Starting phenix.real_space_refine
on Thu Jul 24 00:46:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ey4_31377/07_2025/7ey4_31377.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ey4_31377/07_2025/7ey4_31377.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ey4_31377/07_2025/7ey4_31377.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ey4_31377/07_2025/7ey4_31377.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ey4_31377/07_2025/7ey4_31377.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ey4_31377/07_2025/7ey4_31377.cif"
  }
  resolution = 3.69
  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=   0.023
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      17      5.16       5
     C    3000      2.51       5
     N     772      2.21       5
     O     894      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 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: 4683
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "L"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 6, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 985
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 985
          Classifications: {'peptide': 129}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 126}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "R"
      Number of atoms: 1465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1465
          Classifications: {'peptide': 183}
          Link IDs: {'PTRANS': 9, 'TRANS': 173}
    Chain: "N"
      Number of atoms: 1359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 1359
          Classifications: {'peptide': 165}
          Link IDs: {'PTRANS': 8, 'TRANS': 156}
          Chain breaks: 7
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 4.31, per 1000 atoms: 0.92
  Number of scatterers: 4683
  At special positions: 0
  Unit cell: (62.13, 80.66, 110.09, 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      17     16.00
     O     894      8.00
     N     772      7.00
     C    3000      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 336 " - pdb=" SG  CYS R 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 480 " - pdb=" SG  CYS R 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 131 " - pdb=" SG  CYS N 166 " distance=2.05

  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 A   2 " - " BMA A   3 "
    NAG-ASN
      " NAG A   1 " - " ASN N 165 "
  Time building additional restraints: 1.22
  Conformation dependent library (CDL) restraints added in 557.2 milliseconds
  

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1072

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 11 sheets defined
      7.2% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.648A  pdb=" N   ASP H  31 " --> pdb=" O   ARG H  28 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 28 through 32'
    Processing helix  chain 'H' and resid 74 through 76
      No H-bonds generated for 'chain 'H' and resid 74 through 76'
    Processing helix  chain 'R' and resid 338 through 343
    Processing helix  chain 'R' and resid 349 through 353
    Processing helix  chain 'R' and resid 365 through 370
    Processing helix  chain 'R' and resid 383 through 387
      removed outlier: 3.577A  pdb=" N   LEU R 387 " --> pdb=" O   PRO R 384 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 405 through 410
      removed outlier: 3.653A  pdb=" N   ARG R 408 " --> pdb=" O   ASP R 405 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 417 through 422
    Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5
      removed outlier: 3.923A  pdb=" N   GLU L  70 " --> pdb=" O   PHE L  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 7.193A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL L  85 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.513A  pdb=" N   SER H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASP H  73 " --> pdb=" O   SER H  78 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AA5, first strand: chain 'H' and resid 45 through 47
      removed outlier: 4.277A  pdb=" N   TYR H  33 " --> pdb=" O   GLY H  99 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ASN H  35 " --> pdb=" O   ALA H  97 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ARG H  98 " --> pdb=" O   ASP H 117 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 49 through 50
      removed outlier: 3.668A  pdb=" N   TYR H  50 " --> pdb=" O   TYR H  59 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'R' and resid 356 through 358
      removed outlier: 3.687A  pdb=" N   ILE R 402 " --> pdb=" O   TYR R 508 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   GLY R 431 " --> pdb=" O   TYR R 380 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   TYR R 380 " --> pdb=" O   GLY R 431 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   VAL R 433 " --> pdb=" O   LYS R 378 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LYS R 378 " --> pdb=" O   VAL R 433 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'R' and resid 452 through 454
    Processing sheet with id=AA9, first strand: chain 'R' and resid 473 through 474
    Processing sheet with id=AB1, first strand: chain 'N' and resid 50 through 55
      removed outlier: 3.774A  pdb=" N   ASP N  53 " --> pdb=" O   ARG N 273 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ASP N 287 " --> pdb=" O   LYS N 278 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 63 through 64
  WARNING: can't find start of bonding for strands!
    previous: chain 'N' and resid 63 through 64
    current: chain 'N' and resid 116 through 121
      removed outlier: 4.174A  pdb=" N   ASN N 164 " --> pdb=" O   GLU N 132 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'N' and resid 163 through 164
    current: chain 'N' and resid 200 through 205
      removed outlier: 5.953A  pdb=" N   SER N 205 " --> pdb=" O   PRO N 225 " (cutoff:3.500A)

