Chirality :  0.050   0.254    539
  Planarity :  0.005   0.043    592
  Dihedral  :  5.277  18.838    559
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 17.76
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.90 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  8.20 %
    Allowed  : 25.68 %
    Favored  : 66.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.81 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.71 (0.40), residues: 165
  loop : -1.59 (0.37), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 237 
 TYR   0.016   0.001   TYR L  87 
 PHE   0.024   0.003   PHE A 106 
 TRP   0.013   0.001   TRP A 104 
 HIS   0.003   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 3471)
  covalent geometry    : angle       0.74683 ( 4718)
  SS BOND              : bond        0.00261 (    4)
  SS BOND              : angle       0.61375 (    8)
  hydrogen bonds       : bond        0.04163 (   97)
  hydrogen bonds       : angle       5.43435 (  294)
  link_BETA1-4         : bond        0.00602 (    2)
  link_BETA1-4         : angle       1.70406 (    6)
  link_NAG-ASN         : bond        0.00078 (    3)
  link_NAG-ASN         : angle       2.03002 (    9)

*********************** 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
  158 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8657 (mm)
REVERT: A  153 MET cc_start: 0.8070 (mmm) cc_final: 0.7812 (mmm)
REVERT: A  158 ARG cc_start: 0.7443 (mmt180) cc_final: 0.6661 (mmp-170)
REVERT: A  160 TYR cc_start: 0.8495 (p90) cc_final: 0.8279 (p90)
REVERT: A  239 GLN cc_start: 0.8182 (mt0) cc_final: 0.7883 (mt0)
REVERT: A  244 LEU cc_start: 0.7619 (mp) cc_final: 0.7266 (mp)
REVERT: H   31 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8039 (mt-10)
REVERT: H   38 ARG cc_start: 0.8040 (mtm180) cc_final: 0.7677 (mtp85)
REVERT: H   61 GLN cc_start: 0.8462 (tt0) cc_final: 0.7864 (pm20)
REVERT: H   72 ASP cc_start: 0.9215 (t0) cc_final: 0.8818 (t70)
REVERT: H   81 GLU cc_start: 0.8565 (pp20) cc_final: 0.8197 (pp20)
REVERT: L   36 LEU cc_start: 0.9044 (mp) cc_final: 0.8592 (mt)
REVERT: L   70 ASP cc_start: 0.8594 (t70) cc_final: 0.8313 (t0)
REVERT: L   71 PHE cc_start: 0.7665 (m-80) cc_final: 0.7069 (m-10)
REVERT: L  105 ASP cc_start: 0.6310 (t0) cc_final: 0.5647 (t70)
  outliers start: 30
  outliers final: 17
  residues processed: 143
  average time/residue: 0.0747
  time to fit residues: 12.8171
Evaluate side-chains
  138 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   29 LEU
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 L residue   13 VAL
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   77 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.144229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.122933 restraints weight = 9734.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.126137 restraints weight = 5686.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.128282 restraints weight = 3980.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.129567 restraints weight = 3094.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.130544 restraints weight = 2609.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6967
moved from start:          0.7366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3480  Z= 0.194
  Angle     :  0.837  10.374   4741  Z= 0.431
  Chirality :  0.052   0.378    539
  Planarity :  0.005   0.049    592
  Dihedral  :  5.493  18.862    559
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 18.06
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.39 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  6.83 %
    Allowed  : 26.50 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.98 (0.40), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.80 (0.40), residues: 168
  loop : -1.73 (0.37), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 237 
 TYR   0.018   0.002   TYR L  87 
 PHE   0.027   0.003   PHE A  65 
 TRP   0.016   0.002   TRP A  64 
 HIS   0.020   0.003   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 3471)
  covalent geometry    : angle       0.81386 ( 4718)
  SS BOND              : bond        0.00344 (    4)
  SS BOND              : angle       0.86563 (    8)
  hydrogen bonds       : bond        0.04216 (   97)
  hydrogen bonds       : angle       5.56263 (  294)
  link_BETA1-4         : bond        0.00264 (    2)
  link_BETA1-4         : angle       1.73943 (    6)
  link_NAG-ASN         : bond        0.00320 (    3)
  link_NAG-ASN         : angle       4.36846 (    9)

