Starting phenix.real_space_refine
on Fri Aug 22 14:18:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dt3_27690/08_2025/8dt3_27690_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dt3_27690/08_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_27690/08_2025/8dt3_27690.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dt3_27690/08_2025/8dt3_27690.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dt3_27690/08_2025/8dt3_27690_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dt3_27690/08_2025/8dt3_27690_neut.cif"
  }
  resolution = 3.3
  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=   0.002
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.39, per 1000 atoms: 0.36
  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: 0.28
  Conformation dependent library (CDL) restraints added in 124.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.16
  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: 0.60

  Time building geometry restraints manager: 0.36 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:             3.090
  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:             0.030
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.260
  Find NCS groups from input model:        0.010
  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:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.640
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.65 (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
 ARG   0.010   0.001   ARG L  54 
 TYR   0.025   0.002   TYR C 369 
 PHE   0.013   0.001   PHE C 392 
 TRP   0.012   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 

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

*********************** 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  : 0.127 
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: 0.7938 (m-80)
REVERT: L  105 LEU cc_start: 0.9313 (mp) cc_final: 0.8665 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0686
  time to fit residues: 5.8706
Evaluate side-chains
  57 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.2980
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    0.3980
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0980
   chunk 30 optimal weight:    0.0470
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.3678

-------------------------------------------------------------------------------
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 = 0.3591 r_free = 0.3591 target = 0.077079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.062135 restraints weight = 12980.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 3.89
r_work: 0.3114 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.1167

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= 0.122
  Angle     :  0.685  10.492   5322  Z= 0.335
  Chirality :  0.045   0.155    587
  Planarity :  0.004   0.040    679
  Dihedral  : 12.650 118.567    585
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  8.61 %
    Favored  : 91.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.40), residues: 477
  helix: -3.58 (0.71), residues: 27
  sheet:  1.16 (0.42), residues: 163
  loop : -0.87 (0.38), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  19 
 TYR   0.022   0.001   TYR C 369 
 PHE   0.012   0.001   PHE C 392 
 TRP   0.009   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3908)
  covalent geometry    : angle       0.64563 ( 5301)
  SS BOND              : bond        0.00605 (    6)
  SS BOND              : angle       1.57064 (   12)
  hydrogen bonds       : bond        0.02737 (  123)
  hydrogen bonds       : angle       5.87185 (  291)
  link_BETA1-4         : bond        0.00370 (    1)
  link_BETA1-4         : angle       1.12361 (    3)
  link_BETA1-6         : bond        0.01110 (    1)
  link_BETA1-6         : angle       1.65711 (    3)
  link_NAG-ASN         : bond        0.01124 (    1)
  link_NAG-ASN         : angle       9.00851 (    3)

*********************** 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
  65 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8609 (mm) cc_final: 0.8395 (mt)
REVERT: C  365 TYR cc_start: 0.6128 (p90) cc_final: 0.5910 (p90)
REVERT: C  563 GLN cc_start: 0.8407 (mt0) cc_final: 0.7512 (mm110)
REVERT: H   80 TYR cc_start: 0.8465 (m-80) cc_final: 0.8160 (m-80)
REVERT: L   80 GLU cc_start: 0.8857 (tt0) cc_final: 0.8612 (tt0)
REVERT: L   81 GLN cc_start: 0.8574 (tp-100) cc_final: 0.8296 (tp-100)
REVERT: L   82 GLU cc_start: 0.8681 (pm20) cc_final: 0.8206 (pm20)
  outliers start: 1
  outliers final: 1
  residues processed: 64
  average time/residue: 0.0676
  time to fit residues: 5.5518
Evaluate side-chains
  59 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
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 12 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 17 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 = 0.3507 r_free = 0.3507 target = 0.072943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.057718 restraints weight = 13034.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 3.85
r_work: 0.3015 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.072   3917  Z= 0.304
  Angle     :  0.737  10.350   5322  Z= 0.369
  Chirality :  0.048   0.189    587
  Planarity :  0.004   0.039    679
  Dihedral  : 11.164 106.789    585
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.39), residues: 477
  helix: -3.38 (0.69), residues: 34
  sheet:  1.14 (0.43), residues: 157
  loop : -0.95 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  19 
 TYR   0.019   0.002   TYR C 369 
 PHE   0.016   0.002   PHE C 392 
 TRP   0.013   0.002   TRP H  33 
 HIS   0.006   0.002   HIS L  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00697 ( 3908)
  covalent geometry    : angle       0.69970 ( 5301)
  SS BOND              : bond        0.00705 (    6)
  SS BOND              : angle       2.16174 (   12)
  hydrogen bonds       : bond        0.03363 (  123)
  hydrogen bonds       : angle       5.91227 (  291)
  link_BETA1-4         : bond        0.00029 (    1)
  link_BETA1-4         : angle       0.85800 (    3)
  link_BETA1-6         : bond        0.00115 (    1)
  link_BETA1-6         : angle       2.11808 (    3)
  link_NAG-ASN         : bond        0.00209 (    1)
  link_NAG-ASN         : angle       8.70952 (    3)