    103 hydrogen bonds defined for protein.
    252 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: 1.15

  Time building geometry restraints manager: 1.45 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1473
        1.35 -     1.48: 1418
        1.48 -     1.61: 1891
        1.61 -     1.74: 0
        1.74 -     1.88: 21
  Bond restraints: 4803
  Sorted by residual:
  bond pdb=" CA  SER H 107 "
       pdb=" CB  SER H 107 "
    ideal  model  delta    sigma   weight residual
    1.532  1.464  0.067 1.82e-02 3.02e+03 1.37e+01
  bond pdb=" N   CYS N 166 "
       pdb=" CA  CYS N 166 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.29e-02 6.01e+03 9.58e+00
  bond pdb=" N   PHE N 168 "
       pdb=" CA  PHE N 168 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.033 1.22e-02 6.72e+03 7.54e+00
  bond pdb=" CA  SER H 104 "
       pdb=" CB  SER H 104 "
    ideal  model  delta    sigma   weight residual
    1.524  1.491  0.033 1.22e-02 6.72e+03 7.34e+00
  bond pdb=" N   ASP H 105 "
       pdb=" CA  ASP H 105 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.036 1.34e-02 5.57e+03 7.04e+00
  ... (remaining 4798 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.63: 6374
        2.63 -     5.25: 127
        5.25 -     7.88: 15
        7.88 -    10.50: 1
       10.50 -    13.13: 2
  Bond angle restraints: 6519
  Sorted by residual:
  angle pdb=" N   VAL L  29 "
        pdb=" CA  VAL L  29 "
        pdb=" C   VAL L  29 "
      ideal   model   delta    sigma   weight residual
     111.90  107.22    4.68 8.10e-01 1.52e+00 3.34e+01
  angle pdb=" CA  CYS R 379 "
        pdb=" CB  CYS R 379 "
        pdb=" SG  CYS R 379 "
      ideal   model   delta    sigma   weight residual
     114.40  127.53  -13.13 2.30e+00 1.89e-01 3.26e+01
  angle pdb=" CA  CYS R 432 "
        pdb=" CB  CYS R 432 "
        pdb=" SG  CYS R 432 "
      ideal   model   delta    sigma   weight residual
     114.40  127.18  -12.78 2.30e+00 1.89e-01 3.09e+01
  angle pdb=" N   CYS R 379 "
        pdb=" CA  CYS R 379 "
        pdb=" C   CYS R 379 "
      ideal   model   delta    sigma   weight residual
     108.38  114.13   -5.75 1.35e+00 5.49e-01 1.82e+01
  angle pdb=" N   CYS R 432 "
        pdb=" CA  CYS R 432 "
        pdb=" C   CYS R 432 "
      ideal   model   delta    sigma   weight residual
     108.60  114.65   -6.05 1.46e+00 4.69e-01 1.71e+01
  ... (remaining 6514 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.25: 2582
       21.25 -    42.51: 184
       42.51 -    63.76: 27
       63.76 -    85.01: 13
       85.01 -   106.26: 12
  Dihedral angle restraints: 2818
    sinusoidal: 1129
      harmonic: 1689
  Sorted by residual:
  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
     180.00  132.41   47.59     0      5.00e+00 4.00e-02 9.06e+01
  dihedral pdb=" CB  CYS R 379 "
           pdb=" SG  CYS R 379 "
           pdb=" SG  CYS R 432 "
           pdb=" CB  CYS R 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -10.28  -75.72     1      1.00e+01 1.00e-02 7.23e+01
  dihedral pdb=" CA  CYS R 379 "
           pdb=" C   CYS R 379 "
           pdb=" N   TYR R 380 "
           pdb=" CA  TYR R 380 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.32  -39.68     0      5.00e+00 4.00e-02 6.30e+01
  ... (remaining 2815 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 624
       0.078 -    0.156: 70
       0.156 -    0.233: 4
       0.233 -    0.311: 2
       0.311 -    0.389: 1
  Chirality restraints: 701
  Sorted by residual:
  chirality pdb=" C1  BMA A   3 "
            pdb=" O4  NAG A   2 "
            pdb=" C2  BMA A   3 "
            pdb=" O5  BMA A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-02 2.50e+03 3.79e+02
  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   -2.37   -0.03 2.00e-02 2.50e+03 2.58e+00
  chirality pdb=" CA  CYS R 432 "
            pdb=" N   CYS R 432 "
            pdb=" C   CYS R 432 "
            pdb=" CB  CYS R 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  ... (remaining 698 not shown)

