Starting phenix.real_space_refine
on Wed Jul 23 10:44:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k45_22660/07_2025/7k45_22660.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k45_22660/07_2025/7k45_22660.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k45_22660/07_2025/7k45_22660.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k45_22660/07_2025/7k45_22660.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k45_22660/07_2025/7k45_22660.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k45_22660/07_2025/7k45_22660.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.015
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      16      5.16       5
     C    1960      2.51       5
     N     529      2.21       5
     O     533      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 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: 3038
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 849
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 849
          Classifications: {'peptide': 122}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
          Unresolved non-hydrogen bonds: 81
          Unresolved non-hydrogen angles: 98
          Unresolved non-hydrogen dihedrals: 64
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 30
    Chain: "L"
      Number of atoms: 730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 730
          Classifications: {'peptide': 103}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 96}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "B"
      Number of atoms: 1431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1431
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 135
          Unresolved non-hydrogen dihedrals: 84
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 55
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.59, per 1000 atoms: 1.51
  Number of scatterers: 3038
  At special positions: 0
  Unit cell: (70.35, 55.65, 100.8, 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      16     16.00
     O     533      8.00
     N     529      7.00
     C    1960      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H 101 " - pdb=" SG  CYS H 106 " distance=2.05
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.10
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " 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 A   1 " - " NAG A   2 "
    NAG-ASN
      " NAG A   1 " - " ASN B 343 "
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 396.5 milliseconds
  

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  764

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 10 sheets defined
      15.3% alpha, 33.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 31
    Processing helix  chain 'H' and resid 64 through 66
      No H-bonds generated for 'chain 'H' and resid 64 through 66'
    Processing helix  chain 'H' and resid 74 through 76
      No H-bonds generated for 'chain 'H' and resid 74 through 76'
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'L' and resid 30 through 32
      No H-bonds generated for 'chain 'L' and resid 30 through 32'
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.745A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.815A  pdb=" N   TRP B 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 370
      removed outlier: 4.227A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.295A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing helix  chain 'B' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.052A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.418A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
    Processing sheet with id=AA4, first strand: chain 'H' and resid 101 through 102
    Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 11
      removed outlier: 6.738A  pdb=" N   LEU L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   TYR L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 11
    Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358
    Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 474

    126 hydrogen bonds defined for protein.
    285 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: 0.83

