Starting phenix.real_space_refine
on Wed Jul 23 13:32:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k9k_22751/07_2025/7k9k_22751.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k9k_22751/07_2025/7k9k_22751.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k9k_22751/07_2025/7k9k_22751.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k9k_22751/07_2025/7k9k_22751.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k9k_22751/07_2025/7k9k_22751.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k9k_22751/07_2025/7k9k_22751.cif"
  }
  resolution = 3.14
  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=   0.002 sd=   0.071
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      12      5.16       5
     C    2035      2.51       5
     N     524      2.21       5
     O     631      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 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: 3202
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1400
          Classifications: {'peptide': 175}
          Link IDs: {'PTRANS': 10, 'TRANS': 164}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 947
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
    Chain: "L"
      Number of atoms: 806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 806
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 100}
    Chain: "B"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 49
          Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 2.85, per 1000 atoms: 0.89
  Number of scatterers: 3202
  At special positions: 0
  Unit cell: (79.2, 63.8, 77, 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      12     16.00
     O     631      8.00
     N     524      7.00
     C    2035      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " 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 B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
    BETA1-6
      " NAG B   1 " - " FUC B   4 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG B   1 " - " ASN A 343 "
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 391.4 milliseconds
  

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  740

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 9 sheets defined
      11.7% alpha, 38.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 4.079A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 364 through 371
      removed outlier: 4.322A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 389
      removed outlier: 3.712A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 411
      removed outlier: 3.519A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'L' and resid 79 through 82
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.515A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   THR A 376 " --> pdb=" O   ALA A 435 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6
      removed outlier: 3.667A  pdb=" N   VAL H  18 " --> pdb=" O   LEU H  83 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   CYS H  22 " --> pdb=" O   ALA H  79 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ALA H  79 " --> pdb=" O   CYS H  22 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 9 through 12
      removed outlier: 7.133A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 117 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   ILE H  34 " --> pdb=" O   ASP H  50 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   ASP H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   ARG H  40 " --> pdb=" O   GLY H  44 " (cutoff:3.500A)
      removed outlier: 5.243A  pdb=" N   GLY H  44 " --> pdb=" O   ARG H  40 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 9 through 12
      removed outlier: 7.133A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 117 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   TYR H 109 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 6
      removed outlier: 3.631A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER L  74 " --> pdb=" O   SER L  63 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   SER L  63 " --> pdb=" O   SER L  74 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.817A  pdb=" N   GLU L 105 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU L 104 " --> pdb=" O   ALA L  84 " (cutoff:3.500A)
      removed outlier: 5.250A  pdb=" N   ALA L  84 " --> pdb=" O   LEU L 104 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   ILE L  33 " --> pdb=" O   LYS L  49 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   LYS L  49 " --> pdb=" O   ILE L  33 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLU L  53 " --> pdb=" O   LYS L  49 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.817A  pdb=" N   GLU L 105 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU L 104 " --> pdb=" O   ALA L  84 " (cutoff:3.500A)
      removed outlier: 5.250A  pdb=" N   ALA L  84 " --> pdb=" O   LEU L 104 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)

    107 hydrogen bonds defined for protein.
