Starting phenix.real_space_refine
on Fri Aug 22 15:33:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zqi_11364/08_2025/6zqi_11364.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zqi_11364/08_2025/6zqi_11364.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zqi_11364/08_2025/6zqi_11364.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zqi_11364/08_2025/6zqi_11364.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zqi_11364/08_2025/6zqi_11364.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zqi_11364/08_2025/6zqi_11364.map"
  }
  resolution = 3.8
  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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    3167      2.51       5
     N     875      2.21       5
     O     947      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  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: 5032
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 504, 3835
          Classifications: {'peptide': 504}
          Link IDs: {'PTRANS': 12, 'TRANS': 491}
    Chain: "B"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 790
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 6, 'TRANS': 94}
    Chain: "C"
      Number of atoms: 393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 393
          Classifications: {'peptide': 50}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 47}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.52, per 1000 atoms: 0.30
  Number of scatterers: 5032
  At special positions: 0
  Unit cell: (74.36, 123.37, 138.58, 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      43     16.00
     O     947      8.00
     N     875      7.00
     C    3167      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   3 " - pdb=" SG  CYS A  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  74 " - pdb=" SG  CYS A 105 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  92 " - pdb=" SG  CYS A 116 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 191 " - pdb=" SG  CYS A 292 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 309 " - pdb=" SG  CYS A 340 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  34 " - pdb=" SG  CYS B  69 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  45 " - pdb=" SG  CYS B  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  53 " - pdb=" SG  CYS B  67 " distance=2.04

  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
    NAG-ASN
      " NAG B 201 " - " ASN B  70 "
  Time building additional restraints: 0.32
  Conformation dependent library (CDL) restraints added in 223.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1182

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 12 sheets defined
      23.4% alpha, 29.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 82 through 86
      removed outlier: 3.808A  pdb=" N   ALA A  86 " --> pdb=" O   ASP A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 104
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 216 through 220
      removed outlier: 3.603A  pdb=" N   HIS A 220 " --> pdb=" O   ARG A 216 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 216 through 220'
    Processing helix  chain 'A' and resid 240 through 242
      No H-bonds generated for 'chain 'A' and resid 240 through 242'
    Processing helix  chain 'A' and resid 262 through 270
    Processing helix  chain 'A' and resid 392 through 396
      removed outlier: 3.598A  pdb=" N   THR A 395 " --> pdb=" O   THR A 392 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LYS A 396 " --> pdb=" O   GLY A 393 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 392 through 396'
    Processing helix  chain 'A' and resid 406 through 425
    Processing helix  chain 'A' and resid 437 through 458
      removed outlier: 5.797A  pdb=" N   SER A 452 " --> pdb=" O   GLN A 448 " (cutoff:3.500A)
      removed outlier: 5.750A  pdb=" N   ALA A 453 " --> pdb=" O   VAL A 449 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA A 456 " --> pdb=" O   SER A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 479
      removed outlier: 3.538A  pdb=" N   LEU A 468 " --> pdb=" O   PHE A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 502
      removed outlier: 3.726A  pdb=" N   PHE A 489 " --> pdb=" O   VAL A 485 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 133
    Processing helix  chain 'C' and resid 133 through 146
      removed outlier: 4.026A  pdb=" N   THR C 146 " --> pdb=" O   VAL C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 165
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13
      removed outlier: 7.173A  pdb=" N   ARG A 138 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   THR A  48 " --> pdb=" O   GLU A 136 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   GLU A 136 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13
      removed outlier: 3.690A  pdb=" N   GLU A 277 " --> pdb=" O   THR A 284 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 25
      removed outlier: 3.926A  pdb=" N   LYS A 291 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 228
      removed outlier: 7.034A  pdb=" N   GLY A 127 " --> pdb=" O   VAL A  56 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   SER A  58 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   LEU A 125 " --> pdb=" O   SER A  58 " (cutoff:3.500A)
      removed outlier: 5.084A  pdb=" N   CYS A  60 " --> pdb=" O   LYS A 123 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   LYS A 123 " --> pdb=" O   CYS A  60 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   GLU A  62 " --> pdb=" O   CYS A 121 " (cutoff:3.500A)
      removed outlier: 5.604A  pdb=" N   CYS A 121 " --> pdb=" O   GLU A  62 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   LEU A 274 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 73
    Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 246
    Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 308
      removed outlier: 6.641A  pdb=" N   ALA A 307 " --> pdb=" O   LYS A 341 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 315
      removed outlier: 3.568A  pdb=" N   SER A 320 " --> pdb=" O   THR A 328 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 312 through 315
      removed outlier: 3.965A  pdb=" N   ARG A 358 " --> pdb=" O   ASP A 380 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 347
    Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 5
      removed outlier: 6.199A  pdb=" N   TYR B  10 " --> pdb=" O   TRP B  75 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   VAL B  77 " --> pdb=" O   TYR B  10 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   MET B  12 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   GLY B  79 " --> pdb=" O   MET B  12 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 23 through 26

    213 hydrogen bonds defined for protein.