  Planarity restraints: 836
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   1 "   -0.322 2.00e-02 2.50e+03   2.72e-01 9.26e+02
        pdb=" C7  NAG A   1 "    0.083 2.00e-02 2.50e+03
        pdb=" C8  NAG A   1 "   -0.188 2.00e-02 2.50e+03
        pdb=" N2  NAG A   1 "    0.471 2.00e-02 2.50e+03
        pdb=" O7  NAG A   1 "   -0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   2 "   -0.293 2.00e-02 2.50e+03   2.52e-01 7.94e+02
        pdb=" C7  NAG A   2 "    0.063 2.00e-02 2.50e+03
        pdb=" C8  NAG A   2 "    0.007 2.00e-02 2.50e+03
        pdb=" N2  NAG A   2 "    0.430 2.00e-02 2.50e+03
        pdb=" O7  NAG A   2 "   -0.208 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L   7 "    0.042 5.00e-02 4.00e+02   6.38e-02 6.52e+00
        pdb=" N   PRO L   8 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO L   8 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO L   8 "    0.035 5.00e-02 4.00e+02
  ... (remaining 833 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 180
        2.70 -     3.25: 4472
        3.25 -     3.80: 6731
        3.80 -     4.35: 8835
        4.35 -     4.90: 15297
  Nonbonded interactions: 35515
  Sorted by model distance:
  nonbonded pdb=" OH  TYR N  37 "
            pdb=" O   LEU N  54 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" OD1 ASP N  40 "
            pdb=" OH  TYR N 204 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OH  TYR N  91 "
            pdb=" OE1 GLU N 191 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" NH2 ARG H  98 "
            pdb=" OD2 ASP H 117 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" NH2 ARG L  31 "
            pdb=" OE1 GLU R 340 "
     model   vdw
     2.241 3.120
  ... (remaining 35510 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:             6.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.410
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
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      :  0.007   0.068   4812  Z= 0.328
  Angle     :  0.941  13.127   6540  Z= 0.524
  Chirality :  0.053   0.389    701
  Planarity :  0.014   0.272    835
  Dihedral  : 16.811 106.261   1728
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 13.50 %
    Favored  : 86.15 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.60 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.36 %