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 933
        1.33 -     1.47: 940
        1.47 -     1.60: 1225
        1.60 -     1.73: 2
        1.73 -     1.86: 18
  Bond restraints: 3118
  Sorted by residual:
  bond pdb=" CB  ILE L   2 "
       pdb=" CG1 ILE L   2 "
    ideal  model  delta    sigma   weight residual
    1.530  1.611 -0.081 2.00e-02 2.50e+03 1.65e+01
  bond pdb=" C5  NAG A   2 "
       pdb=" O5  NAG A   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.479 -0.066 2.00e-02 2.50e+03 1.09e+01
  bond pdb=" C5  NAG A   1 "
       pdb=" O5  NAG A   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.474 -0.061 2.00e-02 2.50e+03 9.37e+00
  bond pdb=" NE1 TRP H  50 "
       pdb=" CE2 TRP H  50 "
    ideal  model  delta    sigma   weight residual
    1.370  1.337  0.033 1.10e-02 8.26e+03 8.78e+00
  bond pdb=" CB  ASN B 422 "
       pdb=" CG  ASN B 422 "
    ideal  model  delta    sigma   weight residual
    1.516  1.446  0.070 2.50e-02 1.60e+03 7.94e+00
  ... (remaining 3113 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 3463
        1.63 -     3.26: 641
        3.26 -     4.89: 116
        4.89 -     6.53: 36
        6.53 -     8.16: 11
  Bond angle restraints: 4267
  Sorted by residual:
  angle pdb=" C   GLY H   8 "
        pdb=" N   PRO H   9 "
        pdb=" CA  PRO H   9 "
      ideal   model   delta    sigma   weight residual
     120.03  128.19   -8.16 9.90e-01 1.02e+00 6.79e+01
  angle pdb=" C   ILE L  59 "
        pdb=" N   PRO L  60 "
        pdb=" CA  PRO L  60 "
      ideal   model   delta    sigma   weight residual
     120.21  126.95   -6.74 9.60e-01 1.09e+00 4.93e+01
  angle pdb=" C   SER B 383 "
        pdb=" N   PRO B 384 "
        pdb=" CA  PRO B 384 "
      ideal   model   delta    sigma   weight residual
     119.56  126.42   -6.86 1.02e+00 9.61e-01 4.53e+01
  angle pdb=" C   ALA B 520 "
        pdb=" N   PRO B 521 "
        pdb=" CA  PRO B 521 "
      ideal   model   delta    sigma   weight residual
     119.56  126.33   -6.77 1.02e+00 9.61e-01 4.41e+01
  angle pdb=" C   GLN B 498 "
        pdb=" N   PRO B 499 "
        pdb=" CA  PRO B 499 "
      ideal   model   delta    sigma   weight residual
     119.87  126.70   -6.83 1.04e+00 9.25e-01 4.31e+01
  ... (remaining 4262 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.65: 1752
       16.65 -    33.30: 55
       33.30 -    49.94: 10
       49.94 -    66.59: 4
       66.59 -    83.24: 1
  Dihedral angle restraints: 1822
    sinusoidal: 618
      harmonic: 1204
  Sorted by residual:
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  121.87  -28.87     1      1.00e+01 1.00e-02 1.19e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  89 "
           pdb=" CB  CYS L  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   66.25   26.75     1      1.00e+01 1.00e-02 1.03e+01
  dihedral pdb=" C   TYR L  92 "
           pdb=" N   TYR L  92 "
           pdb=" CA  TYR L  92 "
           pdb=" CB  TYR L  92 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -115.16   -7.44     0      2.50e+00 1.60e-01 8.85e+00
  ... (remaining 1819 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 306
       0.068 -    0.136: 127
       0.136 -    0.204: 28
       0.204 -    0.272: 5
       0.272 -    0.340: 4
  Chirality restraints: 470
  Sorted by residual:
  chirality pdb=" C1  NAG A   2 "
            pdb=" O4  NAG A   1 "
            pdb=" C2  NAG A   2 "
            pdb=" O5  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.54    0.14 2.00e-02 2.50e+03 4.64e+01
  chirality pdb=" C2  NAG A   2 "
            pdb=" C1  NAG A   2 "
            pdb=" C3  NAG A   2 "
            pdb=" N2  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.83    0.34 2.00e-01 2.50e+01 2.89e+00
  chirality pdb=" C2  NAG A   1 "
            pdb=" C1  NAG A   1 "
            pdb=" C3  NAG A   1 "
            pdb=" N2  NAG A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.82    0.33 2.00e-01 2.50e+01 2.65e+00
  ... (remaining 467 not shown)

  Planarity restraints: 561
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  92 "   -0.030 2.00e-02 2.50e+03   1.51e-02 4.56e+00
        pdb=" CG  TYR L  92 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  92 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  92 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  92 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  92 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  92 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR L  92 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  50 "    0.027 2.00e-02 2.50e+03   1.34e-02 4.49e+00
        pdb=" CG  TRP H  50 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  50 "   -0.019 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  50 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  50 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  50 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  50 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  50 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  50 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  47 "   -0.023 2.00e-02 2.50e+03   1.32e-02 4.34e+00
        pdb=" CG  TRP H  47 "    0.013 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  47 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  47 "    0.018 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  47 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  47 "    0.011 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  47 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  47 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  47 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 558 not shown)