    576 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: 0.71

  Time building geometry restraints manager: 0.48 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1646
        1.35 -     1.47: 1271
        1.47 -     1.59: 2159
        1.59 -     1.71: 0
        1.71 -     1.83: 68
  Bond restraints: 5144
  Sorted by residual:
  bond pdb=" N   ARG B  94 "
       pdb=" CA  ARG B  94 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.23e-02 6.61e+03 5.30e+00
  bond pdb=" N   HIS A 250 "
       pdb=" CA  HIS A 250 "
    ideal  model  delta    sigma   weight residual
    1.455  1.482 -0.028 1.25e-02 6.40e+03 4.94e+00
  bond pdb=" N   HIS B 101 "
       pdb=" CA  HIS B 101 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.68e+00
  bond pdb=" CE1 HIS A 250 "
       pdb=" NE2 HIS A 250 "
    ideal  model  delta    sigma   weight residual
    1.321  1.336 -0.015 1.00e-02 1.00e+04 2.22e+00
  bond pdb=" CE1 HIS B 101 "
       pdb=" NE2 HIS B 101 "
    ideal  model  delta    sigma   weight residual
    1.321  1.336 -0.015 1.00e-02 1.00e+04 2.19e+00
  ... (remaining 5139 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.47: 6902
        2.47 -     4.93: 54
        4.93 -     7.40: 4
        7.40 -     9.86: 0
        9.86 -    12.33: 2
  Bond angle restraints: 6962
  Sorted by residual:
  angle pdb=" CA  CYS A 116 "
        pdb=" CB  CYS A 116 "
        pdb=" SG  CYS A 116 "
      ideal   model   delta    sigma   weight residual
     114.40  126.73  -12.33 2.30e+00 1.89e-01 2.87e+01
  angle pdb=" CA  CYS A  92 "
        pdb=" CB  CYS A  92 "
        pdb=" SG  CYS A  92 "
      ideal   model   delta    sigma   weight residual
     114.40  125.70  -11.30 2.30e+00 1.89e-01 2.41e+01
  angle pdb=" N   CYS A 116 "
        pdb=" CA  CYS A 116 "
        pdb=" C   CYS A 116 "
      ideal   model   delta    sigma   weight residual
     109.52  114.59   -5.07 1.55e+00 4.16e-01 1.07e+01
  angle pdb=" C   SER B  71 "
        pdb=" N   THR B  72 "
        pdb=" CA  THR B  72 "
      ideal   model   delta    sigma   weight residual
     122.32  127.75   -5.43 1.76e+00 3.23e-01 9.52e+00
  angle pdb=" C   LYS A 444 "
        pdb=" N   PHE A 445 "
        pdb=" CA  PHE A 445 "
      ideal   model   delta    sigma   weight residual
     120.68  116.13    4.55 1.70e+00 3.46e-01 7.16e+00
  ... (remaining 6957 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 2817
       17.87 -    35.75: 189
       35.75 -    53.62: 39
       53.62 -    71.50: 6
       71.50 -    89.37: 5
  Dihedral angle restraints: 3056
    sinusoidal: 1203
      harmonic: 1853
  Sorted by residual:
  dihedral pdb=" CB  CYS A  74 "
           pdb=" SG  CYS A  74 "
           pdb=" SG  CYS A 105 "
           pdb=" CB  CYS A 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.58  -87.42     1      1.00e+01 1.00e-02 9.17e+01
  dihedral pdb=" CB  CYS B  53 "
           pdb=" SG  CYS B  53 "
           pdb=" SG  CYS B  67 "
           pdb=" CB  CYS B  67 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -23.78  -62.22     1      1.00e+01 1.00e-02 5.13e+01
  dihedral pdb=" CB  CYS B  34 "
           pdb=" SG  CYS B  34 "
           pdb=" SG  CYS B  69 "
           pdb=" CB  CYS B  69 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -28.93  -57.07     1      1.00e+01 1.00e-02 4.38e+01
  ... (remaining 3053 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 602
       0.048 -    0.097: 137
       0.097 -    0.145: 30
       0.145 -    0.193: 3
       0.193 -    0.241: 1
  Chirality restraints: 773
  Sorted by residual:
  chirality pdb=" CA  CYS A 116 "
            pdb=" N   CYS A 116 "
            pdb=" C   CYS A 116 "
            pdb=" CB  CYS A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  CYS A  92 "
            pdb=" N   CYS A  92 "
            pdb=" C   CYS A  92 "
            pdb=" CB  CYS A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.74e-01
  chirality pdb=" CA  ARG B  94 "
            pdb=" N   ARG B  94 "
            pdb=" C   ARG B  94 "
            pdb=" CB  ARG B  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.67e-01
  ... (remaining 770 not shown)

  Planarity restraints: 888
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A  74 "   -0.021 5.00e-02 4.00e+02   3.23e-02 1.66e+00
        pdb=" N   PRO A  75 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A  75 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  75 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B  45 "    0.018 5.00e-02 4.00e+02   2.69e-02 1.16e+00
        pdb=" N   PRO B  46 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO B  46 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B  46 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B  53 "   -0.017 5.00e-02 4.00e+02   2.62e-02 1.10e+00
        pdb=" N   PRO B  54 "    0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO B  54 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B  54 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 885 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 1744
        2.85 -     3.36: 4336
        3.36 -     3.87: 7621
        3.87 -     4.39: 8126
        4.39 -     4.90: 14511
  Nonbonded interactions: 36338
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 380 "
            pdb=" NH1 ARG A 403 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" OG1 THR A 322 "
            pdb=" OG1 THR A 326 "
     model   vdw
     2.361 3.040
  nonbonded pdb=" O   ILE A 497 "