*********************** 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
  58 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8791 (mm) cc_final: 0.8540 (mt)
REVERT: C  365 TYR cc_start: 0.6263 (p90) cc_final: 0.5932 (p90)
REVERT: C  493 GLN cc_start: 0.8343 (mp10) cc_final: 0.8120 (mp10)
REVERT: C  563 GLN cc_start: 0.8476 (mt0) cc_final: 0.7768 (mm110)
REVERT: L   80 GLU cc_start: 0.8825 (tt0) cc_final: 0.8290 (tt0)
  outliers start: 7
  outliers final: 6
  residues processed: 53
  average time/residue: 0.0624
  time to fit residues: 4.3660
Evaluate side-chains
  54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain H residue   46 GLU
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 40 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.6984

-------------------------------------------------------------------------------
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 = 0.3543 r_free = 0.3543 target = 0.074589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.059351 restraints weight = 12777.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 3.85
r_work: 0.3064 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.1727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3917  Z= 0.152
  Angle     :  0.657  10.442   5322  Z= 0.324
  Chirality :  0.045   0.176    587
  Planarity :  0.003   0.034    679
  Dihedral  : 10.406  97.931    585
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.20 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.39), residues: 477
  helix: -3.53 (0.62), residues: 34
  sheet:  1.19 (0.43), residues: 157
  loop : -0.90 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  19 
 TYR   0.017   0.001   TYR C 369 
 PHE   0.013   0.001   PHE C 559 
 TRP   0.010   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 3908)
  covalent geometry    : angle       0.61396 ( 5301)
  SS BOND              : bond        0.00618 (    6)
  SS BOND              : angle       1.86278 (   12)
  hydrogen bonds       : bond        0.02890 (  123)
  hydrogen bonds       : angle       5.68609 (  291)
  link_BETA1-4         : bond        0.00487 (    1)
  link_BETA1-4         : angle       1.07444 (    3)
  link_BETA1-6         : bond        0.00875 (    1)
  link_BETA1-6         : angle       2.10480 (    3)
  link_NAG-ASN         : bond        0.00694 (    1)
  link_NAG-ASN         : angle       8.89852 (    3)

*********************** 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
  64 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8696 (mm) cc_final: 0.8455 (mt)
REVERT: C  434 ILE cc_start: 0.9489 (mt) cc_final: 0.9269 (mt)
REVERT: C  493 GLN cc_start: 0.8192 (mp10) cc_final: 0.7953 (mp10)
REVERT: C  559 PHE cc_start: 0.2792 (OUTLIER) cc_final: 0.1858 (m-80)
REVERT: C  563 GLN cc_start: 0.8562 (mt0) cc_final: 0.7608 (mm110)
REVERT: L   80 GLU cc_start: 0.8832 (tt0) cc_final: 0.8388 (tt0)
  outliers start: 7
  outliers final: 6
  residues processed: 60
  average time/residue: 0.0680
  time to fit residues: 5.2130
Evaluate side-chains
  61 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  559 PHE
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 9 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0770
   chunk 17 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.7740

-------------------------------------------------------------------------------
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 = 0.3546 r_free = 0.3546 target = 0.074656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.059631 restraints weight = 12822.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 3.83
r_work: 0.3066 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.1834

