Starting phenix.real_space_refine
on Thu Sep 10 23:06:09 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6zqi_11364/09_2026/6zqi_11364.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zqi_11364/09_2026/6zqi_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zqi_11364/09_2026/6zqi_11364.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zqi_11364/09_2026/6zqi_11364.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zqi_11364/09_2026/6zqi_11364.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zqi_11364/09_2026/6zqi_11364.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6zqi_11364/09_2026/6zqi_11364.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6zqi_11364/09_2026/6zqi_11364.cif"
  }
  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-2.2.1-6174/lib/python3.11/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 chiralities: 1
  Time building chain proxies: 1.29, per 1000 atoms: 0.26
  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: 0.34
  Conformation dependent library (CDL) restraints added in 188.4 milliseconds
  

  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: 0.65

  Time building geometry restraints manager: 0.49 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: 2799
       17.87 -    35.75: 188
       35.75 -    53.62: 37
       53.62 -    71.50: 6
       71.50 -    89.37: 5
  Dihedral angle restraints: 3035
    sinusoidal: 1182
      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 3032 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.370
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
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  : 12.413  89.370   1826
  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 are 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/Z
  covalent geometry    : bond        0.00242 /  0.13 ( 5144)
  covalent geometry    : angle       0.56453 /  0.32 ( 6962)
  SS BOND              : bond        0.00503 /  0.30 (    9)
  SS BOND              : angle       3.08629 /  1.60 (   18)
  hydrogen bonds       : bond        0.12500 /  7.75 (  203)
  hydrogen bonds       : angle       5.23775 /  3.71 (  576)
  link_NAG-ASN         : bond        0.00635 /  0.33 (    1)
  link_NAG-ASN         : angle       1.64114 /  0.82 (    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  : 0.182 
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: 0.7400 (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: 0.8616 (tpp) cc_final: 0.8022 (tpp)
REVERT: A  432 PHE cc_start: 0.7641 (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: 0.7774 (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: 0.8067 (mt-10)
  outliers start: 6
  outliers final: 1
  residues processed: 192
  average time/residue: 0.0832
  time to fit residues: 19.8752
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  : 0.149 
-------------------------------------------------------------------------------
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...
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 = 0.3952 r_free = 0.3952 target = 0.164297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.132810 restraints weight = 7472.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.137303 restraints weight = 4336.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.140229 restraints weight = 3026.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.142533 restraints weight = 2376.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.144095 restraints weight = 1985.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5154  Z= 0.152
  Angle     :  0.679  14.936   6983  Z= 0.346
  Chirality :  0.046   0.282    773
  Planarity :  0.004   0.058    887
  Dihedral  :  5.761  77.951    705
  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 :  4.28 %
    Allowed  : 14.53 %
    Favored  : 81.19 %
  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 are not related in a simple way.
  whole: -1.27 (0.31), residues: 649
  helix:  1.28 (0.46), residues: 131
  sheet: -0.24 (0.36), residues: 195
  loop : -2.22 (0.29), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 151 
 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/Z
  covalent geometry    : bond        0.00350 /  0.15 ( 5144)
  covalent geometry    : angle       0.65244 /  0.34 ( 6962)
  SS BOND              : bond        0.00675 /  0.30 (    9)
  SS BOND              : angle       3.63002 /  1.98 (   18)
  hydrogen bonds       : bond        0.03735 /  2.36 (  203)
  hydrogen bonds       : angle       4.46580 /  3.19 (  576)
  link_NAG-ASN         : bond        0.01128 /  0.59 (    1)
  link_NAG-ASN         : angle       2.27388 /  1.25 (    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: 23
    poor density    : 159
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8268 (tp40) cc_final: 0.8035 (mt0)
REVERT: A   81 TYR cc_start: 0.8581 (t80) cc_final: 0.8216 (t80)