            pdb=" OG1 THR A 501 "
     model   vdw
     2.370 3.040
  nonbonded pdb=" OE1 GLU A 178 "
            pdb=" OG  SER A 188 "
     model   vdw
     2.385 3.040
  nonbonded pdb=" O   SER A 369 "
            pdb=" OG  SER A 369 "
     model   vdw
     2.389 3.040
  ... (remaining 36333 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.920
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
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      :  0.002   0.031   5154  Z= 0.133
  Angle     :  0.586  12.331   6983  Z= 0.333
  Chirality :  0.044   0.241    773
  Planarity :  0.003   0.032    887
  Dihedral  : 12.439  89.370   1847
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  3.72 %
    Favored  : 95.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.14 (0.29), residues: 649
  helix: -0.02 (0.42), residues: 132
  sheet: -0.56 (0.35), residues: 197
  loop : -2.67 (0.27), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  93 
 TYR   0.010   0.001   TYR A  61 
 PHE   0.017   0.001   PHE A 445 
 TRP   0.006   0.001   TRP A 226 
 HIS   0.002   0.000   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 5144)
  covalent geometry    : angle       0.56453 ( 6962)
  SS BOND              : bond        0.00503 (    9)
  SS BOND              : angle       3.08629 (   18)
  hydrogen bonds       : bond        0.12500 (  203)
  hydrogen bonds       : angle       5.23775 (  576)
  link_NAG-ASN         : bond        0.00635 (    1)
  link_NAG-ASN         : angle       1.64114 (    3)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 189
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.7547 (mtm) cc_final: 0.7153 (mtm)
REVERT: A   77 GLN cc_start: 0.8105 (tp40) cc_final: 0.7775 (mt0)
REVERT: A   81 TYR cc_start: 0.8482 (t80) cc_final: 0.8174 (t80)
REVERT: A  140 LEU cc_start: 0.8661 (mt) cc_final: 0.8299 (mt)
REVERT: A  178 GLU cc_start: 0.7788 (tp30) cc_final: 0.7459 (mm-30)
REVERT: A  201 ASP cc_start: 0.8099 (t0) cc_final: 0.7828 (t0)
REVERT: A  209 ASN cc_start: 0.8389 (t0) cc_final: 0.8051 (t0)
REVERT: A  221 ASP cc_start: 0.7948 (t70) cc_final: 0.7688 (t0)
REVERT: A  330 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7127 (mt-10)
REVERT: A  374 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8178 (mmtm)
REVERT: A  422 MET cc_start: 0.8617 (tpp) cc_final: 0.8022 (tpp)
REVERT: A  432 PHE cc_start: 0.7640 (m-10) cc_final: 0.4940 (p90)
REVERT: A  447 HIS cc_start: 0.8448 (t-90) cc_final: 0.7940 (t-170)
REVERT: A  455 LYS cc_start: 0.7775 (ttmt) cc_final: 0.6999 (mptt)
REVERT: A  471 PHE cc_start: 0.8609 (m-10) cc_final: 0.7968 (t80)
REVERT: B   32 ASN cc_start: 0.6953 (t0) cc_final: 0.6699 (t0)
REVERT: B   39 MET cc_start: 0.7032 (ptt) cc_final: 0.6825 (ttt)
REVERT: B  101 HIS cc_start: 0.7779 (OUTLIER) cc_final: 0.7542 (m-70)
REVERT: C  127 GLU cc_start: 0.8549 (tt0) cc_final: 0.8068 (mt-10)
  outliers start: 6
  outliers final: 1
  residues processed: 192
  average time/residue: 0.0928
  time to fit residues: 21.9441
Evaluate side-chains
  151 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 149
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain B residue  101 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0010
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.9790

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

Flipped N/Q/H residues before XYZ refinement:
A 131 GLN
A 363 ASN
C 153 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.164214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.132821 restraints weight = 7470.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.137265 restraints weight = 4334.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.140435 restraints weight = 3028.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.142413 restraints weight = 2357.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.144023 restraints weight = 1986.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   5154  Z= 0.152
  Angle     :  0.679  15.172   6983  Z= 0.347
  Chirality :  0.047   0.282    773
  Planarity :  0.004   0.060    887
  Dihedral  :  5.822  77.939    726
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 15.27 %
    Favored  : 80.63 %
  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: -1.26 (0.31), residues: 649
  helix:  1.27 (0.46), residues: 131
  sheet: -0.24 (0.36), residues: 195
  loop : -2.21 (0.29), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A   2 
 TYR   0.013   0.001   TYR A  61 
 PHE   0.010   0.001   PHE A 219 
 TRP   0.019   0.001   TRP C 129 
 HIS   0.005   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 5144)
  covalent geometry    : angle       0.65294 ( 6962)
  SS BOND              : bond        0.00727 (    9)
  SS BOND              : angle       3.61318 (   18)
  hydrogen bonds       : bond        0.03733 (  203)
  hydrogen bonds       : angle       4.46121 (  576)
  link_NAG-ASN         : bond        0.01243 (    1)
  link_NAG-ASN         : angle       2.30840 (    3)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 160
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8306 (tp40) cc_final: 0.8050 (mt0)
REVERT: A   81 TYR cc_start: 0.8593 (t80) cc_final: 0.8218 (t80)
REVERT: A  178 GLU cc_start: 0.8151 (tp30) cc_final: 0.7459 (mm-30)
REVERT: A  201 ASP cc_start: 0.8201 (t0) cc_final: 0.7919 (t0)
REVERT: A  203 TYR cc_start: 0.8356 (m-10) cc_final: 0.7940 (m-80)
REVERT: A  221 ASP cc_start: 0.8131 (t70) cc_final: 0.7844 (t0)