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= 0.161
  Angle     :  0.655  10.629   5322  Z= 0.323
  Chirality :  0.045   0.172    587
  Planarity :  0.004   0.033    679
  Dihedral  :  9.841  92.193    585
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 13.16 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.39), residues: 477
  helix: -3.48 (0.64), residues: 34
  sheet:  1.18 (0.43), residues: 157
  loop : -0.90 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  19 
 TYR   0.015   0.002   TYR C 369 
 PHE   0.008   0.001   PHE C 392 
 TRP   0.011   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 3908)
  covalent geometry    : angle       0.61037 ( 5301)
  SS BOND              : bond        0.00610 (    6)
  SS BOND              : angle       1.80254 (   12)
  hydrogen bonds       : bond        0.02826 (  123)
  hydrogen bonds       : angle       5.50748 (  291)
  link_BETA1-4         : bond        0.00404 (    1)
  link_BETA1-4         : angle       1.11655 (    3)
  link_BETA1-6         : bond        0.00953 (    1)
  link_BETA1-6         : angle       2.25767 (    3)
  link_NAG-ASN         : bond        0.00589 (    1)
  link_NAG-ASN         : angle       9.13958 (    3)

*********************** 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
  70 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8671 (mm) cc_final: 0.8434 (mt)
REVERT: C  434 ILE cc_start: 0.9517 (mt) cc_final: 0.9303 (mt)
REVERT: C  563 GLN cc_start: 0.8453 (mt0) cc_final: 0.7889 (mm110)
REVERT: L   80 GLU cc_start: 0.8822 (tt0) cc_final: 0.8344 (tt0)
  outliers start: 13
  outliers final: 9
  residues processed: 65
  average time/residue: 0.0628
  time to fit residues: 5.2252
Evaluate side-chains
  66 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  450 ASN
Chi-restraints excluded: chain C residue  525 CYS
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 25 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3549 r_free = 0.3549 target = 0.074658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.059861 restraints weight = 12941.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 3.81
r_work: 0.3072 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.1970

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= 0.160
  Angle     :  0.664  10.591   5322  Z= 0.324
  Chirality :  0.045   0.173    587
  Planarity :  0.004   0.030    679
  Dihedral  :  9.158  84.470    585
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 14.35 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.39), residues: 477
  helix: -3.30 (0.67), residues: 34
  sheet:  1.17 (0.43), residues: 157
  loop : -0.87 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  19 
 TYR   0.034   0.002   TYR C 365 
 PHE   0.011   0.001   PHE C 565 
 TRP   0.012   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 3908)
  covalent geometry    : angle       0.62065 ( 5301)
  SS BOND              : bond        0.00605 (    6)
  SS BOND              : angle       1.69092 (   12)
  hydrogen bonds       : bond        0.02824 (  123)
  hydrogen bonds       : angle       5.45942 (  291)
  link_BETA1-4         : bond        0.00451 (    1)
  link_BETA1-4         : angle       1.24541 (    3)
  link_BETA1-6         : bond        0.01179 (    1)
  link_BETA1-6         : angle       2.24329 (    3)
  link_NAG-ASN         : bond        0.00582 (    1)
  link_NAG-ASN         : angle       9.16118 (    3)

*********************** 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
  73 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8670 (mm) cc_final: 0.8436 (mt)
REVERT: C  434 ILE cc_start: 0.9534 (mt) cc_final: 0.9316 (mt)
REVERT: C  559 PHE cc_start: 0.3159 (OUTLIER) cc_final: 0.1802 (m-80)
REVERT: C  563 GLN cc_start: 0.8278 (mt0) cc_final: 0.7438 (mm110)
REVERT: L   80 GLU cc_start: 0.8796 (tt0) cc_final: 0.8350 (tt0)
REVERT: L   81 GLN cc_start: 0.8521 (tp-100) cc_final: 0.8241 (tp-100)
  outliers start: 13
  outliers final: 11
  residues processed: 66
  average time/residue: 0.0622
  time to fit residues: 5.1690
Evaluate side-chains
  69 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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   51 TYR
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 11 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.074616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.059730 restraints weight = 13066.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 3.84
r_work: 0.3068 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.2063

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= 0.168
  Angle     :  0.684  10.640   5322  Z= 0.332
  Chirality :  0.045   0.177    587
  Planarity :  0.004   0.030    679
  Dihedral  :  8.350  73.262    585
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 15.55 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.49 (0.39), residues: 477
  helix: -3.15 (0.73), residues: 34
  sheet:  1.17 (0.43), residues: 157
  loop : -0.86 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG L  19 
 TYR   0.030   0.002   TYR C 365 
 PHE   0.008   0.001   PHE C 559 
 TRP   0.011   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 3908)
  covalent geometry    : angle       0.64097 ( 5301)
  SS BOND              : bond        0.00600 (    6)
  SS BOND              : angle       1.71349 (   12)
  hydrogen bonds       : bond        0.02842 (  123)
  hydrogen bonds       : angle       5.44964 (  291)
  link_BETA1-4         : bond        0.00334 (    1)
  link_BETA1-4         : angle       1.26358 (    3)
  link_BETA1-6         : bond        0.01736 (    1)
  link_BETA1-6         : angle       2.05431 (    3)
  link_NAG-ASN         : bond        0.00484 (    1)
  link_NAG-ASN         : angle       9.29606 (    3)