    255 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: 0.80

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 517
        1.32 -     1.45: 1013
        1.45 -     1.57: 1740
        1.57 -     1.70: 0
        1.70 -     1.83: 14
  Bond restraints: 3284
  Sorted by residual:
  bond pdb=" C   VAL A 433 "
       pdb=" O   VAL A 433 "
    ideal  model  delta    sigma   weight residual
    1.238  1.193  0.044 1.17e-02 7.31e+03 1.45e+01
  bond pdb=" C   CYS A 432 "
       pdb=" O   CYS A 432 "
    ideal  model  delta    sigma   weight residual
    1.235  1.198  0.038 1.14e-02 7.69e+03 1.09e+01
  bond pdb=" N   SER L   7 "
       pdb=" CA  SER L   7 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.034 1.04e-02 9.25e+03 1.04e+01
  bond pdb=" CA  ALA A 435 "
       pdb=" CB  ALA A 435 "
    ideal  model  delta    sigma   weight residual
    1.535  1.482  0.053 1.90e-02 2.77e+03 7.83e+00
  bond pdb=" CA  SER L   7 "
       pdb=" CB  SER L   7 "
    ideal  model  delta    sigma   weight residual
    1.537  1.497  0.040 1.47e-02 4.63e+03 7.46e+00
  ... (remaining 3279 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 4002
        1.40 -     2.79: 347
        2.79 -     4.19: 85
        4.19 -     5.58: 21
        5.58 -     6.98: 10
  Bond angle restraints: 4465
  Sorted by residual:
  angle pdb=" CA  SER L   7 "
        pdb=" C   SER L   7 "
        pdb=" N   PRO L   8 "
      ideal   model   delta    sigma   weight residual
     117.96  122.41   -4.45 8.10e-01 1.52e+00 3.02e+01
  angle pdb=" C   PRO L  15 "
        pdb=" CA  PRO L  15 "
        pdb=" CB  PRO L  15 "
      ideal   model   delta    sigma   weight residual
     111.46  105.66    5.80 1.29e+00 6.01e-01 2.02e+01
  angle pdb=" N   GLY L  16 "
        pdb=" CA  GLY L  16 "
        pdb=" C   GLY L  16 "
      ideal   model   delta    sigma   weight residual
     113.79  108.80    4.99 1.17e+00 7.31e-01 1.82e+01
  angle pdb=" CA  ALA L   9 "
        pdb=" C   ALA L   9 "
        pdb=" O   ALA L   9 "
      ideal   model   delta    sigma   weight residual
     120.55  116.59    3.96 1.06e+00 8.90e-01 1.39e+01
  angle pdb=" CA  VAL A 433 "
        pdb=" C   VAL A 433 "
        pdb=" O   VAL A 433 "
      ideal   model   delta    sigma   weight residual
     120.57  116.93    3.64 1.07e+00 8.73e-01 1.16e+01
  ... (remaining 4460 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.39: 1812
       19.39 -    38.78: 120
       38.78 -    58.16: 21
       58.16 -    77.55: 12
       77.55 -    96.94: 7
  Dihedral angle restraints: 1972
    sinusoidal: 807
      harmonic: 1165
  Sorted by residual:
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -0.83  -85.17     1      1.00e+01 1.00e-02 8.79e+01
  dihedral pdb=" CA  SER L   7 "
           pdb=" C   SER L   7 "
           pdb=" N   PRO L   8 "
           pdb=" CA  PRO L   8 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   29.78  -29.78     0      5.00e+00 4.00e-02 3.55e+01
  dihedral pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -41.61  -44.39     1      1.00e+01 1.00e-02 2.74e+01
  ... (remaining 1969 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 395
       0.070 -    0.140: 83
       0.140 -    0.210: 10
       0.210 -    0.280: 2
       0.280 -    0.350: 3
  Chirality restraints: 493
  Sorted by residual:
  chirality pdb=" CA  ILE A 434 "
            pdb=" N   ILE A 434 "
            pdb=" C   ILE A 434 "
            pdb=" CB  ILE A 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.78   -0.35 2.00e-01 2.50e+01 3.06e+00
  chirality pdb=" CA  PHE A 377 "
            pdb=" N   PHE A 377 "
            pdb=" C   PHE A 377 "
            pdb=" CB  PHE A 377 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.82e+00
  chirality pdb=" CA  GLN L   6 "
            pdb=" N   GLN L   6 "
            pdb=" C   GLN L   6 "
            pdb=" CB  GLN L   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.81e+00
  ... (remaining 490 not shown)

  Planarity restraints: 566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE L  58 "   -0.036 5.00e-02 4.00e+02   5.49e-02 4.82e+00
        pdb=" N   PRO L  59 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO L  59 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO L  59 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 431 "    0.010 2.00e-02 2.50e+03   2.03e-02 4.12e+00
        pdb=" C   GLY A 431 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   GLY A 431 "    0.013 2.00e-02 2.50e+03
