Starting phenix.real_space_refine
on Wed Jul 23 18:17:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dt3_27690/07_2025/8dt3_27690_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dt3_27690/07_2025/8dt3_27690.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dt3_27690/07_2025/8dt3_27690.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dt3_27690/07_2025/8dt3_27690.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dt3_27690/07_2025/8dt3_27690_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dt3_27690/07_2025/8dt3_27690_neut.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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      18      5.16       5
     C    2416      2.51       5
     N     636      2.21       5
     O     751      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3821
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 2005
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 2005
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 13, 'TRANS': 239}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 927
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 927
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 3, 'TRANS': 119}
    Chain: "L"
      Number of atoms: 851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 851
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 3, 'TRANS': 105}
    Chain: "T"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 3.20, per 1000 atoms: 0.84
  Number of scatterers: 3821
  At special positions: 0
  Unit cell: (59.4, 97.2, 104.76, 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      18     16.00
     O     751      8.00
     N     636      7.00
     C    2416      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG T   1 " - " NAG T   2 "
    BETA1-6
      " NAG T   1 " - " FUC T   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG T   1 " - " ASN C 343 "
  Time building additional restraints: 1.25
  Conformation dependent library (CDL) restraints added in 510.4 milliseconds
  

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  890

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 9 sheets defined
      12.4% alpha, 34.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 349 through 353
    Processing helix  chain 'C' and resid 364 through 370
      removed outlier: 3.936A  pdb=" N   VAL C 367 " --> pdb=" O   ASP C 364 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   TYR C 369 " --> pdb=" O   SER C 366 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 384 through 390
      removed outlier: 3.794A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU C 390 " --> pdb=" O   LEU C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 411
      removed outlier: 4.296A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
      removed outlier: 3.783A  pdb=" N   ASN C 422 " --> pdb=" O   ILE C 418 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 438 through 443
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.925A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'L' and resid 80 through 84
    Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.547A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLU C 516 " --> pdb=" O   ASN C 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.047A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'C' and resid 538 through 543
      removed outlier: 5.710A  pdb=" N   ASP C 574 " --> pdb=" O   ILE C 587 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   GLY C 566 " --> pdb=" O   ASP C 574 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.218A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   TRP H  33 " --> pdb=" O   GLY H  99 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   MET H  34 " --> pdb=" O   GLN H  50 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   GLN H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.218A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   CYS H  96 " --> pdb=" O   TRP H 111 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   TRP H 111 " --> pdb=" O   CYS H  96 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   ARG H  98 " --> pdb=" O   ASP H 109 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 6
    Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 13
      removed outlier: 6.924A  pdb=" N   LEU L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   TYR L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)