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: -2.54 (0.34), residues: 563
  helix: -3.57 (0.84), residues: 20
  sheet: -0.83 (0.39), residues: 181
  loop : -2.14 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 436 
 HIS   0.001   0.001   HIS N  66 
 PHE   0.028   0.002   PHE H  56 
 TYR   0.024   0.002   TYR H 110 
 ARG   0.017   0.001   ARG N  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.02273 (    1)
  link_NAG-ASN         : angle       7.17095 (    3)
  link_BETA1-4         : bond        0.00559 (    2)
  link_BETA1-4         : angle       3.11479 (    6)
  hydrogen bonds       : bond        0.29872 (  103)
  hydrogen bonds       : angle      10.92957 (  252)
  SS BOND              : bond        0.00982 (    6)
  SS BOND              : angle       4.82403 (   12)
  covalent geometry    : bond        0.00695 ( 4803)
  covalent geometry    : angle       0.90135 ( 6519)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.523 
Fit side-chains
REVERT: H   74 ASP cc_start: 0.8334 (m-30) cc_final: 0.7991 (m-30)
REVERT: N   54 LEU cc_start: 0.7149 (mp) cc_final: 0.6142 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 126
  average time/residue: 0.2158
  time to fit residues: 32.7167
Evaluate side-chains
  98 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 28 optimal weight:    0.1980
   chunk 22 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0040
   chunk 16 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.4392

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

Flipped N/Q/H residues before XYZ refinement:
H 109 ASN
N 164 ASN
N 282 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.148078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.117313 restraints weight = 6484.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.119655 restraints weight = 4909.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.121241 restraints weight = 4069.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4812  Z= 0.157
  Angle     :  0.742   8.089   6540  Z= 0.383
  Chirality :  0.048   0.276    701
  Planarity :  0.005   0.057    835
  Dihedral  : 12.746  85.147    708
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.41 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 11.40 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    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: -2.14 (0.34), residues: 563
  helix: -3.42 (0.95), residues: 20
  sheet: -0.37 (0.39), residues: 192
  loop : -2.01 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 436 
 HIS   0.000   0.000   HIS N  66 
 PHE   0.015   0.002   PHE N  43 
 TYR   0.015   0.001   TYR R 369 
 ARG   0.006   0.001   ARG L  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00724 (    1)
  link_NAG-ASN         : angle       0.12088 (    3)
  link_BETA1-4         : bond        0.00344 (    2)
  link_BETA1-4         : angle       2.85143 (    6)
  hydrogen bonds       : bond        0.04385 (  103)
  hydrogen bonds       : angle       7.43636 (  252)
  SS BOND              : bond        0.00676 (    6)
  SS BOND              : angle       3.17039 (   12)
  covalent geometry    : bond        0.00359 ( 4803)
  covalent geometry    : angle       0.72580 ( 6519)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 110
  time to evaluate  : 0.549 
Fit side-chains
REVERT: H   74 ASP cc_start: 0.8332 (m-30) cc_final: 0.8006 (m-30)
REVERT: R  378 LYS cc_start: 0.7692 (ptpt) cc_final: 0.7484 (ptpp)
REVERT: R  414 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7222 (mm-40)
  outliers start: 5
  outliers final: 3
  residues processed: 114
  average time/residue: 0.1999
  time to fit residues: 27.9754
Evaluate side-chains
  92 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0270
   chunk 23 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 28 optimal weight:    0.1980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.4238

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

Flipped N/Q/H residues before XYZ refinement:
N  81 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.148962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.119275 restraints weight = 6506.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.121362 restraints weight = 4986.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.122768 restraints weight = 4155.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4812  Z= 0.145
  Angle     :  0.709   8.514   6540  Z= 0.361
  Chirality :  0.047   0.229    701
  Planarity :  0.005   0.088    835
  Dihedral  : 10.581  76.632    708
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.88 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.20 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.34), residues: 563
  helix: -3.26 (1.00), residues: 20
  sheet: -0.21 (0.39), residues: 186
  loop : -1.91 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP R 436 
 HIS   0.001   0.001   HIS N  49 
 PHE   0.012   0.001   PHE N  32 
 TYR   0.014   0.001   TYR R 369 
 ARG   0.005   0.001   ARG N 237 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00193 (    1)
  link_NAG-ASN         : angle       1.05049 (    3)
  link_BETA1-4         : bond        0.00989 (    2)
  link_BETA1-4         : angle       2.65422 (    6)
  hydrogen bonds       : bond        0.03772 (  103)
  hydrogen bonds       : angle       6.52670 (  252)
  SS BOND              : bond        0.00532 (    6)
  SS BOND              : angle       3.09610 (   12)
  covalent geometry    : bond        0.00339 ( 4803)
  covalent geometry    : angle       0.69233 ( 6519)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
REVERT: H   74 ASP cc_start: 0.8385 (m-30) cc_final: 0.8034 (m-30)
REVERT: R  414 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7236 (mm-40)
REVERT: N  104 TRP cc_start: 0.8845 (m-90) cc_final: 0.8629 (m-90)
  outliers start: 12
  outliers final: 9
  residues processed: 103
  average time/residue: 0.2249
  time to fit residues: 28.3519
Evaluate side-chains
  92 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain R residue  379 CYS
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 11 optimal weight:    0.0470
   chunk 21 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.8082