  Histogram of nonbonded interaction distances:
        2.57 -     3.03: 1766
        3.03 -     3.50: 2712
        3.50 -     3.97: 4880
        3.97 -     4.43: 5575
        4.43 -     4.90: 9162
  Nonbonded interactions: 24095
  Sorted by model distance:
  nonbonded pdb=" N   LYS B 462 "
            pdb=" O   LYS B 462 "
     model   vdw
     2.568 2.496
  nonbonded pdb=" N   GLU L  80 "
            pdb=" O   GLU L  80 "
     model   vdw
     2.592 2.496
  nonbonded pdb=" CB  GLN H   6 "
            pdb=" OE1 GLN H   6 "
     model   vdw
     2.598 2.752
  nonbonded pdb=" N   GLY B 502 "
            pdb=" O   GLY B 502 "
     model   vdw
     2.601 2.496
  nonbonded pdb=" N   SER B 373 "
            pdb=" N   PHE B 374 "
     model   vdw
     2.605 2.560
  ... (remaining 24090 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.660
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.950
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
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      :  0.015   0.092   3127  Z= 0.793
  Angle     :  1.425   8.157   4287  Z= 0.964
  Chirality :  0.079   0.340    470
  Planarity :  0.006   0.039    560
  Dihedral  :  9.350  83.236   1037
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 0.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.41), residues: 411
  helix: -4.00 (0.49), residues: 33
  sheet:  1.14 (0.43), residues: 150
  loop :  1.17 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.008   TRP H  50 
 HIS   0.002   0.001   HIS H  65 
 PHE   0.013   0.003   PHE H  64 
 TYR   0.030   0.004   TYR L  92 
 ARG   0.004   0.000   ARG H  67 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.06242 (    1)
  link_NAG-ASN         : angle       1.79789 (    3)
  link_BETA1-4         : bond        0.06505 (    1)
  link_BETA1-4         : angle       4.01691 (    3)
  hydrogen bonds       : bond        0.15086 (  116)
  hydrogen bonds       : angle       9.13726 (  285)
  SS BOND              : bond        0.02869 (    7)
  SS BOND              : angle       2.53855 (   14)
  covalent geometry    : bond        0.01446 ( 3118)
  covalent geometry    : angle       1.41601 ( 4267)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.7080 (t80) cc_final: 0.6653 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.2157
  time to fit residues: 20.7585
Evaluate side-chains
  44 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.1980
   chunk 31 optimal weight:    0.3980
   chunk 17 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 20 optimal weight:    0.0870
   chunk 16 optimal weight:    0.3980
   chunk 32 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 19 optimal weight:    0.2980
   chunk 23 optimal weight:    0.8980
   chunk 37 optimal weight:    0.1980
   overall best weight:    0.2358

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
B 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.103617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.094455 restraints weight = 7255.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.096881 restraints weight = 4101.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.098512 restraints weight = 2637.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   3127  Z= 0.171
  Angle     :  0.680   8.553   4287  Z= 0.360
  Chirality :  0.048   0.142    470
  Planarity :  0.005   0.037    560
  Dihedral  :  4.994  21.942    502
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 12.96 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.40), residues: 411
  helix: -3.65 (0.68), residues: 27
  sheet:  0.63 (0.40), residues: 154
  loop :  0.78 (0.40), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 436 
 HIS   0.004   0.003   HIS H  65 
 PHE   0.011   0.002   PHE B 497 
 TYR   0.029   0.002   TYR L  92 
 ARG   0.005   0.001   ARG L  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00121 (    1)
  link_NAG-ASN         : angle       0.71286 (    3)
  link_BETA1-4         : bond        0.00177 (    1)
  link_BETA1-4         : angle       1.70759 (    3)
  hydrogen bonds       : bond        0.03904 (  116)
  hydrogen bonds       : angle       6.68679 (  285)
  SS BOND              : bond        0.00426 (    7)
  SS BOND              : angle       3.11989 (   14)
  covalent geometry    : bond        0.00391 ( 3118)
  covalent geometry    : angle       0.65545 ( 4267)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   37 TYR cc_start: 0.8673 (m-10) cc_final: 0.7902 (m-80)
REVERT: L   72 PHE cc_start: 0.6847 (m-80) cc_final: 0.6613 (m-80)
REVERT: B  369 TYR cc_start: 0.6665 (t80) cc_final: 0.6244 (t80)
  outliers start: 10
  outliers final: 7
  residues processed: 63
  average time/residue: 0.1870
  time to fit residues: 13.9014
Evaluate side-chains
  51 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  480 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    0.0870
   chunk 8 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 36 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
H   6 GLN
H  35 GLN
B 474 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.099577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.090349 restraints weight = 7293.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.092597 restraints weight = 4363.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.094131 restraints weight = 2933.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.3598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   3127  Z= 0.288
  Angle     :  0.738   8.752   4287  Z= 0.396
  Chirality :  0.049   0.134    470
  Planarity :  0.005   0.035    560
  Dihedral  :  5.455  25.810    502
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 12.15 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.39), residues: 411
  helix: -3.24 (0.96), residues: 20
  sheet:  0.23 (0.40), residues: 152
  loop :  0.42 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP L  36 
 HIS   0.006   0.004   HIS H  65 
 PHE   0.012   0.002   PHE B 342 
 TYR   0.035   0.002   TYR L  92 
 ARG   0.004   0.001   ARG L  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00303 (    1)
  link_NAG-ASN         : angle       0.53716 (    3)
  link_BETA1-4         : bond        0.00510 (    1)
  link_BETA1-4         : angle       1.91441 (    3)
  hydrogen bonds       : bond        0.04509 (  116)
  hydrogen bonds       : angle       6.48281 (  285)
  SS BOND              : bond        0.00309 (    7)
  SS BOND              : angle       3.65885 (   14)
  covalent geometry    : bond        0.00648 ( 3118)
  covalent geometry    : angle       0.70697 ( 4267)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: H   90 ASP cc_start: 0.7645 (m-30) cc_final: 0.7267 (m-30)
REVERT: L   72 PHE cc_start: 0.7247 (m-80) cc_final: 0.6798 (m-10)
REVERT: B  461 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8341 (mm)
  outliers start: 14
  outliers final: 10
  residues processed: 55
  average time/residue: 0.1768
  time to fit residues: 11.5630
Evaluate side-chains
  50 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  480 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    0.0270
   chunk 28 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 23 optimal weight:    0.1980
   chunk 38 optimal weight:    0.1980
   chunk 37 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.3238