    127 hydrogen bonds defined for protein.
    291 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: 2.02

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1220
        1.35 -     1.47: 1054
        1.47 -     1.60: 1612
        1.60 -     1.72: 0
        1.72 -     1.85: 22
  Bond restraints: 3908
  Sorted by residual:
  bond pdb=" C1  FUC T   3 "
       pdb=" C2  FUC T   3 "
    ideal  model  delta    sigma   weight residual
    1.528  1.576 -0.048 2.00e-02 2.50e+03 5.81e+00
  bond pdb=" N   ASP H  57 "
       pdb=" CA  ASP H  57 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.030 1.28e-02 6.10e+03 5.58e+00
  bond pdb=" C2  FUC T   3 "
       pdb=" C3  FUC T   3 "
    ideal  model  delta    sigma   weight residual
    1.526  1.554 -0.028 2.00e-02 2.50e+03 2.02e+00
  bond pdb=" C   ALA C 520 "
       pdb=" N   PRO C 521 "
    ideal  model  delta    sigma   weight residual
    1.330  1.346 -0.016 1.19e-02 7.06e+03 1.75e+00
  bond pdb=" C1  NAG T   2 "
       pdb=" O5  NAG T   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.70e+00
  ... (remaining 3903 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 5120
        1.59 -     3.18: 141
        3.18 -     4.78: 31
        4.78 -     6.37: 7
        6.37 -     7.96: 2
  Bond angle restraints: 5301
  Sorted by residual:
  angle pdb=" C   TYR L  51 "
        pdb=" N   THR L  52 "
        pdb=" CA  THR L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  129.01   -7.47 1.91e+00 2.74e-01 1.53e+01
  angle pdb=" CA  CYS C 432 "
        pdb=" CB  CYS C 432 "
        pdb=" SG  CYS C 432 "
      ideal   model   delta    sigma   weight residual
     114.40  122.36   -7.96 2.30e+00 1.89e-01 1.20e+01
  angle pdb=" C   GLY C 431 "
        pdb=" N   CYS C 432 "
        pdb=" CA  CYS C 432 "
      ideal   model   delta    sigma   weight residual
     122.10  116.63    5.47 1.66e+00 3.63e-01 1.09e+01
  angle pdb=" CA  GLY C 431 "
        pdb=" C   GLY C 431 "
        pdb=" O   GLY C 431 "
      ideal   model   delta    sigma   weight residual
     122.65  118.60    4.05 1.28e+00 6.10e-01 1.00e+01
  angle pdb=" N   GLY C 431 "
        pdb=" CA  GLY C 431 "
        pdb=" C   GLY C 431 "
      ideal   model   delta    sigma   weight residual
     112.58  106.99    5.59 1.80e+00 3.09e-01 9.63e+00
  ... (remaining 5296 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.93: 2212
       23.93 -    47.87: 93
       47.87 -    71.80: 21
       71.80 -    95.73: 13
       95.73 -   119.67: 9
  Dihedral angle restraints: 2348
    sinusoidal: 950
      harmonic: 1398
  Sorted by residual:
  dihedral pdb=" CB  CYS C 379 "
           pdb=" SG  CYS C 379 "
           pdb=" SG  CYS C 432 "
           pdb=" CB  CYS C 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.63   55.37     1      1.00e+01 1.00e-02 4.14e+01
  dihedral pdb=" CB  CYS C 336 "
           pdb=" SG  CYS C 336 "
           pdb=" SG  CYS C 361 "
           pdb=" CB  CYS C 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   46.59   46.41     1      1.00e+01 1.00e-02 2.98e+01
  dihedral pdb=" CB  CYS C 480 "
           pdb=" SG  CYS C 480 "
           pdb=" SG  CYS C 488 "
           pdb=" CB  CYS C 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.16   38.84     1      1.00e+01 1.00e-02 2.12e+01
  ... (remaining 2345 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 358
       0.032 -    0.064: 142
       0.064 -    0.095: 47
       0.095 -    0.127: 34
       0.127 -    0.159: 6
  Chirality restraints: 587
  Sorted by residual:
  chirality pdb=" CA  ILE C 434 "
            pdb=" N   ILE C 434 "
            pdb=" C   ILE C 434 "
            pdb=" CB  ILE C 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.31e-01
  chirality pdb=" C5  NAG T   1 "
            pdb=" C4  NAG T   1 "
            pdb=" C6  NAG T   1 "
            pdb=" O5  NAG T   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.56    0.15 2.00e-01 2.50e+01 5.36e-01
  chirality pdb=" CA  ILE L  76 "
            pdb=" N   ILE L  76 "
            pdb=" C   ILE L  76 "
            pdb=" CB  ILE L  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.48e-01
  ... (remaining 584 not shown)

  Planarity restraints: 680
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG H  40 "   -0.043 5.00e-02 4.00e+02   6.48e-02 6.73e+00