*********************** 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  : 0.170 
Fit side-chains
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8672 (mm) cc_final: 0.8443 (mt)
REVERT: C  434 ILE cc_start: 0.9531 (mt) cc_final: 0.9313 (mt)
REVERT: C  559 PHE cc_start: 0.3169 (OUTLIER) cc_final: 0.1548 (m-80)
REVERT: C  563 GLN cc_start: 0.8406 (mt0) cc_final: 0.7560 (mm110)
  outliers start: 13
  outliers final: 11
  residues processed: 65
  average time/residue: 0.0655
  time to fit residues: 5.4578
Evaluate side-chains
  68 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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   51 TYR
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 12 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0070
   chunk 8 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 14 optimal weight:    0.4980
   chunk 37 optimal weight:    3.9990
   chunk 4 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.4798

-------------------------------------------------------------------------------
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 = 0.3570 r_free = 0.3570 target = 0.075635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.060908 restraints weight = 12902.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 3.83
r_work: 0.3099 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.2131

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= 0.130
  Angle     :  0.683  10.977   5322  Z= 0.330
  Chirality :  0.045   0.166    587
  Planarity :  0.004   0.027    679
  Dihedral  :  7.143  54.202    585
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.40), residues: 477
  helix: -3.25 (0.69), residues: 34
  sheet:  1.24 (0.44), residues: 157
  loop : -0.82 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG L  19 
 TYR   0.024   0.001   TYR C 365 
 PHE   0.006   0.001   PHE C 565 
 TRP   0.010   0.001   TRP H  33 
 HIS   0.001   0.000   HIS L  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3908)
  covalent geometry    : angle       0.64041 ( 5301)
  SS BOND              : bond        0.00585 (    6)
  SS BOND              : angle       1.45036 (   12)
  hydrogen bonds       : bond        0.02705 (  123)
  hydrogen bonds       : angle       5.36036 (  291)
  link_BETA1-4         : bond        0.00505 (    1)
  link_BETA1-4         : angle       1.43013 (    3)
  link_BETA1-6         : bond        0.02704 (    1)
  link_BETA1-6         : angle       1.88769 (    3)
  link_NAG-ASN         : bond        0.00622 (    1)
  link_NAG-ASN         : angle       9.37189 (    3)

*********************** 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
  69 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8628 (mm) cc_final: 0.8402 (mt)
REVERT: C  434 ILE cc_start: 0.9525 (mt) cc_final: 0.9312 (mt)
REVERT: C  559 PHE cc_start: 0.3466 (OUTLIER) cc_final: 0.1482 (m-80)
REVERT: C  563 GLN cc_start: 0.8386 (mt0) cc_final: 0.7564 (mm110)
  outliers start: 11
  outliers final: 8
  residues processed: 63
  average time/residue: 0.0678
  time to fit residues: 5.4684
Evaluate side-chains
  64 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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 24 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 32 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.074802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.059515 restraints weight = 12923.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 3.89
r_work: 0.3064 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3917  Z= 0.176
  Angle     :  0.707  10.695   5322  Z= 0.345
  Chirality :  0.045   0.179    587
  Planarity :  0.004   0.032    679
  Dihedral  :  7.237  54.314    585
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.40), residues: 477
  helix: -3.26 (0.69), residues: 34
  sheet:  1.25 (0.44), residues: 157
  loop : -0.80 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG L  19 
 TYR   0.025   0.002   TYR C 365 
 PHE   0.009   0.001   PHE C 562 
 TRP   0.011   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 3908)
  covalent geometry    : angle       0.66582 ( 5301)
  SS BOND              : bond        0.00590 (    6)
  SS BOND              : angle       1.65617 (   12)
  hydrogen bonds       : bond        0.02792 (  123)
  hydrogen bonds       : angle       5.37043 (  291)
  link_BETA1-4         : bond        0.00262 (    1)
  link_BETA1-4         : angle       1.36242 (    3)
  link_BETA1-6         : bond        0.02570 (    1)
  link_BETA1-6         : angle       1.72633 (    3)
  link_NAG-ASN         : bond        0.00406 (    1)
  link_NAG-ASN         : angle       9.31318 (    3)