*********************** 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
  150 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8641 (mm)
REVERT: A  153 MET cc_start: 0.8055 (mmm) cc_final: 0.7829 (mmm)
REVERT: A  158 ARG cc_start: 0.7373 (mmt180) cc_final: 0.6606 (mmp-170)
REVERT: A  160 TYR cc_start: 0.8527 (p90) cc_final: 0.8323 (p90)
REVERT: A  237 ARG cc_start: 0.7373 (ttp-110) cc_final: 0.7026 (ptm-80)
REVERT: A  239 GLN cc_start: 0.8292 (mt0) cc_final: 0.7937 (mt0)
REVERT: H   23 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8223 (mmmt)
REVERT: H   31 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8044 (mt-10)
REVERT: H   38 ARG cc_start: 0.8251 (mtm180) cc_final: 0.7755 (mtp85)
REVERT: H   51 PHE cc_start: 0.8204 (t80) cc_final: 0.7981 (t80)
REVERT: H   72 ASP cc_start: 0.9239 (t0) cc_final: 0.8894 (t70)
REVERT: H   81 GLU cc_start: 0.8632 (pp20) cc_final: 0.8214 (pp20)
REVERT: H  105 GLN cc_start: 0.8268 (pm20) cc_final: 0.8019 (pm20)
REVERT: L   36 LEU cc_start: 0.9067 (mp) cc_final: 0.8486 (mt)
REVERT: L   46 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7690 (tp)
REVERT: L   70 ASP cc_start: 0.8593 (t70) cc_final: 0.8316 (t0)
REVERT: L   71 PHE cc_start: 0.7668 (m-80) cc_final: 0.7260 (m-10)
REVERT: L  105 ASP cc_start: 0.6027 (t0) cc_final: 0.5406 (t70)
  outliers start: 25
  outliers final: 19
  residues processed: 138
  average time/residue: 0.0734
  time to fit residues: 12.1012
Evaluate side-chains
  140 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   29 LEU
Chi-restraints excluded: chain H residue   32 LEU
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue  102 VAL
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain L residue   81 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.145133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.123443 restraints weight = 9583.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.126583 restraints weight = 5707.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.128784 restraints weight = 4016.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.130111 restraints weight = 3125.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.131097 restraints weight = 2618.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6959
moved from start:          0.7621

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= 0.184
  Angle     :  0.809   9.915   4741  Z= 0.418
  Chirality :  0.051   0.291    539
  Planarity :  0.006   0.056    592
  Dihedral  :  5.526  19.531    559
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 20.17
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.62 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 28.14 %
    Favored  : 66.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.12 (0.39), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.63 (0.42), residues: 158
  loop : -2.02 (0.35), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  83 
 TYR   0.015   0.002   TYR A  91 
 PHE   0.023   0.003   PHE A  65 
 TRP   0.012   0.002   TRP A 104 
 HIS   0.004   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 3471)
  covalent geometry    : angle       0.79679 ( 4718)
  SS BOND              : bond        0.00258 (    4)
  SS BOND              : angle       0.87132 (    8)
  hydrogen bonds       : bond        0.04218 (   97)
  hydrogen bonds       : angle       5.58424 (  294)
  link_BETA1-4         : bond        0.00320 (    2)
  link_BETA1-4         : angle       1.63292 (    6)
  link_NAG-ASN         : bond        0.00204 (    3)
  link_NAG-ASN         : angle       3.13554 (    9)

*********************** 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
  137 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8605 (mm)
REVERT: A  153 MET cc_start: 0.7963 (mmm) cc_final: 0.7710 (mmm)
REVERT: A  158 ARG cc_start: 0.7395 (mmt180) cc_final: 0.6630 (mmp-170)
REVERT: A  237 ARG cc_start: 0.7323 (ttp-110) cc_final: 0.7000 (ptm-80)
REVERT: A  239 GLN cc_start: 0.8329 (mt0) cc_final: 0.8116 (mt0)
REVERT: H   23 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8059 (mmmt)
REVERT: H   31 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7998 (mt-10)
REVERT: H   38 ARG cc_start: 0.8183 (mtm180) cc_final: 0.7941 (mtp85)
REVERT: H   43 LYS cc_start: 0.7700 (tmmt) cc_final: 0.7427 (pptt)
REVERT: H   51 PHE cc_start: 0.8222 (t80) cc_final: 0.7989 (t80)
REVERT: H   72 ASP cc_start: 0.9246 (t0) cc_final: 0.8916 (t70)
REVERT: H   81 GLU cc_start: 0.8617 (pp20) cc_final: 0.8286 (pp20)
REVERT: H  100 MET cc_start: 0.8387 (mtt) cc_final: 0.8135 (mmt)
REVERT: H  105 GLN cc_start: 0.8255 (pm20) cc_final: 0.7971 (pm20)
REVERT: L   36 LEU cc_start: 0.9092 (mp) cc_final: 0.8890 (mt)
REVERT: L   70 ASP cc_start: 0.8538 (t70) cc_final: 0.8258 (t0)
REVERT: L   71 PHE cc_start: 0.7617 (m-80) cc_final: 0.7161 (m-10)
REVERT: L  105 ASP cc_start: 0.5924 (t0) cc_final: 0.5367 (t70)
  outliers start: 21
  outliers final: 17
  residues processed: 128
  average time/residue: 0.0834
  time to fit residues: 12.6165
Evaluate side-chains
  132 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   29 LEU
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue  102 VAL
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 17 optimal weight:    0.0980
   chunk 33 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0870
   overall best weight:    0.4358