        pdb=" N   PRO H  41 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO H  41 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO H  41 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 369 "   -0.014 2.00e-02 2.50e+03   1.01e-02 2.06e+00
        pdb=" CG  TYR C 369 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 369 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 369 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 369 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 369 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 369 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR C 369 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L  54 "   -0.098 9.50e-02 1.11e+02   4.40e-02 1.51e+00
        pdb=" NE  ARG L  54 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  ARG L  54 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG L  54 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG L  54 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 677 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 104
        2.68 -     3.24: 3777
        3.24 -     3.79: 5799
        3.79 -     4.35: 7951
        4.35 -     4.90: 13135
  Nonbonded interactions: 30766
  Sorted by model distance:
  nonbonded pdb=" O   SER L  31 "
            pdb=" OH  TYR L  72 "
     model   vdw
     2.125 3.040
  nonbonded pdb=" OG  SER C 469 "
            pdb=" OE1 GLU C 471 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OG  SER C 530 "
            pdb=" OE1 GLN C 580 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OD1 ASP C 442 "
            pdb=" OH  TYR C 451 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" NE2 HIS L  56 "
            pdb=" O3  FUC T   3 "
     model   vdw
     2.262 3.120
  ... (remaining 30761 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 individual isotropic
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:             1.650
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     15.760
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:4.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
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      :  0.004   0.048   3917  Z= 0.174
  Angle     :  0.706  10.039   5322  Z= 0.366
  Chirality :  0.045   0.159    587
  Planarity :  0.004   0.065    679
  Dihedral  : 17.521 119.666   1440
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.40), residues: 477
  helix: -3.69 (0.56), residues: 34
  sheet:  0.93 (0.41), residues: 177
  loop : -0.95 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 
 PHE   0.013   0.001   PHE C 392 
 TYR   0.025   0.002   TYR C 369 
 ARG   0.010   0.001   ARG L  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00836 (    1)
  link_NAG-ASN         : angle       8.33856 (    3)
  link_BETA1-4         : bond        0.01083 (    1)
  link_BETA1-4         : angle       2.58524 (    3)
  hydrogen bonds       : bond        0.13971 (  123)
  hydrogen bonds       : angle       7.40924 (  291)
  link_BETA1-6         : bond        0.00687 (    1)
  link_BETA1-6         : angle       3.06589 (    3)
  SS BOND              : bond        0.00691 (    6)
  SS BOND              : angle       2.03373 (   12)
  covalent geometry    : bond        0.00371 ( 3908)
  covalent geometry    : angle       0.66556 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.392 
Fit side-chains
REVERT: C  365 TYR cc_start: 0.5792 (p90) cc_final: 0.5403 (p90)
REVERT: H   80 TYR cc_start: 0.8183 (m-80) cc_final: 0.7937 (m-80)
REVERT: L  105 LEU cc_start: 0.9313 (mp) cc_final: 0.8676 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.1557
  time to fit residues: 13.2289
Evaluate side-chains
  58 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 14 optimal weight:    0.3980
   chunk 22 optimal weight:    0.0270
   chunk 27 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
L  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.076327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.061584 restraints weight = 12832.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 3.83
r_work: 0.3100 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3917  Z= 0.139
  Angle     :  0.683  10.373   5322  Z= 0.335
  Chirality :  0.045   0.155    587
  Planarity :  0.004   0.042    679
  Dihedral  : 13.002 120.736    585
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  8.13 %
    Favored  : 91.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.40), residues: 477
  helix: -3.55 (0.71), residues: 27
  sheet:  1.14 (0.43), residues: 163