        pdb=" N   CYS A 432 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H  98 "   -0.042 9.50e-02 1.11e+02   2.49e-02 3.50e+00
        pdb=" NE  ARG H  98 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG H  98 "   -0.031 2.00e-02 2.50e+03
        pdb=" NH1 ARG H  98 "    0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG H  98 "    0.009 2.00e-02 2.50e+03
  ... (remaining 563 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 217
        2.73 -     3.27: 3220
        3.27 -     3.82: 4945
        3.82 -     4.36: 6169
        4.36 -     4.90: 10675
  Nonbonded interactions: 25226
  Sorted by model distance:
  nonbonded pdb=" OG  SER H  17 "
            pdb=" O   LEU H  83 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" O   PHE H 107 "
            pdb=" NE1 TRP H 110 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" OG  SER H  66 "
            pdb=" OE1 GLU H  67 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" N   LEU A 455 "
            pdb=" O   PRO A 491 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OD1 ASN A 439 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.301 3.040
  ... (remaining 25221 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:             2.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.880
  Find NCS groups from input model:        0.030
  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:2.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
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      :  0.006   0.053   3293  Z= 0.340
  Angle     :  0.975   7.520   4487  Z= 0.558
  Chirality :  0.063   0.350    493
  Planarity :  0.005   0.055    565
  Dihedral  : 15.505  96.937   1217
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -1.35 (0.39), residues: 394
  helix: -1.50 (0.85), residues: 34
  sheet: -0.41 (0.41), residues: 129
  loop : -1.06 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A 436 
 HIS   0.005   0.003   HIS L  34 
 PHE   0.026   0.002   PHE A 497 
 TYR   0.028   0.003   TYR H  80 
 ARG   0.031   0.003   ARG H  98 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00496 (    1)
  link_NAG-ASN         : angle       2.97039 (    3)
  link_BETA1-4         : bond        0.01425 (    2)
  link_BETA1-4         : angle       3.58342 (    6)
  hydrogen bonds       : bond        0.26370 (  100)
  hydrogen bonds       : angle      10.78116 (  255)
  link_BETA1-6         : bond        0.00546 (    1)
  link_BETA1-6         : angle       2.29257 (    3)
  SS BOND              : bond        0.00741 (    5)
  SS BOND              : angle       1.77181 (   10)
  covalent geometry    : bond        0.00636 ( 3284)
  covalent geometry    : angle       0.96045 ( 4465)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: A  442 ASP cc_start: 0.7791 (m-30) cc_final: 0.7456 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.2229
  time to fit residues: 21.2243
Evaluate side-chains
  63 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 19 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    8.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.131503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.109492 restraints weight = 5848.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 3.22
r_work: 0.3441 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3293  Z= 0.156
  Angle     :  0.727  10.493   4487  Z= 0.363
  Chirality :  0.047   0.173    493
  Planarity :  0.005   0.052    565
  Dihedral  :  9.519  56.312    521
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  8.96 %
    Favored  : 89.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.93 (0.41), residues: 394
  helix: -1.35 (1.10), residues: 28
  sheet: -0.12 (0.41), residues: 140
  loop : -0.80 (0.41), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.013   0.002   PHE A 377 
 TYR   0.014   0.002   TYR A 421 
 ARG   0.005   0.001   ARG A 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00407 (    1)
  link_NAG-ASN         : angle       2.16162 (    3)
  link_BETA1-4         : bond        0.01130 (    2)
  link_BETA1-4         : angle       3.06977 (    6)
  hydrogen bonds       : bond        0.04572 (  100)
  hydrogen bonds       : angle       7.52590 (  255)
  link_BETA1-6         : bond        0.00260 (    1)
  link_BETA1-6         : angle       1.95708 (    3)
  SS BOND              : bond        0.00437 (    5)
  SS BOND              : angle       1.10159 (   10)
  covalent geometry    : bond        0.00338 ( 3284)