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

Flipped N/Q/H residues before XYZ refinement:
N  81 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.144742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.114884 restraints weight = 6603.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.116866 restraints weight = 5206.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.118304 restraints weight = 4421.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   4812  Z= 0.200
  Angle     :  0.729   7.902   6540  Z= 0.374
  Chirality :  0.047   0.249    701
  Planarity :  0.006   0.091    835
  Dihedral  :  9.153  63.990    708
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.59 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 14.60 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.34), residues: 563
  helix: -3.19 (0.93), residues: 20
  sheet: -0.13 (0.39), residues: 185
  loop : -1.98 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 436 
 HIS   0.002   0.001   HIS N  49 
 PHE   0.022   0.002   PHE H  56 
 TYR   0.013   0.002   TYR H 110 
 ARG   0.011   0.001   ARG L  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00010 (    1)
  link_NAG-ASN         : angle       1.41761 (    3)
  link_BETA1-4         : bond        0.01052 (    2)
  link_BETA1-4         : angle       2.86991 (    6)
  hydrogen bonds       : bond        0.03718 (  103)
  hydrogen bonds       : angle       6.26893 (  252)
  SS BOND              : bond        0.00646 (    6)
  SS BOND              : angle       3.15580 (   12)
  covalent geometry    : bond        0.00477 ( 4803)
  covalent geometry    : angle       0.71123 ( 6519)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.492 
Fit side-chains
REVERT: L   93 ASN cc_start: 0.7828 (OUTLIER) cc_final: 0.7620 (m-40)
REVERT: H   74 ASP cc_start: 0.8444 (m-30) cc_final: 0.8119 (m-30)
REVERT: R  378 LYS cc_start: 0.7952 (ptpt) cc_final: 0.7751 (ptpp)
  outliers start: 27
  outliers final: 17
  residues processed: 111
  average time/residue: 0.1908
  time to fit residues: 26.0748
Evaluate side-chains
  103 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   56 THR
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue   93 ASN
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue  113 ASP
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  379 CYS
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0170
   chunk 54 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.5618

-------------------------------------------------------------------------------
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 = 0.3703 r_free = 0.3703 target = 0.146119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.116202 restraints weight = 6576.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.118060 restraints weight = 5157.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.119493 restraints weight = 4378.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.3281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4812  Z= 0.158
  Angle     :  0.699   8.273   6540  Z= 0.356
  Chirality :  0.046   0.238    701
  Planarity :  0.005   0.082    835
  Dihedral  :  8.039  52.495    708
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 16.60 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.90 (0.35), residues: 563
  helix: -2.98 (0.98), residues: 20
  sheet: -0.04 (0.39), residues: 190
  loop : -1.97 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 436 
 HIS   0.001   0.000   HIS N  66 
 PHE   0.013   0.002   PHE N  43 
 TYR   0.011   0.001   TYR H 110 
 ARG   0.012   0.001   ARG L  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00091 (    1)
  link_NAG-ASN         : angle       1.95644 (    3)
  link_BETA1-4         : bond        0.01229 (    2)
  link_BETA1-4         : angle       3.07783 (    6)
  hydrogen bonds       : bond        0.03399 (  103)
  hydrogen bonds       : angle       6.12639 (  252)
  SS BOND              : bond        0.00566 (    6)
  SS BOND              : angle       3.25635 (   12)
  covalent geometry    : bond        0.00376 ( 4803)
  covalent geometry    : angle       0.67850 ( 6519)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.522 
Fit side-chains
REVERT: L   93 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7634 (m-40)
REVERT: H   74 ASP cc_start: 0.8468 (m-30) cc_final: 0.8166 (m-30)
  outliers start: 22
  outliers final: 16
  residues processed: 113
  average time/residue: 0.1901
  time to fit residues: 26.5480
Evaluate side-chains
  105 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue   93 ASN
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  379 CYS
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 44 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0370
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.5058