  loop : -0.87 (0.38), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  33 
 HIS   0.003   0.001   HIS L  56 
 PHE   0.012   0.001   PHE C 392 
 TYR   0.022   0.001   TYR C 369 
 ARG   0.005   0.001   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00934 (    1)
  link_NAG-ASN         : angle       8.98610 (    3)
  link_BETA1-4         : bond        0.00405 (    1)
  link_BETA1-4         : angle       1.04572 (    3)
  hydrogen bonds       : bond        0.02807 (  123)
  hydrogen bonds       : angle       5.97700 (  291)
  link_BETA1-6         : bond        0.01254 (    1)
  link_BETA1-6         : angle       1.79656 (    3)
  SS BOND              : bond        0.00672 (    6)
  SS BOND              : angle       1.68317 (   12)
  covalent geometry    : bond        0.00323 ( 3908)
  covalent geometry    : angle       0.64361 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8658 (mm) cc_final: 0.8439 (mt)
REVERT: C  365 TYR cc_start: 0.6114 (p90) cc_final: 0.5896 (p90)
REVERT: C  563 GLN cc_start: 0.8347 (mt0) cc_final: 0.7449 (mm110)
REVERT: H   80 TYR cc_start: 0.8500 (m-80) cc_final: 0.8204 (m-80)
REVERT: L   80 GLU cc_start: 0.8854 (tt0) cc_final: 0.8602 (tt0)
REVERT: L   81 GLN cc_start: 0.8599 (tp-100) cc_final: 0.8327 (tp-100)
REVERT: L   82 GLU cc_start: 0.8667 (pm20) cc_final: 0.8166 (pm20)
REVERT: L   87 TYR cc_start: 0.8816 (m-80) cc_final: 0.8595 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 65
  average time/residue: 0.1523
  time to fit residues: 12.7620
Evaluate side-chains
  60 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   34 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 29 optimal weight:    0.3980
   chunk 3 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 37 optimal weight:    0.1980
   chunk 39 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.8384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.075148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.060277 restraints weight = 12926.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 3.84
r_work: 0.3080 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.1406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3917  Z= 0.170
  Angle     :  0.652  10.568   5322  Z= 0.322
  Chirality :  0.045   0.186    587
  Planarity :  0.004   0.036    679
  Dihedral  : 10.779 104.828    585
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 10.53 %
    Favored  : 88.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.40), residues: 477
  helix: -3.40 (0.69), residues: 33
  sheet:  1.26 (0.43), residues: 161
  loop : -0.84 (0.38), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  33 
 HIS   0.003   0.001   HIS L  56 
 PHE   0.010   0.001   PHE C 392 
 TYR   0.018   0.001   TYR C 369 
 ARG   0.006   0.001   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00608 (    1)
  link_NAG-ASN         : angle       8.94345 (    3)
  link_BETA1-4         : bond        0.00256 (    1)
  link_BETA1-4         : angle       0.89542 (    3)
  hydrogen bonds       : bond        0.02925 (  123)
  hydrogen bonds       : angle       5.74112 (  291)
  link_BETA1-6         : bond        0.00537 (    1)
  link_BETA1-6         : angle       1.63798 (    3)
  SS BOND              : bond        0.00627 (    6)
  SS BOND              : angle       1.66298 (   12)
  covalent geometry    : bond        0.00396 ( 3908)
  covalent geometry    : angle       0.61069 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8710 (mm) cc_final: 0.8485 (mt)
REVERT: C  365 TYR cc_start: 0.6147 (p90) cc_final: 0.5791 (p90)
REVERT: C  493 GLN cc_start: 0.8206 (mp10) cc_final: 0.7969 (mp10)
REVERT: C  563 GLN cc_start: 0.8375 (mt0) cc_final: 0.7580 (mm110)
REVERT: H   80 TYR cc_start: 0.8527 (m-80) cc_final: 0.8268 (m-80)
REVERT: L   80 GLU cc_start: 0.8777 (tt0) cc_final: 0.8248 (tt0)
REVERT: L   82 GLU cc_start: 0.8623 (pm20) cc_final: 0.7952 (pm20)
  outliers start: 6
  outliers final: 6
  residues processed: 59
  average time/residue: 0.1634
  time to fit residues: 12.2735
Evaluate side-chains
  61 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue  105 LEU
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 19 optimal weight:    0.4980
   chunk 3 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.8784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.074940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.059781 restraints weight = 12887.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 3.86