REVERT: A  178 GLU cc_start: 0.8137 (tp30) cc_final: 0.7450 (mm-30)
REVERT: A  201 ASP cc_start: 0.8193 (t0) cc_final: 0.7913 (t0)
REVERT: A  203 TYR cc_start: 0.8346 (m-10) cc_final: 0.7945 (m-80)
REVERT: A  221 ASP cc_start: 0.8117 (t70) cc_final: 0.7834 (t0)
REVERT: A  241 GLU cc_start: 0.7982 (mp0) cc_final: 0.7746 (mp0)
REVERT: A  301 LEU cc_start: 0.8139 (mt) cc_final: 0.7874 (mp)
REVERT: A  365 VAL cc_start: 0.9153 (p) cc_final: 0.8896 (p)
REVERT: A  422 MET cc_start: 0.8676 (tpp) cc_final: 0.8054 (tpp)
REVERT: A  432 PHE cc_start: 0.7703 (m-10) cc_final: 0.5008 (p90)
REVERT: A  447 HIS cc_start: 0.8565 (t-90) cc_final: 0.8156 (t-170)
REVERT: A  455 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7320 (mptt)
REVERT: A  466 GLN cc_start: 0.8854 (mp10) cc_final: 0.8018 (pm20)
REVERT: A  471 PHE cc_start: 0.8493 (m-10) cc_final: 0.7957 (t80)
REVERT: B   32 ASN cc_start: 0.6873 (t0) cc_final: 0.6472 (t0)
REVERT: C  127 GLU cc_start: 0.8508 (tt0) cc_final: 0.8229 (mt-10)
  outliers start: 23
  outliers final: 14
  residues processed: 170
  average time/residue: 0.0732
  time to fit residues: 15.9723
Evaluate side-chains
  159 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
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:    0.0270
   chunk 43 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 44 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0020
   chunk 35 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.4046

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  59 GLN
C 153 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.166075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.133856 restraints weight = 7394.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.138431 restraints weight = 4320.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.141590 restraints weight = 3025.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.143597 restraints weight = 2367.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.145232 restraints weight = 2002.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.2399

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= 0.113
  Angle     :  0.646  17.620   6983  Z= 0.329
  Chirality :  0.045   0.290    773
  Planarity :  0.003   0.034    887
  Dihedral  :  5.393  80.400    703
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.74 %
    Favored  : 77.09 %
  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 are not related in a simple way.
  whole: -0.91 (0.31), residues: 649
  helix:  1.66 (0.47), residues: 132
  sheet: -0.10 (0.36), residues: 197
  loop : -1.98 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  94 
 TYR   0.009   0.001   TYR A 306 
 PHE   0.018   0.001   PHE A 498 
 TRP   0.032   0.001   TRP C 129 
 HIS   0.005   0.001   HIS A  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.11 ( 5144)
  covalent geometry    : angle       0.61914 /  0.32 ( 6962)
  SS BOND              : bond        0.00730 /  0.34 (    9)
  SS BOND              : angle       3.58924 /  1.95 (   18)
  hydrogen bonds       : bond        0.03209 /  2.00 (  203)
  hydrogen bonds       : angle       4.15561 /  2.98 (  576)
  link_NAG-ASN         : bond        0.00603 /  0.32 (    1)
  link_NAG-ASN         : angle       2.31479 /  1.20 (    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
  178 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 161
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 TYR cc_start: 0.8542 (t80) cc_final: 0.8197 (t80)
REVERT: A  178 GLU cc_start: 0.8218 (tp30) cc_final: 0.7505 (mm-30)
REVERT: A  192 GLU cc_start: 0.8170 (mp0) cc_final: 0.7966 (mp0)
REVERT: A  201 ASP cc_start: 0.8182 (t0) cc_final: 0.7845 (t0)
REVERT: A  203 TYR cc_start: 0.8330 (m-10) cc_final: 0.8072 (m-80)
REVERT: A  221 ASP cc_start: 0.8074 (t70) cc_final: 0.7798 (t0)
REVERT: A  241 GLU cc_start: 0.7952 (mp0) cc_final: 0.7674 (mp0)
REVERT: A  285 ILE cc_start: 0.8843 (mp) cc_final: 0.8626 (mt)
REVERT: A  412 PHE cc_start: 0.7611 (t80) cc_final: 0.7383 (t80)
REVERT: A  422 MET cc_start: 0.8559 (tpp) cc_final: 0.7897 (tpp)
REVERT: A  432 PHE cc_start: 0.7689 (m-10) cc_final: 0.4887 (p90)
REVERT: A  447 HIS cc_start: 0.8642 (t-90) cc_final: 0.8072 (t-170)
REVERT: A  455 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7362 (mptt)
REVERT: A  466 GLN cc_start: 0.8843 (mp10) cc_final: 0.8079 (pm20)
REVERT: A  471 PHE cc_start: 0.8507 (m-10) cc_final: 0.8023 (t80)
REVERT: B   32 ASN cc_start: 0.6772 (t0) cc_final: 0.6379 (t0)
REVERT: C  127 GLU cc_start: 0.8412 (tt0) cc_final: 0.8135 (mt-10)
  outliers start: 17
  outliers final: 12
  residues processed: 169
  average time/residue: 0.0636
  time to fit residues: 14.3581
Evaluate side-chains
  164 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 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  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:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0010