  covalent geometry    : angle       0.71403 ( 4465)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A  406 GLU cc_start: 0.7934 (mp0) cc_final: 0.7260 (mp0)
REVERT: A  442 ASP cc_start: 0.7920 (m-30) cc_final: 0.7631 (m-30)
REVERT: L   86 TYR cc_start: 0.6923 (m-80) cc_final: 0.6698 (m-80)
REVERT: L  105 GLU cc_start: 0.4880 (tp30) cc_final: 0.4643 (tp30)
  outliers start: 7
  outliers final: 3
  residues processed: 74
  average time/residue: 0.2025
  time to fit residues: 18.7987
Evaluate side-chains
  67 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  514 SER
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain L residue   40 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 34 optimal weight:    0.5980
   chunk 12 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 17 optimal weight:    8.9990
   overall best weight:    3.3188

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.127188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.105155 restraints weight = 5786.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 3.18
r_work: 0.3375 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   3293  Z= 0.273
  Angle     :  0.772  11.747   4487  Z= 0.384
  Chirality :  0.049   0.178    493
  Planarity :  0.006   0.052    565
  Dihedral  :  7.937  54.406    521
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 11.27 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.92 (0.41), residues: 394
  helix: -2.17 (0.87), residues: 34
  sheet:  0.19 (0.41), residues: 149
  loop : -0.90 (0.42), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 436 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.019   0.002   PHE A 497 
 TYR   0.013   0.002   TYR H 102 
 ARG   0.004   0.001   ARG A 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00589 (    1)
  link_NAG-ASN         : angle       2.19410 (    3)
  link_BETA1-4         : bond        0.00858 (    2)
  link_BETA1-4         : angle       2.70390 (    6)
  hydrogen bonds       : bond        0.04671 (  100)
  hydrogen bonds       : angle       7.09719 (  255)
  link_BETA1-6         : bond        0.00633 (    1)
  link_BETA1-6         : angle       2.21484 (    3)
  SS BOND              : bond        0.00340 (    5)
  SS BOND              : angle       1.51532 (   10)
  covalent geometry    : bond        0.00620 ( 3284)
  covalent geometry    : angle       0.75968 ( 4465)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8035 (ptm160) cc_final: 0.7484 (ptm-80)
REVERT: A  406 GLU cc_start: 0.8087 (mp0) cc_final: 0.7543 (mp0)
REVERT: A  442 ASP cc_start: 0.7943 (m-30) cc_final: 0.7329 (m-30)
REVERT: H  112 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7139 (mp10)
  outliers start: 13
  outliers final: 11
  residues processed: 74
  average time/residue: 0.2540
  time to fit residues: 22.9498
Evaluate side-chains
  79 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain L residue    1 ASP
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   21 PHE
Chi-restraints excluded: chain L residue   40 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 14 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  41 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.129862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.107997 restraints weight = 5877.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 3.23
r_work: 0.3421 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3293  Z= 0.135
  Angle     :  0.660  12.254   4487  Z= 0.326
  Chirality :  0.045   0.163    493
  Planarity :  0.005   0.053    565
  Dihedral  :  7.000  53.462    521
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 13.87 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.75 (0.42), residues: 394
  helix: -2.23 (0.79), residues: 40
  sheet:  0.40 (0.42), residues: 145
  loop : -0.74 (0.43), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 436 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.015   0.001   PHE A 497 
 TYR   0.019   0.001   TYR H  80 
 ARG   0.004   0.001   ARG A 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00415 (    1)
  link_NAG-ASN         : angle       2.17205 (    3)
  link_BETA1-4         : bond        0.00916 (    2)
  link_BETA1-4         : angle       2.43362 (    6)
  hydrogen bonds       : bond        0.03638 (  100)
  hydrogen bonds       : angle       6.65773 (  255)
  link_BETA1-6         : bond        0.00424 (    1)
  link_BETA1-6         : angle       1.95343 (    3)
