Starting phenix.real_space_refine
on Mon Nov 17 13:29:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k9k_22751/11_2025/7k9k_22751.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k9k_22751/11_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_22751/11_2025/7k9k_22751.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k9k_22751/11_2025/7k9k_22751.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k9k_22751/11_2025/7k9k_22751.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k9k_22751/11_2025/7k9k_22751.cif"
  }
  resolution = 3.14
  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=   0.002 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 0.96, per 1000 atoms: 0.30
  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: 0.33
  Conformation dependent library (CDL) restraints added in 107.9 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: 0.13
  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: 0.45

  Time building geometry restraints manager: 0.35 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:             1.740
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.930
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.100
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (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
 ARG   0.031   0.003   ARG H  98 
 TYR   0.028   0.003   TYR H  80 
 PHE   0.026   0.002   PHE A 497 
 TRP   0.025   0.003   TRP A 436 
 HIS   0.005   0.003   HIS L  34 

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

*********************** 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  : 0.140 
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: 0.0630
  time to fit residues: 6.1689
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  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   chunk 22 optimal weight:    0.0270
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.2044

-------------------------------------------------------------------------------
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 = 0.3860 r_free = 0.3860 target = 0.130870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.109896 restraints weight = 5834.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 3.13
r_work: 0.3452 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3293  Z= 0.153
  Angle     :  0.725  10.253   4487  Z= 0.362
  Chirality :  0.047   0.177    493
  Planarity :  0.005   0.050    565
  Dihedral  :  9.431  55.584    521
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  9.25 %
    Favored  : 88.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.41), residues: 394
  helix: -1.32 (1.12), residues: 28
  sheet: -0.12 (0.41), residues: 140
  loop : -0.79 (0.41), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 355 
 TYR   0.016   0.002   TYR A 421 
 PHE   0.013   0.002   PHE A 377 
 TRP   0.011   0.002   TRP A 436 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3284)
  covalent geometry    : angle       0.71256 ( 4465)
  SS BOND              : bond        0.00316 (    5)
  SS BOND              : angle       1.07683 (   10)
  hydrogen bonds       : bond        0.04522 (  100)
  hydrogen bonds       : angle       7.50327 (  255)
  link_BETA1-4         : bond        0.01306 (    2)
  link_BETA1-4         : angle       3.03502 (    6)
  link_BETA1-6         : bond        0.00300 (    1)
  link_BETA1-6         : angle       1.95732 (    3)
  link_NAG-ASN         : bond        0.00390 (    1)
  link_NAG-ASN         : angle       2.14426 (    3)

*********************** 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
  81 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A  406 GLU cc_start: 0.7966 (mp0) cc_final: 0.7342 (mp0)
REVERT: A  442 ASP cc_start: 0.7907 (m-30) cc_final: 0.7621 (m-30)
REVERT: L   86 TYR cc_start: 0.6888 (m-80) cc_final: 0.6632 (m-80)
REVERT: L  105 GLU cc_start: 0.4897 (tp30) cc_final: 0.4658 (tp30)
  outliers start: 7
  outliers final: 3
  residues processed: 76
  average time/residue: 0.0629
  time to fit residues: 5.8307
Evaluate side-chains
  69 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
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 24 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 21 optimal weight:    0.0670
   chunk 32 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 4 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0570
   chunk 7 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    1.8242

-------------------------------------------------------------------------------
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 = 0.3851 r_free = 0.3851 target = 0.130426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.108219 restraints weight = 5863.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 3.20
r_work: 0.3434 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.1981

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= 0.167
  Angle     :  0.682  11.189   4487  Z= 0.339
  Chirality :  0.046   0.177    493
  Planarity :  0.005   0.050    565
  Dihedral  :  7.426  55.216    521
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 10.69 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.41), residues: 394
  helix: -1.79 (0.94), residues: 34
  sheet:  0.21 (0.41), residues: 143
  loop : -0.74 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  65 
 TYR   0.011   0.001   TYR H 102 
 PHE   0.021   0.002   PHE A 497 
 TRP   0.013   0.001   TRP A 436 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 3284)
  covalent geometry    : angle       0.67011 ( 4465)
  SS BOND              : bond        0.00286 (    5)
  SS BOND              : angle       1.24325 (   10)
  hydrogen bonds       : bond        0.04048 (  100)
  hydrogen bonds       : angle       6.91901 (  255)
  link_BETA1-4         : bond        0.00914 (    2)
  link_BETA1-4         : angle       2.68059 (    6)
  link_BETA1-6         : bond        0.00405 (    1)
  link_BETA1-6         : angle       2.00384 (    3)
  link_NAG-ASN         : bond        0.00504 (    1)
  link_NAG-ASN         : angle       2.06601 (    3)