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.100538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.091412 restraints weight = 7312.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.093672 restraints weight = 4303.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.095215 restraints weight = 2871.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.3930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3127  Z= 0.184
  Angle     :  0.624   6.282   4287  Z= 0.333
  Chirality :  0.047   0.137    470
  Planarity :  0.005   0.037    560
  Dihedral  :  5.145  25.983    502
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 14.98 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.40), residues: 411
  helix: -2.94 (1.07), residues: 20
  sheet:  0.04 (0.39), residues: 152
  loop :  0.43 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 436 
 HIS   0.004   0.003   HIS H  65 
 PHE   0.009   0.002   PHE H  27 
 TYR   0.025   0.002   TYR L  92 
 ARG   0.009   0.001   ARG L  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00311 (    1)
  link_NAG-ASN         : angle       0.26320 (    3)
  link_BETA1-4         : bond        0.00897 (    1)
  link_BETA1-4         : angle       1.50107 (    3)
  hydrogen bonds       : bond        0.03941 (  116)
  hydrogen bonds       : angle       6.19687 (  285)
  SS BOND              : bond        0.00276 (    7)
  SS BOND              : angle       1.69996 (   14)
  covalent geometry    : bond        0.00416 ( 3118)
  covalent geometry    : angle       0.61621 ( 4267)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: H   90 ASP cc_start: 0.7556 (m-30) cc_final: 0.7162 (m-30)
REVERT: B  525 CYS cc_start: 0.5444 (m) cc_final: 0.5208 (m)
  outliers start: 12
  outliers final: 11
  residues processed: 52
  average time/residue: 0.1523
  time to fit residues: 9.6264
Evaluate side-chains
  51 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  480 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    0.0030
   chunk 30 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0770
   overall best weight:    0.4348