  SS BOND              : bond        0.00295 (    5)
  SS BOND              : angle       1.27247 (   10)
  covalent geometry    : bond        0.00294 ( 3284)
  covalent geometry    : angle       0.64833 ( 4465)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 1.518 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8120 (ptm160) cc_final: 0.7467 (ptm-80)
REVERT: A  406 GLU cc_start: 0.8168 (mp0) cc_final: 0.7640 (mp0)
REVERT: A  442 ASP cc_start: 0.7859 (m-30) cc_final: 0.7312 (m-30)
REVERT: H  112 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7229 (mp10)
  outliers start: 11
  outliers final: 6
  residues processed: 76
  average time/residue: 0.3274
  time to fit residues: 30.5735
Evaluate side-chains
  73 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   21 PHE
Chi-restraints excluded: chain L residue   40 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0270
   chunk 36 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0980
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.131990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.110201 restraints weight = 5858.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 3.22
r_work: 0.3449 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3293  Z= 0.106
  Angle     :  0.640  11.501   4487  Z= 0.317
  Chirality :  0.043   0.155    493
  Planarity :  0.004   0.052    565
  Dihedral  :  6.497  48.741    521
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 14.74 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.68 (0.42), residues: 394
  helix: -2.14 (0.86), residues: 34
  sheet:  0.22 (0.41), residues: 155
  loop : -0.62 (0.44), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.002   0.001   HIS L  34 
 PHE   0.036   0.001   PHE A 497 
 TYR   0.011   0.001   TYR A 369 
 ARG   0.005   0.001   ARG H  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00345 (    1)
  link_NAG-ASN         : angle       2.22171 (    3)
  link_BETA1-4         : bond        0.00884 (    2)
  link_BETA1-4         : angle       2.18379 (    6)
  hydrogen bonds       : bond        0.03220 (  100)
  hydrogen bonds       : angle       6.37138 (  255)
  link_BETA1-6         : bond        0.00190 (    1)
  link_BETA1-6         : angle       1.92730 (    3)
  SS BOND              : bond        0.00474 (    5)
  SS BOND              : angle       0.99636 (   10)
  covalent geometry    : bond        0.00224 ( 3284)
  covalent geometry    : angle       0.63068 ( 4465)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.430 
Fit side-chains
REVERT: A  403 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7422 (ptm-80)
REVERT: A  406 GLU cc_start: 0.8229 (mp0) cc_final: 0.7519 (mp0)
REVERT: A  442 ASP cc_start: 0.7853 (m-30) cc_final: 0.7456 (m-30)
REVERT: H  102 TYR cc_start: 0.8489 (m-80) cc_final: 0.7717 (m-80)
REVERT: H  112 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7123 (mp10)
  outliers start: 13
  outliers final: 5
  residues processed: 72
  average time/residue: 0.1583
  time to fit residues: 14.1750
Evaluate side-chains
  71 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   21 PHE
Chi-restraints excluded: chain L residue   40 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 21 optimal weight:    0.1980
   chunk 16 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 8 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0370
   chunk 17 optimal weight:    0.8980
   chunk 14 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    1.6262

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

Flipped N/Q/H residues before XYZ refinement:
H   5 GLN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.130022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.108044 restraints weight = 6031.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 3.28
r_work: 0.3418 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3293  Z= 0.154
  Angle     :  0.642  11.591   4487  Z= 0.319
  Chirality :  0.044   0.157    493
  Planarity :  0.005   0.052    565
  Dihedral  :  6.316  42.805    521
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 16.18 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.70 (0.42), residues: 394
  helix: -2.32 (0.85), residues: 34
  sheet:  0.29 (0.41), residues: 155
  loop : -0.67 (0.44), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  47 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.019   0.002   PHE A 497 
 TYR   0.017   0.001   TYR H  80 