r_work: 0.3071 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.1640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3917  Z= 0.174
  Angle     :  0.652  10.147   5322  Z= 0.323
  Chirality :  0.045   0.167    587
  Planarity :  0.004   0.034    679
  Dihedral  : 10.367  98.382    585
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 10.77 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.39), residues: 477
  helix: -3.48 (0.65), residues: 34
  sheet:  1.23 (0.43), residues: 156
  loop : -0.84 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  33 
 HIS   0.003   0.001   HIS L  56 
 PHE   0.010   0.001   PHE C 392 
 TYR   0.016   0.001   TYR C 369 
 ARG   0.006   0.000   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00646 (    1)
  link_NAG-ASN         : angle       8.78423 (    3)
  link_BETA1-4         : bond        0.00340 (    1)
  link_BETA1-4         : angle       1.16711 (    3)
  hydrogen bonds       : bond        0.02856 (  123)
  hydrogen bonds       : angle       5.61477 (  291)
  link_BETA1-6         : bond        0.00668 (    1)
  link_BETA1-6         : angle       2.24642 (    3)
  SS BOND              : bond        0.00616 (    6)
  SS BOND              : angle       1.66431 (   12)
  covalent geometry    : bond        0.00405 ( 3908)
  covalent geometry    : angle       0.61074 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8713 (mm) cc_final: 0.8485 (mt)
REVERT: C  365 TYR cc_start: 0.6089 (p90) cc_final: 0.5767 (p90)
REVERT: C  434 ILE cc_start: 0.9500 (mt) cc_final: 0.9282 (mt)
REVERT: C  493 GLN cc_start: 0.8169 (mp10) cc_final: 0.7930 (mp10)
REVERT: C  563 GLN cc_start: 0.8409 (mt0) cc_final: 0.7670 (mm110)
REVERT: H   80 TYR cc_start: 0.8564 (m-80) cc_final: 0.8320 (m-80)
REVERT: L   80 GLU cc_start: 0.8813 (tt0) cc_final: 0.8320 (tt0)
REVERT: L   82 GLU cc_start: 0.8564 (pm20) cc_final: 0.7856 (pm20)
  outliers start: 8
  outliers final: 7
  residues processed: 62
  average time/residue: 0.1591
  time to fit residues: 12.6561
Evaluate side-chains
  64 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue  105 LEU
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0870
   chunk 7 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.1962

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.073807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.058322 restraints weight = 13327.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 3.95
r_work: 0.3035 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   3917  Z= 0.223
  Angle     :  0.679  10.142   5322  Z= 0.336
  Chirality :  0.046   0.193    587
  Planarity :  0.004   0.033    679
  Dihedral  : 10.230  95.927    585
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 11.96 %
    Favored  : 85.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.39), residues: 477
  helix: -3.43 (0.65), residues: 34
  sheet:  1.13 (0.43), residues: 157
  loop : -0.91 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  33 
 HIS   0.004   0.001   HIS L  56 
 PHE   0.013   0.002   PHE C 559 
 TYR   0.016   0.001   TYR C 369 
 ARG   0.007   0.000   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00393 (    1)
  link_NAG-ASN         : angle       8.91620 (    3)
  link_BETA1-4         : bond        0.00093 (    1)
  link_BETA1-4         : angle       1.04567 (    3)
  hydrogen bonds       : bond        0.02978 (  123)
  hydrogen bonds       : angle       5.58861 (  291)
  link_BETA1-6         : bond        0.00613 (    1)
  link_BETA1-6         : angle       2.32144 (    3)
  SS BOND              : bond        0.00626 (    6)
  SS BOND              : angle       2.02855 (   12)
  covalent geometry    : bond        0.00513 ( 3908)
  covalent geometry    : angle       0.63679 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8740 (mm) cc_final: 0.8504 (mt)
REVERT: C  434 ILE cc_start: 0.9536 (mt) cc_final: 0.9315 (mt)
REVERT: C  493 GLN cc_start: 0.8263 (mp10) cc_final: 0.8039 (mp10)
REVERT: C  559 PHE cc_start: 0.2887 (OUTLIER) cc_final: 0.1934 (m-80)
REVERT: C  563 GLN cc_start: 0.8520 (mt0) cc_final: 0.7526 (mm110)
REVERT: H   80 TYR cc_start: 0.8642 (m-80) cc_final: 0.8429 (m-80)
REVERT: L   80 GLU cc_start: 0.8827 (tt0) cc_final: 0.8359 (tt0)
REVERT: L   81 GLN cc_start: 0.8581 (tp-100) cc_final: 0.8362 (tp-100)
  outliers start: 11
  outliers final: 9
  residues processed: 61
  average time/residue: 0.1284