*********************** 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
  86 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8031 (ptm160) cc_final: 0.7491 (ptm-80)
REVERT: A  406 GLU cc_start: 0.8116 (mp0) cc_final: 0.7468 (mp0)
REVERT: A  442 ASP cc_start: 0.7966 (m-30) cc_final: 0.7527 (m-30)
REVERT: H  112 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7071 (mp10)
REVERT: L   86 TYR cc_start: 0.7072 (m-80) cc_final: 0.6799 (m-80)
REVERT: L  105 GLU cc_start: 0.5190 (tp30) cc_final: 0.4868 (tp30)
  outliers start: 13
  outliers final: 8
  residues processed: 77
  average time/residue: 0.0743
  time to fit residues: 6.9677
Evaluate side-chains
  76 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
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  424 LYS
Chi-restraints excluded: chain H residue    4 LEU
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 7 optimal weight:    8.9990
   chunk 33 optimal weight:    0.6980
   chunk 17 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    2.5388

-------------------------------------------------------------------------------
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 = 0.3820 r_free = 0.3820 target = 0.128289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.106324 restraints weight = 5894.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 3.23
r_work: 0.3393 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   3293  Z= 0.213
  Angle     :  0.702  12.375   4487  Z= 0.348
  Chirality :  0.046   0.173    493
  Planarity :  0.005   0.050    565
  Dihedral  :  7.056  52.792    521
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 11.56 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.41), residues: 394
  helix: -2.19 (0.86), residues: 34
  sheet:  0.31 (0.42), residues: 146
  loop : -0.82 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 457 
 TYR   0.019   0.002   TYR H  80 
 PHE   0.016   0.002   PHE A 497 
 TRP   0.012   0.002   TRP H  47 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 3284)
  covalent geometry    : angle       0.69124 ( 4465)
  SS BOND              : bond        0.00272 (    5)
  SS BOND              : angle       1.33467 (   10)
  hydrogen bonds       : bond        0.04030 (  100)
  hydrogen bonds       : angle       6.73425 (  255)
  link_BETA1-4         : bond        0.00774 (    2)
  link_BETA1-4         : angle       2.43408 (    6)
  link_BETA1-6         : bond        0.00532 (    1)
  link_BETA1-6         : angle       2.09402 (    3)
  link_NAG-ASN         : bond        0.00536 (    1)
  link_NAG-ASN         : angle       2.13515 (    3)

*********************** 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
  80 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7308 (ptm-80)
REVERT: A  406 GLU cc_start: 0.8173 (mp0) cc_final: 0.7347 (mp0)
REVERT: A  442 ASP cc_start: 0.7930 (m-30) cc_final: 0.7351 (m-30)
REVERT: H   90 ASP cc_start: 0.6797 (t70) cc_final: 0.6571 (t0)
REVERT: H  112 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7200 (mp10)
  outliers start: 12
  outliers final: 7
  residues processed: 71
  average time/residue: 0.0617
  time to fit residues: 5.4150
Evaluate side-chains
  73 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
** 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 = 0.3809 r_free = 0.3809 target = 0.127333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.105607 restraints weight = 5894.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 3.18
r_work: 0.3376 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   3293  Z= 0.229
  Angle     :  0.714  12.749   4487  Z= 0.355
  Chirality :  0.046   0.164    493
  Planarity :  0.005   0.054    565
  Dihedral  :  7.033  49.069    521
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 13.87 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.41), residues: 394
  helix: -2.57 (0.81), residues: 34
  sheet:  0.22 (0.42), residues: 146
  loop : -0.84 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  65 
 TYR   0.015   0.002   TYR H 102 
 PHE   0.013   0.002   PHE A 497 
 TRP   0.014   0.002   TRP H  47 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 ( 3284)
  covalent geometry    : angle       0.70373 ( 4465)
  SS BOND              : bond        0.00196 (    5)
  SS BOND              : angle       1.45369 (   10)
  hydrogen bonds       : bond        0.04016 (  100)
  hydrogen bonds       : angle       6.64537 (  255)
  link_BETA1-4         : bond        0.00805 (    2)
  link_BETA1-4         : angle       2.19587 (    6)
  link_BETA1-6         : bond        0.00694 (    1)
  link_BETA1-6         : angle       2.07745 (    3)
  link_NAG-ASN         : bond        0.00446 (    1)
  link_NAG-ASN         : angle       2.12627 (    3)