 ARG   0.004   0.000   ARG H  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00378 (    1)
  link_NAG-ASN         : angle       2.18873 (    3)
  link_BETA1-4         : bond        0.00774 (    2)
  link_BETA1-4         : angle       1.99297 (    6)
  hydrogen bonds       : bond        0.03445 (  100)
  hydrogen bonds       : angle       6.24984 (  255)
  link_BETA1-6         : bond        0.00313 (    1)
  link_BETA1-6         : angle       2.02808 (    3)
  SS BOND              : bond        0.00148 (    5)
  SS BOND              : angle       0.98058 (   10)
  covalent geometry    : bond        0.00347 ( 3284)
  covalent geometry    : angle       0.63315 ( 4465)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7290 (ptm-80)
REVERT: A  406 GLU cc_start: 0.8232 (mp0) cc_final: 0.7737 (mp0)
REVERT: A  442 ASP cc_start: 0.7882 (m-30) cc_final: 0.7348 (m-30)
REVERT: H  112 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7131 (mp10)
  outliers start: 11
  outliers final: 8
  residues processed: 68
  average time/residue: 0.1614
  time to fit residues: 13.3141
Evaluate side-chains
  76 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain L residue    1 ASP
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   21 PHE
Chi-restraints excluded: chain L residue   40 THR
Chi-restraints excluded: chain L residue   69 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 8 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.129733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.108007 restraints weight = 5855.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 3.20
r_work: 0.3419 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3293  Z= 0.157
  Angle     :  0.640  10.620   4487  Z= 0.320
  Chirality :  0.044   0.157    493
  Planarity :  0.004   0.055    565
  Dihedral  :  6.140  38.975    521
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 16.47 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.76 (0.43), residues: 394
  helix: -2.38 (0.85), residues: 33
  sheet:  0.17 (0.41), residues: 161
  loop : -0.67 (0.45), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  47 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.015   0.001   PHE A 497 
 TYR   0.013   0.001   TYR A 421 
 ARG   0.003   0.000   ARG H  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00338 (    1)
  link_NAG-ASN         : angle       2.15216 (    3)
  link_BETA1-4         : bond        0.00746 (    2)
  link_BETA1-4         : angle       1.90560 (    6)
  hydrogen bonds       : bond        0.03423 (  100)
  hydrogen bonds       : angle       6.20110 (  255)
  link_BETA1-6         : bond        0.00338 (    1)
  link_BETA1-6         : angle       2.00013 (    3)
  SS BOND              : bond        0.00175 (    5)
  SS BOND              : angle       1.03137 (   10)
  covalent geometry    : bond        0.00354 ( 3284)
  covalent geometry    : angle       0.63146 ( 4465)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7393 (ptm-80)
REVERT: A  406 GLU cc_start: 0.8255 (mp0) cc_final: 0.7298 (mp0)
REVERT: A  442 ASP cc_start: 0.7858 (m-30) cc_final: 0.7350 (m-30)
REVERT: A  495 TYR cc_start: 0.7141 (m-80) cc_final: 0.6920 (m-80)
REVERT: H  112 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7206 (mp10)
  outliers start: 14
  outliers final: 11
  residues processed: 73
  average time/residue: 0.1601
  time to fit residues: 14.2594
Evaluate side-chains
  77 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   85 SER
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain L residue    1 ASP
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   21 PHE
Chi-restraints excluded: chain L residue   40 THR
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   78 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 31 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 30 optimal weight:    8.9990
   chunk 0 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  41 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.128534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.106821 restraints weight = 5863.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 3.19
r_work: 0.3405 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3293  Z= 0.186
  Angle     :  0.658  10.266   4487  Z= 0.332
  Chirality :  0.045   0.169    493
  Planarity :  0.005   0.056    565
  Dihedral  :  6.137  39.446    521
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 16.76 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.84 (0.43), residues: 394