   chunk 33 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 62 optimal weight:    0.2980
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 144 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.163319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.131657 restraints weight = 7395.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.136025 restraints weight = 4349.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.139129 restraints weight = 3063.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.141111 restraints weight = 2394.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.142622 restraints weight = 2030.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2763

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= 0.133
  Angle     :  0.657  19.566   6983  Z= 0.336
  Chirality :  0.045   0.300    773
  Planarity :  0.004   0.034    887
  Dihedral  :  5.458  80.044    703
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 20.11 %
    Favored  : 75.42 %
  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 are not related in a simple way.
  whole: -0.65 (0.32), residues: 649
  helix:  1.99 (0.47), residues: 131
  sheet: -0.02 (0.37), residues: 196
  loop : -1.80 (0.30), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  33 
 TYR   0.012   0.001   TYR A  61 
 PHE   0.012   0.001   PHE A 454 
 TRP   0.024   0.001   TRP C 129 
 HIS   0.005   0.001   HIS A  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.13 ( 5144)
  covalent geometry    : angle       0.62930 /  0.32 ( 6962)
  SS BOND              : bond        0.00760 /  0.36 (    9)
  SS BOND              : angle       3.69411 /  1.98 (   18)
  hydrogen bonds       : bond        0.03358 /  2.14 (  203)
  hydrogen bonds       : angle       4.13850 /  3.00 (  576)
  link_NAG-ASN         : bond        0.00513 /  0.27 (    1)
  link_NAG-ASN         : angle       1.62302 /  0.90 (    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
  179 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 155
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 TYR cc_start: 0.8637 (t80) cc_final: 0.8324 (t80)
REVERT: A  178 GLU cc_start: 0.8147 (tp30) cc_final: 0.7448 (mm-30)
REVERT: A  192 GLU cc_start: 0.8123 (mp0) cc_final: 0.7370 (mp0)
REVERT: A  201 ASP cc_start: 0.8157 (t0) cc_final: 0.7867 (t0)
REVERT: A  203 TYR cc_start: 0.8369 (m-10) cc_final: 0.8145 (m-80)
REVERT: A  221 ASP cc_start: 0.8099 (t70) cc_final: 0.7820 (t0)
REVERT: A  241 GLU cc_start: 0.8033 (mp0) cc_final: 0.7719 (mp0)
REVERT: A  332 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7473 (tt0)
REVERT: A  412 PHE cc_start: 0.7603 (t80) cc_final: 0.7364 (t80)
REVERT: A  422 MET cc_start: 0.8519 (tpp) cc_final: 0.7956 (tpp)
REVERT: A  447 HIS cc_start: 0.8708 (t-90) cc_final: 0.8125 (t-170)
REVERT: A  455 LYS cc_start: 0.8053 (ttmt) cc_final: 0.7386 (mptt)
REVERT: A  461 MET cc_start: 0.4562 (mpp) cc_final: 0.4252 (mpp)
REVERT: A  466 GLN cc_start: 0.8837 (mp10) cc_final: 0.8111 (pm20)
REVERT: A  471 PHE cc_start: 0.8498 (m-10) cc_final: 0.8025 (t80)
REVERT: B   32 ASN cc_start: 0.6843 (t0) cc_final: 0.6339 (t0)
REVERT: C  127 GLU cc_start: 0.8193 (tt0) cc_final: 0.7879 (mt-10)
REVERT: C  161 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8186 (mm)
  outliers start: 24
  outliers final: 18
  residues processed: 167
  average time/residue: 0.0662
  time to fit residues: 14.5670
Evaluate side-chains
  161 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
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  113 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  151 MET
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  365 VAL
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 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:    0.0970
   chunk 52 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 33 optimal weight:    0.1980
   chunk 48 optimal weight:   10.0000
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.5578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3944 r_free = 0.3944 target = 0.164171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.132164 restraints weight = 7545.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.136564 restraints weight = 4394.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.139735 restraints weight = 3089.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.141926 restraints weight = 2413.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.143288 restraints weight = 2025.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5154  Z= 0.115
  Angle     :  0.636  13.730   6983  Z= 0.327
  Chirality :  0.044   0.229    773
  Planarity :  0.003   0.035    887
  Dihedral  :  5.467  80.492    703
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 21.42 %
    Favored  : 73.18 %
  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 are not related in a simple way.