*********************** 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: 14
    poor density    : 68
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8161 (ptm160) cc_final: 0.7441 (ptm-80)
REVERT: A  406 GLU cc_start: 0.8207 (mp0) cc_final: 0.7559 (mp0)
REVERT: A  442 ASP cc_start: 0.7853 (m-30) cc_final: 0.7330 (m-30)
REVERT: H   90 ASP cc_start: 0.6838 (t70) cc_final: 0.6612 (t0)
REVERT: H  112 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7231 (mp10)
  outliers start: 14
  outliers final: 10
  residues processed: 74
  average time/residue: 0.0653
  time to fit residues: 5.9391
Evaluate side-chains
  75 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
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  424 LYS
Chi-restraints excluded: chain H residue    4 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 16 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 33 optimal weight:    0.5980
   chunk 30 optimal weight:    6.9990
   chunk 12 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
** 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 = 0.3847 r_free = 0.3847 target = 0.130285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.108549 restraints weight = 5810.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 3.21
r_work: 0.3427 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3293  Z= 0.112
  Angle     :  0.631  11.134   4487  Z= 0.315
  Chirality :  0.044   0.155    493
  Planarity :  0.005   0.055    565
  Dihedral  :  6.412  44.694    521
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 15.32 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.42), residues: 394
  helix: -2.51 (0.76), residues: 40
  sheet:  0.10 (0.41), residues: 160
  loop : -0.70 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  65 
 TYR   0.015   0.001   TYR H  80 
 PHE   0.009   0.001   PHE A 497 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3284)
  covalent geometry    : angle       0.62124 ( 4465)
  SS BOND              : bond        0.00314 (    5)
  SS BOND              : angle       1.04881 (   10)
  hydrogen bonds       : bond        0.03266 (  100)
  hydrogen bonds       : angle       6.39620 (  255)
  link_BETA1-4         : bond        0.00804 (    2)
  link_BETA1-4         : angle       2.03404 (    6)
  link_BETA1-6         : bond        0.00268 (    1)
  link_BETA1-6         : angle       1.96521 (    3)
  link_NAG-ASN         : bond        0.00277 (    1)
  link_NAG-ASN         : angle       2.23315 (    3)

*********************** 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
  84 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7497 (ptm-80)
REVERT: A  406 GLU cc_start: 0.8296 (mp0) cc_final: 0.7821 (mp0)
REVERT: A  442 ASP cc_start: 0.7846 (m-30) cc_final: 0.7346 (m-30)
REVERT: H  102 TYR cc_start: 0.8493 (m-80) cc_final: 0.8256 (m-80)
REVERT: H  112 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7188 (mp10)
  outliers start: 14
  outliers final: 9
  residues processed: 74
  average time/residue: 0.0664
  time to fit residues: 5.9659
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  : 0.086 
-------------------------------------------------------------------------------
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  106 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 19 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.128323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.107284 restraints weight = 6035.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 3.16
r_work: 0.3413 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3293  Z= 0.158
  Angle     :  0.653   9.778   4487  Z= 0.328
  Chirality :  0.045   0.160    493
  Planarity :  0.005   0.055    565
  Dihedral  :  6.246  39.161    521
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 17.34 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.90 (0.42), residues: 394
  helix: -2.55 (0.75), residues: 40
  sheet:  0.19 (0.41), residues: 160
  loop : -0.76 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  65 
 TYR   0.016   0.001   TYR A 369 
 PHE   0.008   0.001   PHE A 497 
 TRP   0.012   0.001   TRP H  47 
 HIS   0.001   0.001   HIS L  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3284)
  covalent geometry    : angle       0.64097 ( 4465)
  SS BOND              : bond        0.00239 (    5)
  SS BOND              : angle       1.82642 (   10)
  hydrogen bonds       : bond        0.03567 (  100)
  hydrogen bonds       : angle       6.34208 (  255)
  link_BETA1-4         : bond        0.00765 (    2)
  link_BETA1-4         : angle       1.90530 (    6)
  link_BETA1-6         : bond        0.00364 (    1)
  link_BETA1-6         : angle       2.03330 (    3)
  link_NAG-ASN         : bond        0.00355 (    1)
  link_NAG-ASN         : angle       2.15863 (    3)