REVERT: A  241 GLU cc_start: 0.8005 (mp0) cc_final: 0.7768 (mp0)
REVERT: A  301 LEU cc_start: 0.8148 (mt) cc_final: 0.7884 (mp)
REVERT: A  365 VAL cc_start: 0.9161 (p) cc_final: 0.8900 (p)
REVERT: A  422 MET cc_start: 0.8677 (tpp) cc_final: 0.8055 (tpp)
REVERT: A  432 PHE cc_start: 0.7722 (m-10) cc_final: 0.5010 (p90)
REVERT: A  447 HIS cc_start: 0.8564 (t-90) cc_final: 0.8158 (t-170)
REVERT: A  455 LYS cc_start: 0.8118 (ttmt) cc_final: 0.7309 (mptt)
REVERT: A  466 GLN cc_start: 0.8864 (mp10) cc_final: 0.8036 (pm20)
REVERT: A  471 PHE cc_start: 0.8521 (m-10) cc_final: 0.7963 (t80)
REVERT: B   32 ASN cc_start: 0.6883 (t0) cc_final: 0.6477 (t0)
REVERT: C  127 GLU cc_start: 0.8524 (tt0) cc_final: 0.8241 (mt-10)
  outliers start: 22
  outliers final: 14
  residues processed: 170
  average time/residue: 0.0749
  time to fit residues: 16.2540
Evaluate side-chains
  158 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain C residue  130 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 22 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0870
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
B  59 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.164184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.133001 restraints weight = 7439.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.137437 restraints weight = 4287.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.140408 restraints weight = 2970.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.142652 restraints weight = 2326.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.143988 restraints weight = 1944.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5154  Z= 0.121
  Angle     :  0.651  17.934   6983  Z= 0.332
  Chirality :  0.045   0.281    773
  Planarity :  0.003   0.035    887
  Dihedral  :  5.488  80.271    724
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 19.74 %
    Favored  : 76.35 %
  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: -0.88 (0.32), residues: 649
  helix:  1.69 (0.47), residues: 132
  sheet: -0.12 (0.36), residues: 197
  loop : -1.95 (0.30), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 151 
 TYR   0.010   0.001   TYR A  61 
 PHE   0.017   0.001   PHE A 498 
 TRP   0.033   0.001   TRP C 129 
 HIS   0.005   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 5144)
  covalent geometry    : angle       0.62405 ( 6962)
  SS BOND              : bond        0.00425 (    9)
  SS BOND              : angle       3.61084 (   18)
  hydrogen bonds       : bond        0.03280 (  203)
  hydrogen bonds       : angle       4.17143 (  576)
  link_NAG-ASN         : bond        0.00618 (    1)
  link_NAG-ASN         : angle       2.05253 (    3)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 155
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8214 (tp40) cc_final: 0.8008 (mt0)
REVERT: A   81 TYR cc_start: 0.8603 (t80) cc_final: 0.8234 (t80)
REVERT: A  178 GLU cc_start: 0.8224 (tp30) cc_final: 0.7506 (mm-30)
REVERT: A  192 GLU cc_start: 0.8081 (mp0) cc_final: 0.7442 (mp0)
REVERT: A  201 ASP cc_start: 0.8207 (t0) cc_final: 0.7863 (t0)
REVERT: A  203 TYR cc_start: 0.8355 (m-10) cc_final: 0.8082 (m-80)
REVERT: A  221 ASP cc_start: 0.8107 (t70) cc_final: 0.7826 (t0)
REVERT: A  241 GLU cc_start: 0.8017 (mp0) cc_final: 0.7739 (mp0)
REVERT: A  285 ILE cc_start: 0.8833 (mp) cc_final: 0.8623 (mt)
REVERT: A  368 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7238 (mp0)
REVERT: A  412 PHE cc_start: 0.7640 (t80) cc_final: 0.7409 (t80)
REVERT: A  422 MET cc_start: 0.8565 (tpp) cc_final: 0.7922 (tpp)
REVERT: A  432 PHE cc_start: 0.7774 (m-10) cc_final: 0.4928 (p90)
REVERT: A  447 HIS cc_start: 0.8664 (t-90) cc_final: 0.8117 (t-170)
REVERT: A  455 LYS cc_start: 0.8087 (ttmt) cc_final: 0.7360 (mptt)
REVERT: A  466 GLN cc_start: 0.8857 (mp10) cc_final: 0.8099 (pm20)
REVERT: A  471 PHE cc_start: 0.8539 (m-10) cc_final: 0.8021 (t80)
REVERT: B   32 ASN cc_start: 0.6829 (t0) cc_final: 0.6437 (t0)
REVERT: C  127 GLU cc_start: 0.8336 (tt0) cc_final: 0.8078 (mt-10)
  outliers start: 21
  outliers final: 14
  residues processed: 166
  average time/residue: 0.0686
  time to fit residues: 14.8094
Evaluate side-chains
  167 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 152
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  151 MET
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0570
   chunk 14 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 56 optimal weight:    0.3980
   chunk 33 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.6904

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

Flipped N/Q/H residues before XYZ refinement:
A 144 HIS
A 159 GLN
A 227 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.157314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.125978 restraints weight = 7458.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.130167 restraints weight = 4443.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.133049 restraints weight = 3158.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.135063 restraints weight = 2499.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.136449 restraints weight = 2114.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   5154  Z= 0.215
  Angle     :  0.707  14.648   6983  Z= 0.366
  Chirality :  0.047   0.258    773
  Planarity :  0.004   0.039    887
  Dihedral  :  5.775  78.268    724
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 21.42 %
    Favored  : 73.37 %