  whole: -0.52 (0.32), residues: 649
  helix:  2.26 (0.47), residues: 131
  sheet:  0.12 (0.37), residues: 195
  loop : -1.84 (0.30), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  33 
 TYR   0.018   0.001   TYR B  60 
 PHE   0.028   0.001   PHE A 454 
 TRP   0.018   0.001   TRP C 129 
 HIS   0.005   0.001   HIS A  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.11 ( 5144)
  covalent geometry    : angle       0.60593 /  0.31 ( 6962)
  SS BOND              : bond        0.00646 /  0.27 (    9)
  SS BOND              : angle       3.74269 /  1.87 (   18)
  hydrogen bonds       : bond        0.03100 /  2.01 (  203)
  hydrogen bonds       : angle       4.02802 /  2.90 (  576)
  link_NAG-ASN         : bond        0.00530 /  0.28 (    1)
  link_NAG-ASN         : angle       2.00934 /  1.08 (    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
  179 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 TYR cc_start: 0.8654 (t80) cc_final: 0.8344 (t80)
REVERT: A  178 GLU cc_start: 0.8132 (tp30) cc_final: 0.7370 (mm-30)
REVERT: A  192 GLU cc_start: 0.8097 (mp0) cc_final: 0.7255 (mp0)
REVERT: A  201 ASP cc_start: 0.8183 (t0) cc_final: 0.7866 (t0)
REVERT: A  203 TYR cc_start: 0.8361 (m-10) cc_final: 0.8152 (m-80)
REVERT: A  221 ASP cc_start: 0.8082 (t70) cc_final: 0.7806 (t0)
REVERT: A  241 GLU cc_start: 0.8058 (mp0) cc_final: 0.7720 (mp0)
REVERT: A  332 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7699 (tt0)
REVERT: A  376 MET cc_start: 0.8699 (tmm) cc_final: 0.8498 (tmm)
REVERT: A  412 PHE cc_start: 0.7610 (t80) cc_final: 0.7376 (t80)
REVERT: A  422 MET cc_start: 0.8467 (tpp) cc_final: 0.7893 (tpp)
REVERT: A  455 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7189 (mptt)
REVERT: A  461 MET cc_start: 0.5779 (mpp) cc_final: 0.5099 (mpp)
REVERT: A  466 GLN cc_start: 0.8801 (mp10) cc_final: 0.8069 (pm20)
REVERT: A  471 PHE cc_start: 0.8524 (m-10) cc_final: 0.8007 (t80)
REVERT: B   32 ASN cc_start: 0.6439 (t0) cc_final: 0.6062 (t0)
REVERT: C  127 GLU cc_start: 0.8112 (tt0) cc_final: 0.7827 (mt-10)
REVERT: C  161 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8039 (mm)
  outliers start: 29
  outliers final: 19
  residues processed: 168
  average time/residue: 0.0631
  time to fit residues: 14.1449
Evaluate side-chains
  161 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
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  115 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  189 MET
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  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   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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 38 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.5388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 159 GLN
A 227 HIS
** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.156989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.125802 restraints weight = 7605.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.130045 restraints weight = 4462.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.133034 restraints weight = 3157.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.134904 restraints weight = 2484.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.136348 restraints weight = 2112.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.3371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   5154  Z= 0.204
  Angle     :  0.741  22.624   6983  Z= 0.381
  Chirality :  0.048   0.346    773
  Planarity :  0.004   0.038    887
  Dihedral  :  5.753  79.742    703
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 22.91 %
    Favored  : 72.07 %
  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 are not related in a simple way.