-------------------------------------------------------------------------------
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 = 0.3667 r_free = 0.3667 target = 0.143504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.112959 restraints weight = 6499.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.115021 restraints weight = 4964.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.116655 restraints weight = 4152.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.3555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4812  Z= 0.150
  Angle     :  0.700   8.092   6540  Z= 0.356
  Chirality :  0.046   0.212    701
  Planarity :  0.005   0.091    835
  Dihedral  :  7.113  41.124    708
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 18.40 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.84 (0.35), residues: 563
  helix: -2.74 (1.03), residues: 20
  sheet:  0.14 (0.38), residues: 201
  loop : -2.10 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 436 
 HIS   0.001   0.000   HIS N  49 
 PHE   0.027   0.002   PHE N 168 
 TYR   0.010   0.001   TYR H 110 
 ARG   0.011   0.001   ARG L  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00018 (    1)
  link_NAG-ASN         : angle       2.13271 (    3)
  link_BETA1-4         : bond        0.01223 (    2)
  link_BETA1-4         : angle       3.22787 (    6)
  hydrogen bonds       : bond        0.03255 (  103)
  hydrogen bonds       : angle       5.83591 (  252)
  SS BOND              : bond        0.00612 (    6)
  SS BOND              : angle       2.98330 (   12)
  covalent geometry    : bond        0.00361 ( 4803)
  covalent geometry    : angle       0.68111 ( 6519)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.501 
Fit side-chains
  outliers start: 20
  outliers final: 15
  residues processed: 106
  average time/residue: 0.1861
  time to fit residues: 24.3953
Evaluate side-chains
  103 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  379 CYS
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 28 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
R 360 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.142029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.111108 restraints weight = 6524.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.113211 restraints weight = 5022.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.114544 restraints weight = 4214.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.3650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4812  Z= 0.177
  Angle     :  0.719   7.636   6540  Z= 0.369
  Chirality :  0.046   0.177    701
  Planarity :  0.005   0.090    835
  Dihedral  :  6.487  38.668    708
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.41 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 19.20 %
    Favored  : 76.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.34), residues: 563
  helix: -2.76 (1.02), residues: 20
  sheet:  0.10 (0.38), residues: 202
  loop : -2.09 (0.31), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 436 
 HIS   0.001   0.001   HIS N  49 
 PHE   0.026   0.002   PHE N  43 
 TYR   0.013   0.001   TYR H 110 
 ARG   0.011   0.001   ARG L  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00040 (    1)
  link_NAG-ASN         : angle       2.77050 (    3)
  link_BETA1-4         : bond        0.01338 (    2)
  link_BETA1-4         : angle       3.44378 (    6)
  hydrogen bonds       : bond        0.03419 (  103)
  hydrogen bonds       : angle       5.88858 (  252)
  SS BOND              : bond        0.00574 (    6)
  SS BOND              : angle       3.33503 (   12)
  covalent geometry    : bond        0.00429 ( 4803)
  covalent geometry    : angle       0.69510 ( 6519)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.612 
Fit side-chains
REVERT: N   44 ARG cc_start: 0.5737 (ttm170) cc_final: 0.4871 (mpt180)
REVERT: N   52 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7652 (pp30)
  outliers start: 21
  outliers final: 17
  residues processed: 107
  average time/residue: 0.2285
  time to fit residues: 30.1799
Evaluate side-chains
  107 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue  103 THR
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  379 CYS
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0070
   chunk 4 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.6198