*********************** 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
  80 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7387 (ptm-80)
REVERT: A  406 GLU cc_start: 0.8271 (mp0) cc_final: 0.7296 (mp0)
REVERT: A  442 ASP cc_start: 0.7842 (m-30) cc_final: 0.7412 (m-30)
REVERT: H  112 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7157 (mp10)
  outliers start: 15
  outliers final: 9
  residues processed: 70
  average time/residue: 0.0685
  time to fit residues: 5.8108
Evaluate side-chains
  74 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0060
   chunk 9 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0980
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 22 optimal weight:    0.4980
   overall best weight:    0.7198

-------------------------------------------------------------------------------
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 = 0.3884 r_free = 0.3884 target = 0.132569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.110450 restraints weight = 5992.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 3.24
r_work: 0.3457 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.2958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3293  Z= 0.106
  Angle     :  0.609   8.207   4487  Z= 0.307
  Chirality :  0.043   0.172    493
  Planarity :  0.004   0.056    565
  Dihedral  :  5.559  37.591    521
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 17.63 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.42), residues: 394
  helix: -2.62 (0.75), residues: 39
  sheet:  0.20 (0.41), residues: 160
  loop : -0.71 (0.45), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  65 
 TYR   0.015   0.001   TYR H  80 
 PHE   0.007   0.001   PHE A 497 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.001   0.000   HIS L  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 3284)
  covalent geometry    : angle       0.59865 ( 4465)
  SS BOND              : bond        0.00248 (    5)
  SS BOND              : angle       1.46637 (   10)
  hydrogen bonds       : bond        0.02982 (  100)
  hydrogen bonds       : angle       6.12200 (  255)
  link_BETA1-4         : bond        0.00775 (    2)
  link_BETA1-4         : angle       1.80487 (    6)
  link_BETA1-6         : bond        0.00044 (    1)
  link_BETA1-6         : angle       1.74650 (    3)
  link_NAG-ASN         : bond        0.00184 (    1)
  link_NAG-ASN         : angle       2.25355 (    3)

*********************** 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
  82 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.095 
Fit side-chains
REVERT: A  403 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7739 (ptm-80)
REVERT: A  442 ASP cc_start: 0.7895 (m-30) cc_final: 0.7396 (m-30)
REVERT: H   46 GLU cc_start: 0.8029 (pt0) cc_final: 0.7781 (pt0)
REVERT: H  112 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7080 (mp10)
  outliers start: 12
  outliers final: 6
  residues processed: 74
  average time/residue: 0.0744
  time to fit residues: 6.5085
Evaluate side-chains
  71 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain L residue   69 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    2.3388

-------------------------------------------------------------------------------
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 = 0.3835 r_free = 0.3835 target = 0.128688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.106749 restraints weight = 6059.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 3.20
r_work: 0.3406 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3293  Z= 0.202
  Angle     :  0.681   8.409   4487  Z= 0.343
  Chirality :  0.045   0.181    493
  Planarity :  0.005   0.057    565
  Dihedral  :  5.934  39.089    521
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 17.63 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.89 (0.42), residues: 394
  helix: -2.66 (0.72), residues: 40
  sheet:  0.21 (0.42), residues: 160
  loop : -0.74 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  65 
 TYR   0.013   0.001   TYR A 369 
 PHE   0.011   0.002   PHE L  71 
 TRP   0.013   0.001   TRP H  47 
 HIS   0.001   0.001   HIS L  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 3284)
  covalent geometry    : angle       0.67127 ( 4465)
  SS BOND              : bond        0.00190 (    5)
  SS BOND              : angle       1.64414 (   10)
  hydrogen bonds       : bond        0.03616 (  100)
  hydrogen bonds       : angle       6.22827 (  255)
  link_BETA1-4         : bond        0.00619 (    2)
  link_BETA1-4         : angle       1.71801 (    6)
  link_BETA1-6         : bond        0.00414 (    1)
  link_BETA1-6         : angle       2.10137 (    3)
  link_NAG-ASN         : bond        0.00363 (    1)
  link_NAG-ASN         : angle       2.07981 (    3)