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.096518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.086715 restraints weight = 7312.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.089145 restraints weight = 4140.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.090819 restraints weight = 2698.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.4298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   3127  Z= 0.232
  Angle     :  0.645   6.089   4287  Z= 0.344
  Chirality :  0.047   0.157    470
  Planarity :  0.005   0.044    560
  Dihedral  :  5.223  28.914    502
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 14.17 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.41), residues: 411
  helix: -2.97 (1.08), residues: 20
  sheet: -0.11 (0.39), residues: 155
  loop :  0.34 (0.41), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 436 
 HIS   0.005   0.003   HIS H  65 
 PHE   0.016   0.002   PHE B 392 
 TYR   0.028   0.002   TYR L  92 
 ARG   0.006   0.001   ARG L  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00268 (    1)
  link_NAG-ASN         : angle       0.29795 (    3)
  link_BETA1-4         : bond        0.00502 (    1)
  link_BETA1-4         : angle       1.54467 (    3)
  hydrogen bonds       : bond        0.03988 (  116)
  hydrogen bonds       : angle       6.21503 (  285)
  SS BOND              : bond        0.00211 (    7)
  SS BOND              : angle       1.45031 (   14)
  covalent geometry    : bond        0.00531 ( 3118)
  covalent geometry    : angle       0.63996 ( 4267)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 40
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   90 ASP cc_start: 0.7911 (m-30) cc_final: 0.7362 (m-30)
REVERT: L  102 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7229 (mp10)
  outliers start: 14
  outliers final: 11
  residues processed: 51
  average time/residue: 0.1587
  time to fit residues: 9.9147
Evaluate side-chains
  50 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 38
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue  102 GLN
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  480 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 4 optimal weight:    0.0050
   chunk 5 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0870
   chunk 35 optimal weight:    0.0770
   chunk 40 optimal weight:    0.0980
   chunk 28 optimal weight:    0.2980
   chunk 22 optimal weight:    0.0970
   chunk 32 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 7 optimal weight:    0.1980
   overall best weight:    0.0728

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
B 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.100577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.090255 restraints weight = 7437.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.092910 restraints weight = 4092.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.094639 restraints weight = 2607.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.4397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3127  Z= 0.100
  Angle     :  0.555   5.752   4287  Z= 0.291
  Chirality :  0.045   0.147    470
  Planarity :  0.004   0.038    560
  Dihedral  :  4.628  28.733    502
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 15.79 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.41), residues: 411
  helix: -2.78 (1.09), residues: 20
  sheet: -0.12 (0.39), residues: 155
  loop :  0.39 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 436 
 HIS   0.001   0.001   HIS H  65 
 PHE   0.012   0.001   PHE B 392 
 TYR   0.015   0.001   TYR L  92 
 ARG   0.005   0.001   ARG L  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00324 (    1)
  link_NAG-ASN         : angle       0.22815 (    3)
  link_BETA1-4         : bond        0.00424 (    1)
  link_BETA1-4         : angle       1.20113 (    3)
  hydrogen bonds       : bond        0.03204 (  116)
  hydrogen bonds       : angle       5.99911 (  285)
  SS BOND              : bond        0.00245 (    7)
  SS BOND              : angle       1.18224 (   14)
  covalent geometry    : bond        0.00224 ( 3118)
  covalent geometry    : angle       0.55083 ( 4267)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: H   90 ASP cc_start: 0.7822 (m-30) cc_final: 0.7452 (m-30)
REVERT: L   37 TYR cc_start: 0.8658 (m-10) cc_final: 0.8059 (m-80)
REVERT: L  102 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.6829 (mp10)
  outliers start: 11
  outliers final: 9
  residues processed: 52
  average time/residue: 0.1749
  time to fit residues: 10.9515
Evaluate side-chains
  49 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue  102 GLN
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  471 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 40 optimal weight:    0.4980
   chunk 5 optimal weight:    0.8980
   chunk 17 optimal weight:    0.4980
   chunk 3 optimal weight:    0.1980
   chunk 27 optimal weight:    0.0980
   chunk 22 optimal weight:    0.0970
   chunk 39 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0770
   chunk 19 optimal weight:    0.0050
   overall best weight:    0.0950