  helix: -2.51 (0.82), residues: 34
  sheet:  0.14 (0.42), residues: 161
  loop : -0.71 (0.44), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  47 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.012   0.002   PHE A 497 
 TYR   0.018   0.002   TYR H  80 
 ARG   0.004   0.000   ARG H  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00399 (    1)
  link_NAG-ASN         : angle       2.14750 (    3)
  link_BETA1-4         : bond        0.00713 (    2)
  link_BETA1-4         : angle       1.84139 (    6)
  hydrogen bonds       : bond        0.03589 (  100)
  hydrogen bonds       : angle       6.23218 (  255)
  link_BETA1-6         : bond        0.00427 (    1)
  link_BETA1-6         : angle       2.07227 (    3)
  SS BOND              : bond        0.00179 (    5)
  SS BOND              : angle       1.34780 (   10)
  covalent geometry    : bond        0.00422 ( 3284)
  covalent geometry    : angle       0.64829 ( 4465)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7422 (ptm-80)
REVERT: A  406 GLU cc_start: 0.8264 (mp0) cc_final: 0.7363 (mp0)
REVERT: A  442 ASP cc_start: 0.7857 (m-30) cc_final: 0.7356 (m-30)
REVERT: H  112 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7168 (mp10)
  outliers start: 16
  outliers final: 12
  residues processed: 70
  average time/residue: 0.2405
  time to fit residues: 20.3048
Evaluate side-chains
  78 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   85 SER
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain L residue    1 ASP
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   21 PHE
Chi-restraints excluded: chain L residue   40 THR
Chi-restraints excluded: chain L residue   41 ASN
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   78 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 34 optimal weight:    7.9990
   chunk 35 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.129506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.108767 restraints weight = 5839.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 3.10
r_work: 0.3433 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3293  Z= 0.127
  Angle     :  0.647   9.608   4487  Z= 0.326
  Chirality :  0.045   0.190    493
  Planarity :  0.004   0.056    565
  Dihedral  :  5.841  39.160    521
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 18.50 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.84 (0.43), residues: 394
  helix: -2.67 (0.72), residues: 40
  sheet:  0.22 (0.42), residues: 160
  loop : -0.67 (0.46), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.002   0.001   HIS L  34 
 PHE   0.013   0.001   PHE A 497 
 TYR   0.014   0.001   TYR A 369 
 ARG   0.004   0.000   ARG H  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00310 (    1)
  link_NAG-ASN         : angle       2.20295 (    3)
  link_BETA1-4         : bond        0.00760 (    2)
  link_BETA1-4         : angle       1.81930 (    6)
  hydrogen bonds       : bond        0.03335 (  100)
  hydrogen bonds       : angle       6.27902 (  255)
  link_BETA1-6         : bond        0.00243 (    1)
  link_BETA1-6         : angle       1.99593 (    3)
  SS BOND              : bond        0.00388 (    5)
  SS BOND              : angle       2.17015 (   10)
  covalent geometry    : bond        0.00285 ( 3284)
  covalent geometry    : angle       0.63224 ( 4465)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7585 (ptm-80)
REVERT: A  406 GLU cc_start: 0.8263 (mp0) cc_final: 0.7995 (mm-30)
REVERT: A  442 ASP cc_start: 0.7856 (m-30) cc_final: 0.7278 (m-30)
REVERT: H  112 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7142 (mp10)
REVERT: L  105 GLU cc_start: 0.5088 (tp30) cc_final: 0.4752 (tp30)
  outliers start: 12
  outliers final: 9
  residues processed: 68
  average time/residue: 0.2425
  time to fit residues: 19.9483
Evaluate side-chains
  73 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain L residue    1 ASP
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   21 PHE
Chi-restraints excluded: chain L residue   40 THR
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   78 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 25 optimal weight:    0.0000
   chunk 32 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0670
   chunk 1 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 2 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.3526