-------------------------------------------------------------------------------
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**
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.147486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.126087 restraints weight = 9460.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.129321 restraints weight = 5521.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.131405 restraints weight = 3887.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.132753 restraints weight = 3050.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.133717 restraints weight = 2564.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6897
moved from start:          0.7775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   3480  Z= 0.156
  Angle     :  0.793   9.842   4741  Z= 0.408
  Chirality :  0.050   0.255    539
  Planarity :  0.006   0.060    592
  Dihedral  :  5.424  19.196    559
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 19.72
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.88 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 28.69 %
    Favored  : 66.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.18 (0.39), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.64 (0.42), residues: 155
  loop : -2.09 (0.34), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG H  83 
 TYR   0.011   0.001   TYR L  49 
 PHE   0.022   0.002   PHE A 106 
 TRP   0.016   0.001   TRP A 104 
 HIS   0.002   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 3471)
  covalent geometry    : angle       0.78463 ( 4718)
  SS BOND              : bond        0.00180 (    4)
  SS BOND              : angle       0.67081 (    8)
  hydrogen bonds       : bond        0.04066 (   97)
  hydrogen bonds       : angle       5.49662 (  294)
  link_BETA1-4         : bond        0.00389 (    2)
  link_BETA1-4         : angle       1.46046 (    6)
  link_NAG-ASN         : bond        0.00072 (    3)
  link_NAG-ASN         : angle       2.54193 (    9)

********************** 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
  137 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8509 (mm)
REVERT: A  153 MET cc_start: 0.7949 (mmm) cc_final: 0.7707 (mmm)
REVERT: A  158 ARG cc_start: 0.7477 (mmt180) cc_final: 0.6943 (mmp-170)
REVERT: A  237 ARG cc_start: 0.7165 (ttp-110) cc_final: 0.6908 (ptm-80)
REVERT: H   31 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8001 (mt-10)
REVERT: H   38 ARG cc_start: 0.8103 (mtm180) cc_final: 0.7844 (mtp85)
REVERT: H   51 PHE cc_start: 0.8178 (t80) cc_final: 0.7961 (t80)
REVERT: H   72 ASP cc_start: 0.9228 (t0) cc_final: 0.8910 (t70)
REVERT: H   81 GLU cc_start: 0.8556 (pp20) cc_final: 0.8148 (pp20)
REVERT: H  105 GLN cc_start: 0.8253 (pm20) cc_final: 0.7935 (pm20)
REVERT: L   36 LEU cc_start: 0.9101 (mp) cc_final: 0.8891 (mt)
REVERT: L   71 PHE cc_start: 0.7485 (m-80) cc_final: 0.7245 (m-10)
REVERT: L  105 ASP cc_start: 0.5560 (t0) cc_final: 0.4990 (t70)
  outliers start: 19
  outliers final: 17
  residues processed: 129
  average time/residue: 0.0811
  time to fit residues: 12.4195
Evaluate side-chains
  132 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   29 LEU
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 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 4 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0070
   chunk 28 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 25 optimal weight:    0.2980
   chunk 9 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.4998

-------------------------------------------------------------------------------
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  81 ASN ** 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**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  30 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.147400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.125539 restraints weight = 9663.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.128907 restraints weight = 5592.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.131119 restraints weight = 3879.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.132583 restraints weight = 3005.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.133402 restraints weight = 2511.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6919
moved from start:          0.8029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   3480  Z= 0.156
  Angle     :  0.783   9.635   4741  Z= 0.405
  Chirality :  0.050   0.239    539
  Planarity :  0.006   0.062    592
  Dihedral  :  5.361  21.251    559
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 19.27
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.37 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 28.69 %
    Favored  : 66.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.16 (0.39), residues: 406
  helix:  None (None), residues: 0
  sheet: -0.63 (0.42), residues: 155
  loop : -2.06 (0.35), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 102 
 TYR   0.015   0.002   TYR L  49 
 PHE   0.020   0.003   PHE A 106 
 TRP   0.015   0.001   TRP A 104 
 HIS   0.002   0.001   HIS A 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 3471)
  covalent geometry    : angle       0.77581 ( 4718)
  SS BOND              : bond        0.00317 (    4)
  SS BOND              : angle       0.84845 (    8)
  hydrogen bonds       : bond        0.03975 (   97)
  hydrogen bonds       : angle       5.39855 (  294)
  link_BETA1-4         : bond        0.00509 (    2)
  link_BETA1-4         : angle       1.56000 (    6)
  link_NAG-ASN         : bond        0.00158 (    3)
  link_NAG-ASN         : angle       2.20244 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1278.17 seconds
wall clock time: 22 minutes 46.96 seconds (1366.96 seconds total)