  time to fit residues: 10.3366
Evaluate side-chains
  63 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain C residue  581 THR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue  105 LEU
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.073984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.059121 restraints weight = 12758.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 3.79
r_work: 0.3061 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3917  Z= 0.173
  Angle     :  0.676  10.360   5322  Z= 0.331
  Chirality :  0.046   0.182    587
  Planarity :  0.003   0.031    679
  Dihedral  :  9.497  88.149    585
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 14.11 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.39), residues: 477
  helix: -3.37 (0.65), residues: 33
  sheet:  1.15 (0.43), residues: 157
  loop : -0.89 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 
 PHE   0.007   0.001   PHE C 392 
 TYR   0.016   0.001   TYR C 365 
 ARG   0.004   0.000   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00504 (    1)
  link_NAG-ASN         : angle       9.06525 (    3)
  link_BETA1-4         : bond        0.00335 (    1)
  link_BETA1-4         : angle       1.15832 (    3)
  hydrogen bonds       : bond        0.02834 (  123)
  hydrogen bonds       : angle       5.54382 (  291)
  link_BETA1-6         : bond        0.01165 (    1)
  link_BETA1-6         : angle       2.29196 (    3)
  SS BOND              : bond        0.00621 (    6)
  SS BOND              : angle       1.83292 (   12)
  covalent geometry    : bond        0.00402 ( 3908)
  covalent geometry    : angle       0.63276 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8685 (mm) cc_final: 0.8444 (mt)
REVERT: C  434 ILE cc_start: 0.9526 (mt) cc_final: 0.9308 (mt)
REVERT: C  493 GLN cc_start: 0.8221 (mp10) cc_final: 0.7970 (mp10)
REVERT: C  563 GLN cc_start: 0.8466 (mt0) cc_final: 0.7907 (mm110)
REVERT: H   80 TYR cc_start: 0.8601 (m-80) cc_final: 0.8380 (m-80)
REVERT: L   80 GLU cc_start: 0.8828 (tt0) cc_final: 0.8390 (tt0)
REVERT: L   81 GLN cc_start: 0.8539 (tp-100) cc_final: 0.8261 (tp-100)
  outliers start: 12
  outliers final: 9
  residues processed: 64
  average time/residue: 0.1482
  time to fit residues: 12.2922
Evaluate side-chains
  67 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  450 ASN
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue  105 LEU
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 9 optimal weight:    0.2980
   chunk 7 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.9584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.074050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.059068 restraints weight = 12873.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 3.82
r_work: 0.3050 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3917  Z= 0.189
  Angle     :  0.689  10.575   5322  Z= 0.334
  Chirality :  0.046   0.187    587
  Planarity :  0.004   0.030    679
  Dihedral  :  8.696  77.665    585
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 15.07 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.39), residues: 477
  helix: -3.18 (0.71), residues: 33
  sheet:  1.14 (0.44), residues: 157
  loop : -0.88 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  33 
 HIS   0.003   0.001   HIS L  56 
 PHE   0.008   0.001   PHE C 392 
 TYR   0.039   0.002   TYR C 365 
 ARG   0.009   0.001   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00398 (    1)
  link_NAG-ASN         : angle       9.21954 (    3)
  link_BETA1-4         : bond        0.00263 (    1)
  link_BETA1-4         : angle       1.19288 (    3)
  hydrogen bonds       : bond        0.02867 (  123)
  hydrogen bonds       : angle       5.50284 (  291)
  link_BETA1-6         : bond        0.01529 (    1)
  link_BETA1-6         : angle       2.21708 (    3)
  SS BOND              : bond        0.00630 (    6)
  SS BOND              : angle       1.84262 (   12)
  covalent geometry    : bond        0.00434 ( 3908)
  covalent geometry    : angle       0.64622 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8688 (mm) cc_final: 0.8448 (mt)
REVERT: C  434 ILE cc_start: 0.9538 (mt) cc_final: 0.9316 (mt)
REVERT: C  493 GLN cc_start: 0.8295 (mp10) cc_final: 0.8079 (mp10)
REVERT: C  559 PHE cc_start: 0.2899 (OUTLIER) cc_final: 0.1524 (m-80)
REVERT: C  563 GLN cc_start: 0.8320 (mt0) cc_final: 0.7484 (mm110)