-------------------------------------------------------------------------------
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 = 0.3652 r_free = 0.3652 target = 0.142135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.111169 restraints weight = 6537.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.113120 restraints weight = 5069.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.114704 restraints weight = 4289.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.3805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   4812  Z= 0.176
  Angle     :  0.792  21.179   6540  Z= 0.401
  Chirality :  0.047   0.280    701
  Planarity :  0.005   0.081    835
  Dihedral  :  6.059  38.468    708
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.40 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.35), residues: 563
  helix: -2.64 (1.06), residues: 20
  sheet:  0.09 (0.38), residues: 200
  loop : -1.98 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 436 
 HIS   0.001   0.001   HIS N  49 
 PHE   0.032   0.002   PHE N  43 
 TYR   0.012   0.001   TYR H 110 
 ARG   0.012   0.001   ARG L  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00043 (    1)
  link_NAG-ASN         : angle       4.30136 (    3)
  link_BETA1-4         : bond        0.01574 (    2)
  link_BETA1-4         : angle       3.52199 (    6)
  hydrogen bonds       : bond        0.03428 (  103)
  hydrogen bonds       : angle       5.84769 (  252)
  SS BOND              : bond        0.00973 (    6)
  SS BOND              : angle       4.21722 (   12)
  covalent geometry    : bond        0.00430 ( 4803)
  covalent geometry    : angle       0.75979 ( 6519)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.585 
Fit side-chains
REVERT: N   44 ARG cc_start: 0.5808 (ttm170) cc_final: 0.4796 (mpt180)
REVERT: N   52 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7687 (pp30)
  outliers start: 19
  outliers final: 16
  residues processed: 105
  average time/residue: 0.2633
  time to fit residues: 35.0765
Evaluate side-chains
  105 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  379 CYS
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0970
   chunk 6 optimal weight:    0.7980
   chunk 11 optimal weight:    0.1980
   chunk 16 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 41 optimal weight:    0.3980
   overall best weight:    0.3978

-------------------------------------------------------------------------------
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 = 0.3673 r_free = 0.3673 target = 0.143896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.112760 restraints weight = 6542.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.114939 restraints weight = 5034.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.116526 restraints weight = 4211.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   4812  Z= 0.145
  Angle     :  0.751  17.751   6540  Z= 0.383
  Chirality :  0.046   0.294    701
  Planarity :  0.005   0.082    835
  Dihedral  :  5.698  36.642    708
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 21.60 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.35), residues: 563
  helix: -2.58 (1.08), residues: 20
  sheet:  0.27 (0.40), residues: 180
  loop : -1.86 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 436 
 HIS   0.001   0.000   HIS N  49 
 PHE   0.031   0.001   PHE N  43 
 TYR   0.011   0.001   TYR H 110 
 ARG   0.012   0.001   ARG L  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00002 (    1)
  link_NAG-ASN         : angle       3.67886 (    3)
  link_BETA1-4         : bond        0.01558 (    2)
  link_BETA1-4         : angle       3.19990 (    6)
  hydrogen bonds       : bond        0.03184 (  103)
  hydrogen bonds       : angle       5.75432 (  252)
  SS BOND              : bond        0.00728 (    6)
  SS BOND              : angle       3.80791 (   12)
  covalent geometry    : bond        0.00349 ( 4803)
  covalent geometry    : angle       0.72396 ( 6519)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 1.226 
Fit side-chains
REVERT: L   74 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8369 (p)
REVERT: H   34 MET cc_start: 0.8219 (mmm) cc_final: 0.7677 (mtm)
REVERT: H   87 ARG cc_start: 0.7703 (ptp-170) cc_final: 0.7480 (ptp-170)
REVERT: R  493 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7883 (mm-40)
REVERT: N   44 ARG cc_start: 0.6038 (ttm170) cc_final: 0.4765 (mpt180)
REVERT: N   52 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7731 (pp30)
  outliers start: 18
  outliers final: 15
  residues processed: 101
  average time/residue: 0.2951
  time to fit residues: 37.1873
Evaluate side-chains
  103 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  379 CYS
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  105 ILE
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 13 optimal weight:    0.3980
   chunk 4 optimal weight:    0.3980
   chunk 16 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0370
   chunk 51 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.4258