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.101346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.090818 restraints weight = 7148.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.093547 restraints weight = 3945.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.095388 restraints weight = 2516.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.4574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3127  Z= 0.102
  Angle     :  0.558   7.774   4287  Z= 0.287
  Chirality :  0.045   0.142    470
  Planarity :  0.004   0.038    560
  Dihedral  :  4.415  27.981    502
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 15.38 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.41), residues: 411
  helix: -2.74 (1.10), residues: 20
  sheet:  0.02 (0.40), residues: 154
  loop :  0.43 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 436 
 HIS   0.001   0.001   HIS H  65 
 PHE   0.009   0.001   PHE H  27 
 TYR   0.017   0.001   TYR H 100 
 ARG   0.006   0.001   ARG L  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00293 (    1)
  link_NAG-ASN         : angle       0.34754 (    3)
  link_BETA1-4         : bond        0.00431 (    1)
  link_BETA1-4         : angle       1.17694 (    3)
  hydrogen bonds       : bond        0.03087 (  116)
  hydrogen bonds       : angle       5.87939 (  285)
  SS BOND              : bond        0.00228 (    7)
  SS BOND              : angle       1.00557 (   14)
  covalent geometry    : bond        0.00227 ( 3118)
  covalent geometry    : angle       0.55538 ( 4267)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: H   90 ASP cc_start: 0.7765 (m-30) cc_final: 0.7399 (m-30)
REVERT: L   37 TYR cc_start: 0.8615 (m-10) cc_final: 0.8021 (m-80)
REVERT: L  102 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.6775 (mp10)
  outliers start: 12
  outliers final: 8
  residues processed: 51
  average time/residue: 0.1834
  time to fit residues: 11.1347
Evaluate side-chains
  49 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue  102 GLN
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  471 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    0.0570
   chunk 6 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 3 optimal weight:    0.1980
   chunk 39 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 29 optimal weight:    0.1980
   chunk 31 optimal weight:    0.5980
   chunk 8 optimal weight:    0.3980
   overall best weight:    0.2898

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.098968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.089319 restraints weight = 7146.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.091693 restraints weight = 4155.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.093294 restraints weight = 2748.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.4675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3127  Z= 0.162
  Angle     :  0.577   7.461   4287  Z= 0.303
  Chirality :  0.045   0.134    470
  Planarity :  0.004   0.035    560
  Dihedral  :  4.597  29.163    502
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 13.77 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.41), residues: 411
  helix: -2.83 (1.07), residues: 20
  sheet:  0.07 (0.40), residues: 156
  loop :  0.39 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 436 
 HIS   0.002   0.001   HIS H  65 
 PHE   0.009   0.001   PHE H  27 
 TYR   0.022   0.001   TYR L  92 
 ARG   0.003   0.000   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00244 (    1)
  link_NAG-ASN         : angle       0.47328 (    3)
  link_BETA1-4         : bond        0.00340 (    1)
  link_BETA1-4         : angle       1.28734 (    3)
  hydrogen bonds       : bond        0.03390 (  116)
  hydrogen bonds       : angle       5.89659 (  285)
  SS BOND              : bond        0.00238 (    7)
  SS BOND              : angle       0.97185 (   14)
  covalent geometry    : bond        0.00371 ( 3118)
  covalent geometry    : angle       0.57492 ( 4267)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: H   90 ASP cc_start: 0.7825 (m-30) cc_final: 0.7473 (m-30)
REVERT: L  102 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7024 (mp10)
  outliers start: 14
  outliers final: 9
  residues processed: 52
  average time/residue: 0.1931
  time to fit residues: 11.9926
Evaluate side-chains
  49 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue  102 GLN
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  471 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    0.0980
   chunk 30 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 18 optimal weight:    0.3980
   chunk 4 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0670
   chunk 16 optimal weight:    0.1980
   overall best weight:    0.2518