REVERT: L   80 GLU cc_start: 0.8905 (tt0) cc_final: 0.8444 (tt0)
  outliers start: 13
  outliers final: 10
  residues processed: 65
  average time/residue: 0.1558
  time to fit residues: 12.8140
Evaluate side-chains
  66 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  450 ASN
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue  105 LEU
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 42 optimal weight:    0.1980
   chunk 34 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 9 optimal weight:    0.4980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.075057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.060180 restraints weight = 12939.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 3.82
r_work: 0.3079 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3917  Z= 0.144
  Angle     :  0.684  10.710   5322  Z= 0.331
  Chirality :  0.045   0.168    587
  Planarity :  0.004   0.030    679
  Dihedral  :  7.585  61.282    585
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.51 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.39), residues: 477
  helix: -3.09 (0.74), residues: 33
  sheet:  1.20 (0.44), residues: 157
  loop : -0.85 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  93 
 PHE   0.008   0.001   PHE C 562 
 TYR   0.030   0.002   TYR C 365 
 ARG   0.008   0.001   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00501 (    1)
  link_NAG-ASN         : angle       9.30405 (    3)
  link_BETA1-4         : bond        0.00380 (    1)
  link_BETA1-4         : angle       1.33405 (    3)
  hydrogen bonds       : bond        0.02721 (  123)
  hydrogen bonds       : angle       5.44755 (  291)
  link_BETA1-6         : bond        0.02351 (    1)
  link_BETA1-6         : angle       1.76053 (    3)
  SS BOND              : bond        0.00604 (    6)
  SS BOND              : angle       1.63601 (   12)
  covalent geometry    : bond        0.00334 ( 3908)
  covalent geometry    : angle       0.64214 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8647 (mm) cc_final: 0.8410 (mt)
REVERT: C  434 ILE cc_start: 0.9524 (mt) cc_final: 0.9314 (mt)
REVERT: C  493 GLN cc_start: 0.8239 (mp10) cc_final: 0.8019 (mp10)
REVERT: C  559 PHE cc_start: 0.3079 (OUTLIER) cc_final: 0.1498 (m-80)
REVERT: C  563 GLN cc_start: 0.8396 (mt0) cc_final: 0.7574 (mm110)
REVERT: L   80 GLU cc_start: 0.8836 (tt0) cc_final: 0.8348 (tt0)
  outliers start: 11
  outliers final: 10
  residues processed: 64
  average time/residue: 0.1684
  time to fit residues: 13.6534
Evaluate side-chains
  68 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  105 LEU
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.074562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.059707 restraints weight = 12861.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 3.83
r_work: 0.3065 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3917  Z= 0.170
  Angle     :  0.700  10.809   5322  Z= 0.341
  Chirality :  0.045   0.179    587
  Planarity :  0.004   0.031    679
  Dihedral  :  7.295  54.959    585
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.27 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.39), residues: 477
  helix: -2.96 (0.80), residues: 33
  sheet:  1.15 (0.44), residues: 157
  loop : -0.86 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 
 PHE   0.008   0.001   PHE C 559 
 TYR   0.033   0.002   TYR C 369 
 ARG   0.009   0.001   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00361 (    1)
  link_NAG-ASN         : angle       9.33471 (    3)
  link_BETA1-4         : bond        0.00235 (    1)
  link_BETA1-4         : angle       1.29993 (    3)
  hydrogen bonds       : bond        0.02784 (  123)
  hydrogen bonds       : angle       5.53789 (  291)
  link_BETA1-6         : bond        0.02545 (    1)
  link_BETA1-6         : angle       1.65521 (    3)
  SS BOND              : bond        0.00608 (    6)
  SS BOND              : angle       1.70651 (   12)
  covalent geometry    : bond        0.00393 ( 3908)
  covalent geometry    : angle       0.65821 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.438 
Fit side-chains
REVERT: C  358 ILE cc_start: 0.8676 (mm) cc_final: 0.8440 (mt)
REVERT: C  434 ILE cc_start: 0.9536 (mt) cc_final: 0.9316 (mt)
REVERT: C  493 GLN cc_start: 0.8264 (mp10) cc_final: 0.8046 (mp10)
REVERT: C  516 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7546 (tm-30)
REVERT: C  559 PHE cc_start: 0.3219 (OUTLIER) cc_final: 0.1405 (m-80)