  whole: -0.65 (0.32), residues: 649
  helix:  2.07 (0.45), residues: 131
  sheet: -0.08 (0.37), residues: 196
  loop : -1.79 (0.31), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  94 
 TYR   0.019   0.002   TYR A  61 
 PHE   0.023   0.002   PHE A 498 
 TRP   0.014   0.001   TRP B  68 
 HIS   0.006   0.001   HIS A 447 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00469 /  0.20 ( 5144)
  covalent geometry    : angle       0.71360 /  0.37 ( 6962)
  SS BOND              : bond        0.00744 /  0.36 (    9)
  SS BOND              : angle       3.96709 /  2.08 (   18)
  hydrogen bonds       : bond        0.03903 /  2.52 (  203)
  hydrogen bonds       : angle       4.29297 /  3.08 (  576)
  link_NAG-ASN         : bond        0.00521 /  0.27 (    1)
  link_NAG-ASN         : angle       1.53296 /  0.83 (    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
  175 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 148
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 TYR cc_start: 0.8466 (t80) cc_final: 0.7990 (t80)
REVERT: A  178 GLU cc_start: 0.8109 (tp30) cc_final: 0.7562 (mm-30)
REVERT: A  192 GLU cc_start: 0.8267 (mp0) cc_final: 0.7379 (mp0)
REVERT: A  201 ASP cc_start: 0.8307 (t0) cc_final: 0.8025 (t0)
REVERT: A  221 ASP cc_start: 0.8207 (t70) cc_final: 0.7908 (t0)
REVERT: A  241 GLU cc_start: 0.8380 (mp0) cc_final: 0.8045 (mp0)
REVERT: A  332 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7621 (tm-30)
REVERT: A  412 PHE cc_start: 0.7792 (t80) cc_final: 0.7584 (t80)
REVERT: A  422 MET cc_start: 0.8483 (tpp) cc_final: 0.7947 (tpp)
REVERT: A  455 LYS cc_start: 0.7857 (ttmt) cc_final: 0.7186 (mptt)
REVERT: A  461 MET cc_start: 0.4675 (mpp) cc_final: 0.4265 (mpp)
REVERT: A  471 PHE cc_start: 0.8662 (m-10) cc_final: 0.8050 (t80)
REVERT: C  161 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7737 (mm)
  outliers start: 27
  outliers final: 23
  residues processed: 162
  average time/residue: 0.0662
  time to fit residues: 14.1810
Evaluate side-chains
  164 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
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  113 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  189 MET
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  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    6 LYS
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   41 ILE
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:    0.9990
   chunk 47 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 38 optimal weight:    0.4980
   chunk 22 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    0.2980
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 447 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.157022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.126397 restraints weight = 7470.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.130566 restraints weight = 4568.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.133445 restraints weight = 3275.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.135395 restraints weight = 2591.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.136612 restraints weight = 2196.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.3562

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= 0.184
  Angle     :  0.742  17.168   6983  Z= 0.380
  Chirality :  0.047   0.302    773
  Planarity :  0.004   0.038    887
  Dihedral  :  5.868  81.197    703
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 24.77 %
    Favored  : 70.39 %
  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 are not related in a simple way.