*********************** 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
  67 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8668 (mm) cc_final: 0.8444 (mt)
REVERT: C  434 ILE cc_start: 0.9525 (mt) cc_final: 0.9307 (mt)
REVERT: C  516 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7605 (tm-30)
REVERT: C  559 PHE cc_start: 0.3524 (OUTLIER) cc_final: 0.1448 (m-80)
REVERT: C  563 GLN cc_start: 0.8352 (mt0) cc_final: 0.7532 (mm110)
  outliers start: 11
  outliers final: 9
  residues processed: 61
  average time/residue: 0.0649
  time to fit residues: 5.0770
Evaluate side-chains
  64 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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   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 25 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3552 r_free = 0.3552 target = 0.074755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.059604 restraints weight = 13004.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 3.88
r_work: 0.3058 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3917  Z= 0.168
  Angle     :  0.709  10.896   5322  Z= 0.345
  Chirality :  0.045   0.184    587
  Planarity :  0.004   0.033    679
  Dihedral  :  6.937  51.861    585
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.40), residues: 477
  helix: -3.28 (0.68), residues: 34
  sheet:  1.23 (0.44), residues: 157
  loop : -0.83 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG L  19 
 TYR   0.028   0.002   TYR C 369 
 PHE   0.009   0.001   PHE C 562 
 TRP   0.011   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 3908)
  covalent geometry    : angle       0.66850 ( 5301)
  SS BOND              : bond        0.00600 (    6)
  SS BOND              : angle       1.60487 (   12)
  hydrogen bonds       : bond        0.02754 (  123)
  hydrogen bonds       : angle       5.36994 (  291)
  link_BETA1-4         : bond        0.00258 (    1)
  link_BETA1-4         : angle       1.39019 (    3)
  link_BETA1-6         : bond        0.02961 (    1)
  link_BETA1-6         : angle       1.88387 (    3)
  link_NAG-ASN         : bond        0.00407 (    1)
  link_NAG-ASN         : angle       9.24398 (    3)

********************** 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
  67 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8656 (mm) cc_final: 0.8434 (mt)
REVERT: C  434 ILE cc_start: 0.9523 (mt) cc_final: 0.9304 (mt)
REVERT: C  559 PHE cc_start: 0.3451 (OUTLIER) cc_final: 0.1319 (m-80)
REVERT: C  563 GLN cc_start: 0.8298 (mt0) cc_final: 0.7495 (mm110)
REVERT: L   82 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8856 (pm20)
  outliers start: 11
  outliers final: 9
  residues processed: 61
  average time/residue: 0.0600
  time to fit residues: 4.7876
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  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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   34 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue   82 GLU
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 34 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 38 optimal weight:    6.9990
   chunk 5 optimal weight:    0.3980
   chunk 45 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0970
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3562 r_free = 0.3562 target = 0.075380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.060287 restraints weight = 12821.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 3.87
r_work: 0.3075 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.2297

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= 0.147
  Angle     :  0.697  10.852   5322  Z= 0.339
  Chirality :  0.045   0.196    587
  Planarity :  0.004   0.032    679
  Dihedral  :  6.692  51.569    585
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 16.99 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.40), residues: 477
  helix: -3.27 (0.69), residues: 34
  sheet:  1.25 (0.44), residues: 157
  loop : -0.82 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG L  19 
 TYR   0.023   0.002   TYR C 365 
 PHE   0.009   0.001   PHE C 562 
 TRP   0.010   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3908)
  covalent geometry    : angle       0.65523 ( 5301)
  SS BOND              : bond        0.00587 (    6)
  SS BOND              : angle       1.51827 (   12)
  hydrogen bonds       : bond        0.02670 (  123)
  hydrogen bonds       : angle       5.33758 (  291)
  link_BETA1-4         : bond        0.00292 (    1)
  link_BETA1-4         : angle       1.43866 (    3)
  link_BETA1-6         : bond        0.03429 (    1)
  link_BETA1-6         : angle       2.38325 (    3)
  link_NAG-ASN         : bond        0.00446 (    1)
  link_NAG-ASN         : angle       9.34387 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1098.40 seconds
wall clock time: 19 minutes 43.52 seconds (1183.52 seconds total)