REVERT: C  563 GLN cc_start: 0.8490 (mt0) cc_final: 0.7667 (mm110)
  outliers start: 11
  outliers final: 10
  residues processed: 61
  average time/residue: 0.1647
  time to fit residues: 12.8013
Evaluate side-chains
  66 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  105 LEU
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    0.2980
   chunk 1 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0980
   chunk 42 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0970
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.3578

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.076220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.061183 restraints weight = 12703.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 3.87
r_work: 0.3096 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3917  Z= 0.127
  Angle     :  0.688  11.033   5322  Z= 0.335
  Chirality :  0.045   0.191    587
  Planarity :  0.004   0.030    679
  Dihedral  :  6.595  50.746    585
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.51 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.39), residues: 477
  helix: -3.17 (0.74), residues: 33
  sheet:  1.25 (0.44), residues: 157
  loop : -0.82 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  33 
 HIS   0.001   0.000   HIS L  93 
 PHE   0.008   0.001   PHE C 562 
 TYR   0.021   0.001   TYR C 365 
 ARG   0.010   0.001   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00631 (    1)
  link_NAG-ASN         : angle       9.34181 (    3)
  link_BETA1-4         : bond        0.00381 (    1)
  link_BETA1-4         : angle       1.52196 (    3)
  hydrogen bonds       : bond        0.02637 (  123)
  hydrogen bonds       : angle       5.44436 (  291)
  link_BETA1-6         : bond        0.03594 (    1)
  link_BETA1-6         : angle       2.83924 (    3)
  SS BOND              : bond        0.00581 (    6)
  SS BOND              : angle       1.42885 (   12)
  covalent geometry    : bond        0.00287 ( 3908)
  covalent geometry    : angle       0.64498 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.455 
Fit side-chains
REVERT: C  358 ILE cc_start: 0.8608 (mm) cc_final: 0.8381 (mt)
REVERT: C  434 ILE cc_start: 0.9517 (mt) cc_final: 0.9310 (mt)
REVERT: C  493 GLN cc_start: 0.8227 (mp10) cc_final: 0.7989 (mp10)
REVERT: C  516 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7506 (tm-30)
REVERT: C  559 PHE cc_start: 0.3525 (OUTLIER) cc_final: 0.1462 (m-80)
REVERT: C  563 GLN cc_start: 0.8402 (mt0) cc_final: 0.7692 (mm110)
  outliers start: 11
  outliers final: 9
  residues processed: 61
  average time/residue: 0.1605
  time to fit residues: 12.5188
Evaluate side-chains
  67 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  105 LEU
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 30 optimal weight:    0.2980
   chunk 44 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.075235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.060121 restraints weight = 12641.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 3.84
r_work: 0.3073 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3917  Z= 0.158
  Angle     :  0.705  10.730   5322  Z= 0.346
  Chirality :  0.045   0.194    587
  Planarity :  0.004   0.032    679
  Dihedral  :  6.757  52.199    585
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.75 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.40), residues: 477
  helix: -3.12 (0.76), residues: 33
  sheet:  1.23 (0.44), residues: 157
  loop : -0.79 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 
 PHE   0.007   0.001   PHE C 562 
 TYR   0.027   0.002   TYR C 369 
 ARG   0.010   0.001   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00433 (    1)
  link_NAG-ASN         : angle       9.35335 (    3)
  link_BETA1-4         : bond        0.00340 (    1)
  link_BETA1-4         : angle       1.43383 (    3)
  hydrogen bonds       : bond        0.02720 (  123)
  hydrogen bonds       : angle       5.42086 (  291)
  link_BETA1-6         : bond        0.03205 (    1)
  link_BETA1-6         : angle       2.22127 (    3)
  SS BOND              : bond        0.00595 (    6)
  SS BOND              : angle       1.57341 (   12)
  covalent geometry    : bond        0.00361 ( 3908)
  covalent geometry    : angle       0.66300 ( 5301)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2377.80 seconds
wall clock time: 42 minutes 7.03 seconds (2527.03 seconds total)