  whole: -0.69 (0.32), residues: 649
  helix:  1.91 (0.46), residues: 131
  sheet: -0.08 (0.37), residues: 194
  loop : -1.76 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  94 
 TYR   0.017   0.002   TYR A  61 
 PHE   0.023   0.002   PHE A 498 
 TRP   0.039   0.002   TRP C 129 
 HIS   0.006   0.001   HIS A  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00426 /  0.18 ( 5144)
  covalent geometry    : angle       0.71260 /  0.37 ( 6962)
  SS BOND              : bond        0.00706 /  0.34 (    9)
  SS BOND              : angle       4.06501 /  1.99 (   18)
  hydrogen bonds       : bond        0.03793 /  2.45 (  203)
  hydrogen bonds       : angle       4.25987 /  3.04 (  576)
  link_NAG-ASN         : bond        0.00582 /  0.31 (    1)
  link_NAG-ASN         : angle       1.57191 /  0.88 (    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
  167 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 MET cc_start: 0.8004 (mtm) cc_final: 0.7658 (mtp)
REVERT: A   81 TYR cc_start: 0.8370 (t80) cc_final: 0.7936 (t80)
REVERT: A  178 GLU cc_start: 0.8071 (tp30) cc_final: 0.7549 (mm-30)
REVERT: A  192 GLU cc_start: 0.8298 (mp0) cc_final: 0.7453 (mp0)
REVERT: A  201 ASP cc_start: 0.8355 (t0) cc_final: 0.8051 (t0)
REVERT: A  221 ASP cc_start: 0.8195 (t70) cc_final: 0.7917 (t0)
REVERT: A  332 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7727 (tm-30)
REVERT: A  412 PHE cc_start: 0.7712 (t80) cc_final: 0.7497 (t80)
REVERT: A  422 MET cc_start: 0.8493 (tpp) cc_final: 0.7989 (tpp)
REVERT: A  455 LYS cc_start: 0.7885 (ttmt) cc_final: 0.7241 (mptt)
REVERT: A  471 PHE cc_start: 0.8616 (m-10) cc_final: 0.8011 (t80)
REVERT: B   32 ASN cc_start: 0.6758 (t0) cc_final: 0.6312 (t0)
REVERT: C  161 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7355 (mm)
  outliers start: 26
  outliers final: 25
  residues processed: 156
  average time/residue: 0.0621
  time to fit residues: 12.6693
Evaluate side-chains
  160 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 134
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
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  189 MET
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  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 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:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 3 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.159336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.130157 restraints weight = 7414.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.134381 restraints weight = 4226.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.137366 restraints weight = 2906.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.139347 restraints weight = 2237.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.140778 restraints weight = 1864.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.3624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5154  Z= 0.134
  Angle     :  0.723  19.462   6983  Z= 0.366
  Chirality :  0.046   0.295    773
  Planarity :  0.004   0.037    887
  Dihedral  :  5.684  80.599    703
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 25.70 %
    Favored  : 70.02 %
  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 are not related in a simple way.
  whole: -0.58 (0.33), residues: 649
  helix:  2.03 (0.46), residues: 131
  sheet:  0.08 (0.38), residues: 190
  loop : -1.77 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  90 
 TYR   0.011   0.001   TYR A  61 
 PHE   0.018   0.001   PHE A 454 
 TRP   0.026   0.001   TRP C 129 
 HIS   0.005   0.001   HIS A  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.13 ( 5144)
  covalent geometry    : angle       0.69553 /  0.35 ( 6962)
  SS BOND              : bond        0.00778 /  0.38 (    9)
  SS BOND              : angle       3.90845 /  1.96 (   18)
  hydrogen bonds       : bond        0.03457 /  2.20 (  203)
  hydrogen bonds       : angle       4.14708 /  2.96 (  576)
  link_NAG-ASN         : bond        0.00525 /  0.28 (    1)
  link_NAG-ASN         : angle       1.71194 /  1.00 (    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
  166 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 TYR cc_start: 0.8381 (t80) cc_final: 0.7913 (t80)
REVERT: A  178 GLU cc_start: 0.8082 (tp30) cc_final: 0.7535 (mm-30)
REVERT: A  192 GLU cc_start: 0.8236 (mp0) cc_final: 0.7411 (mp0)
REVERT: A  221 ASP cc_start: 0.8163 (t70) cc_final: 0.7882 (t0)
REVERT: A  332 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7629 (tm-30)
REVERT: A  412 PHE cc_start: 0.7737 (t80) cc_final: 0.7527 (t80)
REVERT: A  422 MET cc_start: 0.8489 (tpp) cc_final: 0.7919 (tpp)
REVERT: A  455 LYS cc_start: 0.7701 (ttmt) cc_final: 0.6956 (mptt)
REVERT: A  471 PHE cc_start: 0.8589 (m-10) cc_final: 0.7996 (t80)
REVERT: B   32 ASN cc_start: 0.6696 (t0) cc_final: 0.6259 (t0)
REVERT: B   60 TYR cc_start: 0.8779 (m-80) cc_final: 0.8500 (m-80)
REVERT: B  101 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7517 (m-70)
REVERT: C  161 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8118 (mm)
  outliers start: 23
  outliers final: 20
  residues processed: 156
  average time/residue: 0.0538
  time to fit residues: 11.1300
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  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  189 MET
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 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 B residue  101 HIS
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:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 58 optimal weight:    0.0570
   chunk 8 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 32 optimal weight:    0.4980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.5298

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 236 HIS ** 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 = 0.3914 r_free = 0.3914 target = 0.161176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.129788 restraints weight = 7494.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.134204 restraints weight = 4317.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.137233 restraints weight = 3017.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.139191 restraints weight = 2363.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.140738 restraints weight = 1996.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.3695

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= 0.127
  Angle     :  0.719  18.005   6983  Z= 0.370
  Chirality :  0.047   0.302    773
  Planarity :  0.004   0.039    887
  Dihedral  :  5.577  81.129    703
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 25.33 %
    Favored  : 70.02 %
  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 are not related in a simple way.