*********************** 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: 13
    poor density    : 64
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7658 (ptm-80)
REVERT: A  406 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8073 (mm-30)
REVERT: A  442 ASP cc_start: 0.7940 (m-30) cc_final: 0.7487 (m-30)
REVERT: H   46 GLU cc_start: 0.8062 (pt0) cc_final: 0.7822 (pt0)
REVERT: H  112 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7119 (mp10)
  outliers start: 13
  outliers final: 9
  residues processed: 68
  average time/residue: 0.0695
  time to fit residues: 5.6640
Evaluate side-chains
  74 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
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    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 17 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 21 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0000
   chunk 8 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.3388

-------------------------------------------------------------------------------
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 = 0.3859 r_free = 0.3859 target = 0.130386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.108344 restraints weight = 5960.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 3.20
r_work: 0.3430 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3293  Z= 0.137
  Angle     :  0.641   8.313   4487  Z= 0.325
  Chirality :  0.045   0.195    493
  Planarity :  0.005   0.056    565
  Dihedral  :  5.695  39.411    521
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 18.21 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.42), residues: 394
  helix: -2.74 (0.71), residues: 40
  sheet:  0.20 (0.41), residues: 160
  loop : -0.77 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  65 
 TYR   0.012   0.001   TYR A 369 
 PHE   0.010   0.001   PHE L  71 
 TRP   0.010   0.001   TRP H  47 
 HIS   0.001   0.001   HIS L  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3284)
  covalent geometry    : angle       0.63135 ( 4465)
  SS BOND              : bond        0.00206 (    5)
  SS BOND              : angle       1.36764 (   10)
  hydrogen bonds       : bond        0.03323 (  100)
  hydrogen bonds       : angle       6.18750 (  255)
  link_BETA1-4         : bond        0.00803 (    2)
  link_BETA1-4         : angle       1.70556 (    6)
  link_BETA1-6         : bond        0.00254 (    1)
  link_BETA1-6         : angle       1.93918 (    3)
  link_NAG-ASN         : bond        0.00249 (    1)
  link_NAG-ASN         : angle       2.17354 (    3)

********************** 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
  72 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A  403 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7653 (ptm-80)
REVERT: A  406 GLU cc_start: 0.8246 (mm-30) cc_final: 0.8015 (mm-30)
REVERT: A  442 ASP cc_start: 0.7907 (m-30) cc_final: 0.7448 (m-30)
REVERT: H   46 GLU cc_start: 0.8008 (pt0) cc_final: 0.7775 (pt0)
REVERT: H  112 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7090 (mp10)
  outliers start: 10
  outliers final: 6
  residues processed: 64
  average time/residue: 0.0619
  time to fit residues: 4.9105
Evaluate side-chains
  69 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
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    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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0060
   chunk 2 optimal weight:    0.9980
   chunk 28 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 35 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   overall best weight:    0.6596

-------------------------------------------------------------------------------
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 = 0.3887 r_free = 0.3887 target = 0.132435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.110211 restraints weight = 6003.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 3.24
r_work: 0.3458 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   3293  Z= 0.107
  Angle     :  0.627   7.215   4487  Z= 0.314
  Chirality :  0.044   0.195    493
  Planarity :  0.004   0.055    565
  Dihedral  :  5.269  37.345    521
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 18.50 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.42), residues: 394
  helix: -2.84 (0.69), residues: 40
  sheet:  0.27 (0.42), residues: 160
  loop : -0.73 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  65 
 TYR   0.011   0.001   TYR A 369 
 PHE   0.009   0.001   PHE A 464 
 TRP   0.011   0.001   TRP A 436 
 HIS   0.001   0.000   HIS L  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 3284)
  covalent geometry    : angle       0.61885 ( 4465)
  SS BOND              : bond        0.00229 (    5)
  SS BOND              : angle       1.13461 (   10)
  hydrogen bonds       : bond        0.02949 (  100)
  hydrogen bonds       : angle       6.01870 (  255)
  link_BETA1-4         : bond        0.00740 (    2)
  link_BETA1-4         : angle       1.62963 (    6)
  link_BETA1-6         : bond        0.00094 (    1)
  link_BETA1-6         : angle       1.82948 (    3)
  link_NAG-ASN         : bond        0.00181 (    1)
  link_NAG-ASN         : angle       2.17381 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 902.27 seconds
wall clock time: 16 minutes 14.20 seconds (974.20 seconds total)