  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: -0.81 (0.32), residues: 649
  helix:  1.72 (0.46), residues: 131
  sheet: -0.19 (0.36), residues: 196
  loop : -1.79 (0.31), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  90 
 TYR   0.020   0.002   TYR A  61 
 PHE   0.015   0.002   PHE A 219 
 TRP   0.016   0.002   TRP B  68 
 HIS   0.006   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 5144)
  covalent geometry    : angle       0.68344 ( 6962)
  SS BOND              : bond        0.00691 (    9)
  SS BOND              : angle       3.58407 (   18)
  hydrogen bonds       : bond        0.03973 (  203)
  hydrogen bonds       : angle       4.45490 (  576)
  link_NAG-ASN         : bond        0.00567 (    1)
  link_NAG-ASN         : angle       1.51904 (    3)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 146
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 TYR cc_start: 0.8478 (t80) cc_final: 0.8091 (t80)
REVERT: A  192 GLU cc_start: 0.8173 (mp0) cc_final: 0.7355 (mp0)
REVERT: A  201 ASP cc_start: 0.8290 (t0) cc_final: 0.8038 (t0)
REVERT: A  221 ASP cc_start: 0.8183 (t70) cc_final: 0.7896 (t0)
REVERT: A  241 GLU cc_start: 0.8237 (mp0) cc_final: 0.7901 (mp0)
REVERT: A  332 GLN cc_start: 0.7837 (tm-30) cc_final: 0.7395 (tt0)
REVERT: A  412 PHE cc_start: 0.7755 (t80) cc_final: 0.7550 (t80)
REVERT: A  422 MET cc_start: 0.8736 (tpp) cc_final: 0.8163 (tpp)
REVERT: A  447 HIS cc_start: 0.8776 (t-90) cc_final: 0.8211 (t-170)
REVERT: A  466 GLN cc_start: 0.8873 (mp10) cc_final: 0.8172 (pm20)
REVERT: A  471 PHE cc_start: 0.8599 (m-10) cc_final: 0.8005 (t80)
REVERT: B   34 CYS cc_start: 0.6992 (t) cc_final: 0.6571 (t)
REVERT: C  129 TRP cc_start: 0.7876 (t60) cc_final: 0.7552 (t60)
  outliers start: 28
  outliers final: 21
  residues processed: 160
  average time/residue: 0.0681
  time to fit residues: 14.2994
Evaluate side-chains
  159 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 52 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    1.3184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.156675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.125540 restraints weight = 7597.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.129816 restraints weight = 4417.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.132768 restraints weight = 3102.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.134816 restraints weight = 2436.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.136085 restraints weight = 2050.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.3268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   5154  Z= 0.182
  Angle     :  0.713  21.172   6983  Z= 0.367
  Chirality :  0.047   0.319    773
  Planarity :  0.004   0.039    887
  Dihedral  :  5.745  79.276    724
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 22.91 %
    Favored  : 71.69 %
  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: -0.77 (0.32), residues: 649
  helix:  1.90 (0.46), residues: 130
  sheet: -0.11 (0.37), residues: 192
  loop : -1.83 (0.31), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  94 
 TYR   0.016   0.002   TYR A  61 
 PHE   0.027   0.002   PHE A 454 
 TRP   0.010   0.001   TRP C 129 
 HIS   0.006   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 5144)
  covalent geometry    : angle       0.68601 ( 6962)
  SS BOND              : bond        0.00767 (    9)
  SS BOND              : angle       3.82074 (   18)
  hydrogen bonds       : bond        0.03800 (  203)
  hydrogen bonds       : angle       4.29261 (  576)
  link_NAG-ASN         : bond        0.00720 (    1)
  link_NAG-ASN         : angle       1.88875 (    3)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 147
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8317 (mm110) cc_final: 0.7912 (mm-40)
REVERT: A   81 TYR cc_start: 0.8283 (t80) cc_final: 0.7859 (t80)
REVERT: A  192 GLU cc_start: 0.8259 (mp0) cc_final: 0.7427 (mp0)
REVERT: A  201 ASP cc_start: 0.8347 (t0) cc_final: 0.8044 (t0)
REVERT: A  221 ASP cc_start: 0.8155 (t70) cc_final: 0.7871 (t0)
REVERT: A  412 PHE cc_start: 0.7688 (t80) cc_final: 0.7484 (t80)
REVERT: A  422 MET cc_start: 0.8687 (tpp) cc_final: 0.8233 (tpp)
REVERT: A  447 HIS cc_start: 0.8826 (t-90) cc_final: 0.8273 (t-170)
REVERT: A  466 GLN cc_start: 0.8908 (mp10) cc_final: 0.8235 (pm20)
REVERT: A  471 PHE cc_start: 0.8567 (m-10) cc_final: 0.8024 (t80)
REVERT: B   32 ASN cc_start: 0.6807 (t0) cc_final: 0.6389 (t0)
REVERT: C  161 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7809 (mm)
  outliers start: 29
  outliers final: 21
  residues processed: 165
  average time/residue: 0.0730
  time to fit residues: 15.6822
Evaluate side-chains
  157 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 27 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 63 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 47 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   overall best weight:    1.2784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.155991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.124943 restraints weight = 7618.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.129176 restraints weight = 4465.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.132112 restraints weight = 3145.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.134118 restraints weight = 2474.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.135434 restraints weight = 2090.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.3487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   5154  Z= 0.176