  whole: -0.44 (0.33), residues: 649
  helix:  2.23 (0.46), residues: 131
  sheet:  0.21 (0.38), residues: 190
  loop : -1.75 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  33 
 TYR   0.009   0.001   TYR A  61 
 PHE   0.018   0.001   PHE A 454 
 TRP   0.039   0.001   TRP C 129 
 HIS   0.005   0.001   HIS A  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 ( 5144)
  covalent geometry    : angle       0.69077 /  0.36 ( 6962)
  SS BOND              : bond        0.00697 /  0.34 (    9)
  SS BOND              : angle       3.92659 /  1.92 (   18)
  hydrogen bonds       : bond        0.03316 /  2.10 (  203)
  hydrogen bonds       : angle       4.04969 /  2.91 (  576)
  link_NAG-ASN         : bond        0.00503 /  0.26 (    1)
  link_NAG-ASN         : angle       1.56247 /  0.92 (    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
  165 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.6794 (ttm) cc_final: 0.6579 (mtm)
REVERT: A   81 TYR cc_start: 0.8389 (t80) cc_final: 0.7903 (t80)
REVERT: A  178 GLU cc_start: 0.8130 (tp30) cc_final: 0.7700 (mm-30)
REVERT: A  192 GLU cc_start: 0.8214 (mp0) cc_final: 0.7400 (mp0)
REVERT: A  221 ASP cc_start: 0.8133 (t70) cc_final: 0.7844 (t0)
REVERT: A  350 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.8814 (t)
REVERT: A  368 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7130 (mp0)
REVERT: A  412 PHE cc_start: 0.7734 (t80) cc_final: 0.7515 (t80)
REVERT: A  422 MET cc_start: 0.8421 (tpp) cc_final: 0.7766 (tpp)
REVERT: A  455 LYS cc_start: 0.7787 (ttmt) cc_final: 0.6924 (mmtm)
REVERT: A  471 PHE cc_start: 0.8629 (m-10) cc_final: 0.7967 (t80)
REVERT: B   32 ASN cc_start: 0.6610 (t0) cc_final: 0.6121 (t0)
REVERT: B  101 HIS cc_start: 0.7933 (OUTLIER) cc_final: 0.7302 (m-70)
REVERT: C  161 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8119 (mm)
  outliers start: 25
  outliers final: 20
  residues processed: 155
  average time/residue: 0.0625
  time to fit residues: 12.9549
Evaluate side-chains
  158 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 134
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
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  115 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  189 MET
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  368 GLU
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   22 VAL
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 B residue  101 HIS
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:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 49 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9990
   chunk 60 optimal weight:    0.4980
   chunk 20 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0370
   chunk 55 optimal weight:    0.0870
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.3636

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 236 HIS ** 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 = 0.3923 r_free = 0.3923 target = 0.161462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.130913 restraints weight = 7460.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.135222 restraints weight = 4408.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.138161 restraints weight = 3101.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.140132 restraints weight = 2435.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.141633 restraints weight = 2057.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.3812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5154  Z= 0.123
  Angle     :  0.754  18.865   6983  Z= 0.378
  Chirality :  0.046   0.295    773
  Planarity :  0.004   0.036    887
  Dihedral  :  5.436  81.046    703
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 26.26 %
    Favored  : 70.02 %
  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 are not related in a simple way.