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  41 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.129192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.108468 restraints weight = 5861.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 3.09
r_work: 0.3428 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.101   3293  Z= 0.157
  Angle     :  0.703  11.556   4487  Z= 0.354
  Chirality :  0.046   0.303    493
  Planarity :  0.005   0.055    565
  Dihedral  :  5.782  38.637    521
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 17.63 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.82 (0.43), residues: 394
  helix: -2.68 (0.71), residues: 40
  sheet:  0.24 (0.42), residues: 160
  loop : -0.66 (0.46), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.001   0.001   HIS L  34 
 PHE   0.012   0.001   PHE A 497 
 TYR   0.019   0.001   TYR H  80 
 ARG   0.004   0.000   ARG H  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00321 (    1)
  link_NAG-ASN         : angle       2.17196 (    3)
  link_BETA1-4         : bond        0.00700 (    2)
  link_BETA1-4         : angle       1.72464 (    6)
  hydrogen bonds       : bond        0.03406 (  100)
  hydrogen bonds       : angle       6.38192 (  255)
  link_BETA1-6         : bond        0.00266 (    1)
  link_BETA1-6         : angle       1.98815 (    3)
  SS BOND              : bond        0.00922 (    5)
  SS BOND              : angle       3.68679 (   10)
  covalent geometry    : bond        0.00386 ( 3284)
  covalent geometry    : angle       0.67597 ( 4465)

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

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

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  788 Ramachandran restraints generated.
    394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7602 (ptm-80)
REVERT: A  406 GLU cc_start: 0.8275 (mp0) cc_final: 0.7978 (mm-30)
REVERT: A  442 ASP cc_start: 0.7842 (m-30) cc_final: 0.7205 (m-30)
REVERT: H  112 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7178 (mp10)
REVERT: L  105 GLU cc_start: 0.4970 (tp30) cc_final: 0.4647 (tp30)
  outliers start: 14
  outliers final: 11
  residues processed: 70
  average time/residue: 0.3068
  time to fit residues: 26.4167
Evaluate side-chains
  75 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain H residue   85 SER
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain L residue    1 ASP
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   21 PHE
Chi-restraints excluded: chain L residue   40 THR
Chi-restraints excluded: chain L residue   41 ASN
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   78 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0020
   chunk 15 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0020
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  41 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.132562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.110438 restraints weight = 5834.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 3.19
r_work: 0.3459 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.3146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.104   3293  Z= 0.129
  Angle     :  0.708  14.261   4487  Z= 0.354
  Chirality :  0.045   0.221    493
  Planarity :  0.004   0.055    565
  Dihedral  :  5.597  38.037    521
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 18.50 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.78 (0.43), residues: 394
  helix: -2.64 (0.71), residues: 40
  sheet:  0.27 (0.42), residues: 160
  loop : -0.63 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.001   0.001   HIS L  34 
 PHE   0.013   0.001   PHE A 497 
 TYR   0.012   0.001   TYR A 369 
 ARG   0.004   0.000   ARG H  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00284 (    1)
  link_NAG-ASN         : angle       2.22704 (    3)
  link_BETA1-4         : bond        0.00803 (    2)
  link_BETA1-4         : angle       1.72205 (    6)
  hydrogen bonds       : bond        0.03127 (  100)
  hydrogen bonds       : angle       6.33911 (  255)
  link_BETA1-6         : bond        0.00137 (    1)
  link_BETA1-6         : angle       1.87356 (    3)
  SS BOND              : bond        0.00948 (    5)
  SS BOND              : angle       3.97023 (   10)
  covalent geometry    : bond        0.00320 ( 3284)
  covalent geometry    : angle       0.67733 ( 4465)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2736.24 seconds
wall clock time: 51 minutes 32.76 seconds (3092.76 seconds total)