  Angle     :  0.709  15.618   6983  Z= 0.366
  Chirality :  0.047   0.292    773
  Planarity :  0.004   0.039    887
  Dihedral  :  5.787  80.046    724
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 24.58 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -0.68 (0.32), residues: 649
  helix:  1.93 (0.46), residues: 131
  sheet: -0.01 (0.38), residues: 187
  loop : -1.78 (0.30), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 293 
 TYR   0.016   0.002   TYR A  61 
 PHE   0.021   0.002   PHE A 454 
 TRP   0.021   0.001   TRP C 129 
 HIS   0.006   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 5144)
  covalent geometry    : angle       0.68131 ( 6962)
  SS BOND              : bond        0.00554 (    9)
  SS BOND              : angle       3.86011 (   18)
  hydrogen bonds       : bond        0.03711 (  203)
  hydrogen bonds       : angle       4.26701 (  576)
  link_NAG-ASN         : bond        0.00600 (    1)
  link_NAG-ASN         : angle       1.78637 (    3)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8551 (mm110) cc_final: 0.8163 (mm-40)
REVERT: A   81 TYR cc_start: 0.8371 (t80) cc_final: 0.8094 (t80)
REVERT: A  178 GLU cc_start: 0.8053 (tp30) cc_final: 0.7575 (mm-30)
REVERT: A  192 GLU cc_start: 0.8259 (mp0) cc_final: 0.7507 (mp0)
REVERT: A  201 ASP cc_start: 0.8321 (t0) cc_final: 0.8037 (t0)
REVERT: A  221 ASP cc_start: 0.8199 (t70) cc_final: 0.7915 (t0)
REVERT: A  332 GLN cc_start: 0.7646 (tm-30) cc_final: 0.7141 (tt0)
REVERT: A  412 PHE cc_start: 0.7716 (t80) cc_final: 0.7508 (t80)
REVERT: A  422 MET cc_start: 0.8693 (tpp) cc_final: 0.8240 (tpp)
REVERT: A  447 HIS cc_start: 0.8854 (t-90) cc_final: 0.8289 (t-170)
REVERT: A  466 GLN cc_start: 0.8922 (mp10) cc_final: 0.8267 (pm20)
REVERT: A  471 PHE cc_start: 0.8636 (m-10) cc_final: 0.8071 (t80)
REVERT: B   32 ASN cc_start: 0.6737 (t0) cc_final: 0.6416 (t0)
REVERT: C  154 LYS cc_start: 0.4403 (mttt) cc_final: 0.3643 (mtmm)
REVERT: C  161 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7664 (mm)
  outliers start: 28
  outliers final: 23
  residues processed: 160
  average time/residue: 0.0719
  time to fit residues: 14.9990
Evaluate side-chains
  159 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 34 optimal weight:    0.3980
   chunk 47 optimal weight:    7.9990
   chunk 41 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 22 optimal weight:    0.2980
   chunk 58 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 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 = 0.3890 r_free = 0.3890 target = 0.159245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.128395 restraints weight = 7429.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.132653 restraints weight = 4339.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.135602 restraints weight = 3052.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.137562 restraints weight = 2394.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.138827 restraints weight = 2026.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.3546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5154  Z= 0.135
  Angle     :  0.727  23.048   6983  Z= 0.368
  Chirality :  0.047   0.317    773
  Planarity :  0.004   0.041    887
  Dihedral  :  5.719  80.893    724
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 25.70 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -0.53 (0.33), residues: 649
  helix:  2.12 (0.47), residues: 131
  sheet:  0.08 (0.38), residues: 192
  loop : -1.74 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A   2 
 TYR   0.011   0.001   TYR A  61 
 PHE   0.018   0.001   PHE A 454 
 TRP   0.013   0.001   TRP C 129 
 HIS   0.005   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 5144)
  covalent geometry    : angle       0.69850 ( 6962)
  SS BOND              : bond        0.00968 (    9)
  SS BOND              : angle       3.99266 (   18)
  hydrogen bonds       : bond        0.03523 (  203)
  hydrogen bonds       : angle       4.08876 (  576)
  link_NAG-ASN         : bond        0.00581 (    1)
  link_NAG-ASN         : angle       1.84567 (    3)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8559 (mm110) cc_final: 0.8152 (mm-40)
REVERT: A  178 GLU cc_start: 0.7914 (tp30) cc_final: 0.7285 (mm-30)
REVERT: A  192 GLU cc_start: 0.8218 (mp0) cc_final: 0.7446 (mp0)
REVERT: A  201 ASP cc_start: 0.8312 (t0) cc_final: 0.8033 (t0)
REVERT: A  221 ASP cc_start: 0.8187 (t70) cc_final: 0.7890 (t0)
REVERT: A  412 PHE cc_start: 0.7767 (t80) cc_final: 0.7552 (t80)
REVERT: A  422 MET cc_start: 0.8503 (tpp) cc_final: 0.8029 (tpp)
REVERT: A  447 HIS cc_start: 0.8744 (t-90) cc_final: 0.8065 (t-170)
REVERT: A  455 LYS cc_start: 0.7766 (ttmt) cc_final: 0.7196 (mptt)
REVERT: A  466 GLN cc_start: 0.8908 (mp10) cc_final: 0.8601 (mp10)
REVERT: A  471 PHE cc_start: 0.8610 (m-10) cc_final: 0.7949 (t80)
REVERT: B   32 ASN cc_start: 0.6687 (t0) cc_final: 0.6365 (t0)
REVERT: B   60 TYR cc_start: 0.8908 (m-80) cc_final: 0.8705 (m-80)
REVERT: C  161 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8110 (mm)
  outliers start: 22
  outliers final: 19
  residues processed: 153
  average time/residue: 0.0675
  time to fit residues: 13.6739
Evaluate side-chains
  158 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 53 optimal weight:    7.9990
   chunk 3 optimal weight:    0.0010
   chunk 29 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    1.1992