  whole: -0.33 (0.33), residues: 649
  helix:  2.26 (0.47), residues: 132
  sheet:  0.27 (0.38), residues: 190
  loop : -1.65 (0.31), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  33 
 TYR   0.025   0.001   TYR B  60 
 PHE   0.016   0.001   PHE A 454 
 TRP   0.039   0.001   TRP C 129 
 HIS   0.005   0.001   HIS A  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 ( 5144)
  covalent geometry    : angle       0.72693 /  0.37 ( 6962)
  SS BOND              : bond        0.00761 /  0.37 (    9)
  SS BOND              : angle       3.95518 /  1.95 (   18)
  hydrogen bonds       : bond        0.03287 /  2.07 (  203)
  hydrogen bonds       : angle       3.93293 /  2.83 (  576)
  link_NAG-ASN         : bond        0.00465 /  0.24 (    1)
  link_NAG-ASN         : angle       1.48085 /  0.87 (    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: 20
    poor density    : 140
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.6706 (ttm) cc_final: 0.6492 (mtm)
REVERT: A   81 TYR cc_start: 0.8385 (t80) cc_final: 0.7883 (t80)
REVERT: A  178 GLU cc_start: 0.8155 (tp30) cc_final: 0.7497 (tp30)
REVERT: A  192 GLU cc_start: 0.8306 (mp0) cc_final: 0.7577 (mp0)
REVERT: A  221 ASP cc_start: 0.8113 (t70) cc_final: 0.7832 (t0)
REVERT: A  368 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7087 (mp0)
REVERT: A  376 MET cc_start: 0.8633 (tmm) cc_final: 0.8410 (tmm)
REVERT: A  412 PHE cc_start: 0.7715 (t80) cc_final: 0.7499 (t80)
REVERT: A  422 MET cc_start: 0.8296 (tpp) cc_final: 0.7648 (tpp)
REVERT: A  455 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7071 (mmtm)
REVERT: A  471 PHE cc_start: 0.8545 (m-10) cc_final: 0.7848 (t80)
REVERT: B   32 ASN cc_start: 0.6482 (t0) cc_final: 0.5968 (t0)
REVERT: B  101 HIS cc_start: 0.7839 (OUTLIER) cc_final: 0.7057 (m-70)
REVERT: C  161 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8021 (mm)
  outliers start: 20
  outliers final: 16
  residues processed: 153
  average time/residue: 0.0634
  time to fit residues: 13.0419
Evaluate side-chains
  153 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
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  115 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  189 MET
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  365 VAL
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  101 HIS
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:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 58 optimal weight:    0.4980
   chunk 1 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 236 HIS ** 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 = 0.3904 r_free = 0.3904 target = 0.159423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.128117 restraints weight = 7614.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.132580 restraints weight = 4395.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.135591 restraints weight = 3051.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.137708 restraints weight = 2382.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.139033 restraints weight = 1996.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.3885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5154  Z= 0.142
  Angle     :  0.759  17.515   6983  Z= 0.382
  Chirality :  0.046   0.289    773
  Planarity :  0.004   0.038    887
  Dihedral  :  5.519  80.366    703
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 26.44 %
    Favored  : 69.27 %
  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 are not related in a simple way.
  whole: -0.33 (0.33), residues: 649
  helix:  2.27 (0.46), residues: 132
  sheet:  0.29 (0.38), residues: 190
  loop : -1.66 (0.31), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  33 
 TYR   0.026   0.001   TYR B  60 
 PHE   0.016   0.001   PHE A 454 
 TRP   0.036   0.002   TRP C 129 
 HIS   0.005   0.001   HIS A  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.14 ( 5144)
  covalent geometry    : angle       0.73212 /  0.37 ( 6962)
  SS BOND              : bond        0.00722 /  0.34 (    9)
  SS BOND              : angle       3.95682 /  1.95 (   18)
  hydrogen bonds       : bond        0.03416 /  2.18 (  203)
  hydrogen bonds       : angle       4.00059 /  2.87 (  576)
  link_NAG-ASN         : bond        0.00415 /  0.22 (    1)
  link_NAG-ASN         : angle       1.28222 /  0.74 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1048.65 seconds
wall clock time: 18 minutes 50.70 seconds (1130.70 seconds total)