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.098997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.088889 restraints weight = 7274.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.091425 restraints weight = 4134.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.093154 restraints weight = 2680.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.4844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3127  Z= 0.150
  Angle     :  0.573   7.593   4287  Z= 0.301
  Chirality :  0.045   0.135    470
  Planarity :  0.004   0.036    560
  Dihedral  :  4.645  30.487    502
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 14.57 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.42), residues: 411
  helix: -2.87 (1.06), residues: 20
  sheet:  0.07 (0.41), residues: 156
  loop :  0.43 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 436 
 HIS   0.002   0.002   HIS H  65 
 PHE   0.009   0.001   PHE H  27 
 TYR   0.021   0.001   TYR L  92 
 ARG   0.003   0.000   ARG L  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00246 (    1)
  link_NAG-ASN         : angle       0.48900 (    3)
  link_BETA1-4         : bond        0.00411 (    1)
  link_BETA1-4         : angle       1.18182 (    3)
  hydrogen bonds       : bond        0.03291 (  116)
  hydrogen bonds       : angle       5.92448 (  285)
  SS BOND              : bond        0.00225 (    7)
  SS BOND              : angle       0.93569 (   14)
  covalent geometry    : bond        0.00345 ( 3118)
  covalent geometry    : angle       0.57095 ( 4267)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
REVERT: H   90 ASP cc_start: 0.7871 (m-30) cc_final: 0.7449 (m-30)
REVERT: L  102 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.6857 (mp10)
  outliers start: 13
  outliers final: 9
  residues processed: 51
  average time/residue: 0.1622
  time to fit residues: 10.0449
Evaluate side-chains
  48 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 38
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue  102 GLN
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  461 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0970
   chunk 5 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 474 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 = 0.3546 r_free = 0.3546 target = 0.095422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.085836 restraints weight = 7235.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.088147 restraints weight = 4274.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.089637 restraints weight = 2858.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.5023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068   3127  Z= 0.291
  Angle     :  0.683   7.685   4287  Z= 0.364
  Chirality :  0.047   0.142    470
  Planarity :  0.005   0.041    560
  Dihedral  :  5.344  34.446    502
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 14.57 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.42), residues: 411
  helix: -3.04 (1.06), residues: 20
  sheet: -0.00 (0.41), residues: 151
  loop :  0.32 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP L  36 
 HIS   0.005   0.003   HIS H  65 
 PHE   0.010   0.002   PHE B 377 
 TYR   0.032   0.002   TYR L  92 
 ARG   0.009   0.001   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00146 (    1)
  link_NAG-ASN         : angle       0.63082 (    3)
  link_BETA1-4         : bond        0.00222 (    1)
  link_BETA1-4         : angle       1.43792 (    3)
  hydrogen bonds       : bond        0.04053 (  116)
  hydrogen bonds       : angle       6.34075 (  285)
  SS BOND              : bond        0.00260 (    7)
  SS BOND              : angle       1.06422 (   14)
  covalent geometry    : bond        0.00665 ( 3118)
  covalent geometry    : angle       0.68082 ( 4267)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 36
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
REVERT: H   90 ASP cc_start: 0.7980 (m-30) cc_final: 0.7526 (m-30)
REVERT: L  102 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7145 (mp10)
  outliers start: 15
  outliers final: 10
  residues processed: 48
  average time/residue: 0.1696
  time to fit residues: 9.8799
Evaluate side-chains
  47 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 36
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue  102 GLN
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  461 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.2980
   chunk 31 optimal weight:    0.4980
   chunk 20 optimal weight:    0.0970
   chunk 25 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 34 optimal weight:    0.1980
   chunk 8 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.3378

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 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 = 0.3577 r_free = 0.3577 target = 0.097125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.087544 restraints weight = 7292.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.089870 restraints weight = 4270.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.091393 restraints weight = 2836.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.5087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3127  Z= 0.184
  Angle     :  0.604   7.445   4287  Z= 0.320
  Chirality :  0.046   0.133    470
  Planarity :  0.005   0.038    560
  Dihedral  :  5.094  34.816    502
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 16.60 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.42), residues: 411
  helix: -2.92 (1.08), residues: 20
  sheet:  0.01 (0.42), residues: 151
  loop :  0.26 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 436 
 HIS   0.003   0.002   HIS H  65 
 PHE   0.009   0.001   PHE H  27 
 TYR   0.024   0.002   TYR L  92 
 ARG   0.003   0.001   ARG L  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00275 (    1)
  link_NAG-ASN         : angle       0.69774 (    3)
  link_BETA1-4         : bond        0.00397 (    1)
  link_BETA1-4         : angle       1.18047 (    3)
  hydrogen bonds       : bond        0.03558 (  116)
  hydrogen bonds       : angle       6.20577 (  285)
  SS BOND              : bond        0.00229 (    7)
  SS BOND              : angle       0.95887 (   14)
  covalent geometry    : bond        0.00420 ( 3118)
  covalent geometry    : angle       0.60219 ( 4267)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1751.26 seconds
wall clock time: 30 minutes 52.19 seconds (1852.19 seconds total)