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

Flipped N/Q/H residues before XYZ refinement:
** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 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 = 0.3863 r_free = 0.3863 target = 0.156806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.125663 restraints weight = 7594.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.129868 restraints weight = 4475.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.132772 restraints weight = 3162.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.134595 restraints weight = 2489.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.136059 restraints weight = 2117.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.3718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   5154  Z= 0.170
  Angle     :  0.729  18.332   6983  Z= 0.372
  Chirality :  0.047   0.310    773
  Planarity :  0.004   0.044    887
  Dihedral  :  5.779  80.178    724
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 25.33 %
    Favored  : 69.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -0.54 (0.32), residues: 649
  helix:  2.05 (0.46), residues: 131
  sheet:  0.10 (0.38), residues: 192
  loop : -1.73 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   2 
 TYR   0.016   0.002   TYR A  61 
 PHE   0.015   0.001   PHE A 454 
 TRP   0.010   0.001   TRP A 226 
 HIS   0.005   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 5144)
  covalent geometry    : angle       0.70005 ( 6962)
  SS BOND              : bond        0.00685 (    9)
  SS BOND              : angle       3.99340 (   18)
  hydrogen bonds       : bond        0.03746 (  203)
  hydrogen bonds       : angle       4.20588 (  576)
  link_NAG-ASN         : bond        0.00482 (    1)
  link_NAG-ASN         : angle       1.59443 (    3)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8640 (mm110) cc_final: 0.8220 (mm-40)
REVERT: A   81 TYR cc_start: 0.8450 (t80) cc_final: 0.8198 (t80)
REVERT: A  192 GLU cc_start: 0.8312 (mp0) cc_final: 0.7474 (mp0)
REVERT: A  201 ASP cc_start: 0.8326 (t0) cc_final: 0.8043 (t0)
REVERT: A  221 ASP cc_start: 0.8218 (t70) cc_final: 0.7928 (t0)
REVERT: A  332 GLN cc_start: 0.7109 (tt0) cc_final: 0.6732 (tm-30)
REVERT: A  412 PHE cc_start: 0.7737 (t80) cc_final: 0.7521 (t80)
REVERT: A  422 MET cc_start: 0.8578 (tpp) cc_final: 0.8132 (tpp)
REVERT: A  455 LYS cc_start: 0.7815 (ttmt) cc_final: 0.7215 (mptt)
REVERT: A  466 GLN cc_start: 0.8836 (mp10) cc_final: 0.8474 (mp10)
REVERT: A  468 LEU cc_start: 0.8573 (mt) cc_final: 0.8295 (mm)
REVERT: A  471 PHE cc_start: 0.8721 (m-10) cc_final: 0.8030 (t80)
REVERT: B   32 ASN cc_start: 0.6794 (t0) cc_final: 0.6531 (t0)
REVERT: B   60 TYR cc_start: 0.8915 (m-80) cc_final: 0.8675 (m-80)
REVERT: C  161 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7752 (mm)
  outliers start: 26
  outliers final: 23
  residues processed: 153
  average time/residue: 0.0640
  time to fit residues: 13.0877
Evaluate side-chains
  155 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 58 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 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 = 0.3864 r_free = 0.3864 target = 0.156571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.126979 restraints weight = 7458.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.131115 restraints weight = 4289.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.133973 restraints weight = 2982.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.135750 restraints weight = 2326.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.137312 restraints weight = 1966.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.3833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   5154  Z= 0.171
  Angle     :  0.751  20.248   6983  Z= 0.381
  Chirality :  0.048   0.330    773
  Planarity :  0.004   0.042    887
  Dihedral  :  5.819  79.646    724
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 25.88 %
    Favored  : 69.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -0.69 (0.32), residues: 649
  helix:  1.86 (0.46), residues: 136
  sheet: -0.01 (0.38), residues: 192
  loop : -1.85 (0.31), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   2 
 TYR   0.015   0.002   TYR A  61 
 PHE   0.015   0.001   PHE A 454 
 TRP   0.016   0.001   TRP A 212 
 HIS   0.007   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 5144)
  covalent geometry    : angle       0.72221 ( 6962)
  SS BOND              : bond        0.00862 (    9)
  SS BOND              : angle       4.08306 (   18)
  hydrogen bonds       : bond        0.03778 (  203)
  hydrogen bonds       : angle       4.13179 (  576)
  link_NAG-ASN         : bond        0.00529 (    1)
  link_NAG-ASN         : angle       1.69799 (    3)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 135
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8581 (mm110) cc_final: 0.8089 (mm-40)
REVERT: A   81 TYR cc_start: 0.8464 (t80) cc_final: 0.8156 (t80)
REVERT: A  178 GLU cc_start: 0.7961 (tp30) cc_final: 0.7509 (mm-30)
REVERT: A  192 GLU cc_start: 0.8410 (mp0) cc_final: 0.7646 (mp0)
REVERT: A  201 ASP cc_start: 0.8565 (t0) cc_final: 0.8364 (t0)
REVERT: A  412 PHE cc_start: 0.7716 (t80) cc_final: 0.7508 (t80)
REVERT: A  422 MET cc_start: 0.8580 (tpp) cc_final: 0.8131 (tpp)
REVERT: A  455 LYS cc_start: 0.7814 (ttmt) cc_final: 0.7234 (mptt)
REVERT: A  466 GLN cc_start: 0.8802 (mp10) cc_final: 0.8437 (mp10)