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.143935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.112345 restraints weight = 6482.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.114382 restraints weight = 5078.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.116037 restraints weight = 4280.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.4098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4812  Z= 0.147
  Angle     :  0.738  16.126   6540  Z= 0.379
  Chirality :  0.046   0.266    701
  Planarity :  0.006   0.095    835
  Dihedral  :  5.496  38.113    708
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 21.60 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.35), residues: 563
  helix: -3.07 (0.86), residues: 26
  sheet:  0.11 (0.39), residues: 190
  loop : -1.77 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 436 
 HIS   0.001   0.001   HIS N  49 
 PHE   0.032   0.002   PHE N  43 
 TYR   0.011   0.001   TYR H 110 
 ARG   0.012   0.001   ARG L  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00006 (    1)
  link_NAG-ASN         : angle       3.38304 (    3)
  link_BETA1-4         : bond        0.01503 (    2)
  link_BETA1-4         : angle       3.00296 (    6)
  hydrogen bonds       : bond        0.03162 (  103)
  hydrogen bonds       : angle       5.68344 (  252)
  SS BOND              : bond        0.00653 (    6)
  SS BOND              : angle       3.51281 (   12)
  covalent geometry    : bond        0.00354 ( 4803)
  covalent geometry    : angle       0.71436 ( 6519)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.531 
Fit side-chains
REVERT: L   74 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8368 (p)
REVERT: H   34 MET cc_start: 0.8252 (mmm) cc_final: 0.7684 (mtm)
REVERT: R  493 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7982 (mm-40)
REVERT: N   52 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7805 (pp30)
  outliers start: 18
  outliers final: 17
  residues processed: 98
  average time/residue: 0.2209
  time to fit residues: 26.6890
Evaluate side-chains
  105 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  379 CYS
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  105 ILE
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 20 optimal weight:    0.0050
   chunk 9 optimal weight:    0.0870
   chunk 14 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.4372

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

Flipped N/Q/H residues before XYZ refinement:
N 173 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.144113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.113997 restraints weight = 6525.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.116100 restraints weight = 5578.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.117197 restraints weight = 4545.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.4168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4812  Z= 0.146
  Angle     :  0.727  15.394   6540  Z= 0.374
  Chirality :  0.045   0.250    701
  Planarity :  0.005   0.099    835
  Dihedral  :  5.457  36.178    708
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 21.80 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.35), residues: 563
  helix: -2.97 (0.90), residues: 26
  sheet:  0.13 (0.39), residues: 190
  loop : -1.75 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 436 
 HIS   0.001   0.001   HIS N  49 
 PHE   0.031   0.001   PHE N  43 
 TYR   0.012   0.001   TYR H 110 
 ARG   0.012   0.001   ARG L  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00053 (    1)
  link_NAG-ASN         : angle       3.14114 (    3)
  link_BETA1-4         : bond        0.01430 (    2)
  link_BETA1-4         : angle       2.79864 (    6)
  hydrogen bonds       : bond        0.03112 (  103)
  hydrogen bonds       : angle       5.60731 (  252)
  SS BOND              : bond        0.00622 (    6)
  SS BOND              : angle       3.39454 (   12)
  covalent geometry    : bond        0.00351 ( 4803)
  covalent geometry    : angle       0.70538 ( 6519)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2802.17 seconds
wall clock time: 51 minutes 56.27 seconds (3116.27 seconds total)