REVERT: A  468 LEU cc_start: 0.8614 (mt) cc_final: 0.8334 (mm)
REVERT: A  471 PHE cc_start: 0.8657 (m-10) cc_final: 0.8000 (t80)
REVERT: B   11 TYR cc_start: 0.8435 (m-10) cc_final: 0.8222 (m-10)
REVERT: B   32 ASN cc_start: 0.6665 (t0) cc_final: 0.6378 (t0)
REVERT: C  161 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7741 (mm)
  outliers start: 25
  outliers final: 23
  residues processed: 150
  average time/residue: 0.0662
  time to fit residues: 13.2591
Evaluate side-chains
  156 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 41 optimal weight:    9.9990
   chunk 10 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 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 = 0.3875 r_free = 0.3875 target = 0.157905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.126518 restraints weight = 7633.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.130780 restraints weight = 4480.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.133740 restraints weight = 3150.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.135587 restraints weight = 2475.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.137170 restraints weight = 2102.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5154  Z= 0.142
  Angle     :  0.725  18.031   6983  Z= 0.370
  Chirality :  0.047   0.298    773
  Planarity :  0.004   0.038    887
  Dihedral  :  5.741  79.824    724
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 26.63 %
    Favored  : 69.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -0.61 (0.32), residues: 649
  helix:  1.95 (0.46), residues: 136
  sheet:  0.08 (0.38), residues: 192
  loop : -1.83 (0.31), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A   2 
 TYR   0.012   0.001   TYR A  61 
 PHE   0.016   0.001   PHE A 454 
 TRP   0.023   0.001   TRP A 212 
 HIS   0.005   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5144)
  covalent geometry    : angle       0.69650 ( 6962)
  SS BOND              : bond        0.00734 (    9)
  SS BOND              : angle       3.96075 (   18)
  hydrogen bonds       : bond        0.03531 (  203)
  hydrogen bonds       : angle       4.02498 (  576)
  link_NAG-ASN         : bond        0.00551 (    1)
  link_NAG-ASN         : angle       1.76044 (    3)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 137
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8602 (mm110) cc_final: 0.8108 (mm-40)
REVERT: A  178 GLU cc_start: 0.8063 (tp30) cc_final: 0.7625 (mm-30)
REVERT: A  192 GLU cc_start: 0.8392 (mp0) cc_final: 0.7615 (mp0)
REVERT: A  412 PHE cc_start: 0.7797 (t80) cc_final: 0.7593 (t80)
REVERT: A  422 MET cc_start: 0.8548 (tpp) cc_final: 0.8022 (tpp)
REVERT: A  455 LYS cc_start: 0.7698 (ttmt) cc_final: 0.6937 (mptt)
REVERT: A  466 GLN cc_start: 0.8816 (mp10) cc_final: 0.8373 (mp10)
REVERT: A  468 LEU cc_start: 0.8849 (mt) cc_final: 0.8562 (mm)
REVERT: A  471 PHE cc_start: 0.8726 (m-10) cc_final: 0.8008 (t80)
REVERT: B   32 ASN cc_start: 0.6631 (t0) cc_final: 0.6347 (t0)
REVERT: C  161 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7990 (mm)
  outliers start: 23
  outliers final: 20
  residues processed: 148
  average time/residue: 0.0626
  time to fit residues: 12.4232
Evaluate side-chains
  154 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   41 ILE
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0980
   chunk 7 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0270
   chunk 24 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 13 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   overall best weight:    0.4438

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

Flipped N/Q/H residues before XYZ refinement:
** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 GLN
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 153 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.179332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.146504 restraints weight = 7278.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.151269 restraints weight = 4372.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.154589 restraints weight = 3110.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.156816 restraints weight = 2458.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.158405 restraints weight = 2080.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5154  Z= 0.120
  Angle     :  0.720  18.193   6983  Z= 0.365
  Chirality :  0.046   0.282    773
  Planarity :  0.004   0.037    887
  Dihedral  :  5.530  80.604    724
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 26.82 %
    Favored  : 68.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -0.38 (0.33), residues: 649
  helix:  2.39 (0.46), residues: 131
  sheet:  0.20 (0.38), residues: 190
  loop : -1.73 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  94 
 TYR   0.031   0.001   TYR B  60 
 PHE   0.017   0.001   PHE A 454 
 TRP   0.022   0.001   TRP A 212 
 HIS   0.004   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 5144)
  covalent geometry    : angle       0.69265 ( 6962)
  SS BOND              : bond        0.00715 (    9)
  SS BOND              : angle       3.89282 (   18)
  hydrogen bonds       : bond        0.03232 (  203)
  hydrogen bonds       : angle       3.84109 (  576)
  link_NAG-ASN         : bond        0.00522 (    1)
  link_NAG-ASN         : angle       1.75961 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1085.71 seconds
wall clock time: 19 minutes 28.23 seconds (1168.23 seconds total)