Starting phenix.real_space_refine
on Tue Mar  3 11:22:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k45_22660/03_2026/7k45_22660.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k45_22660/03_2026/7k45_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_22660/03_2026/7k45_22660.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k45_22660/03_2026/7k45_22660.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k45_22660/03_2026/7k45_22660.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k45_22660/03_2026/7k45_22660.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.015
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1}
          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: {'GLU:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 5, 'GLN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 1}
          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: 0.81, per 1000 atoms: 0.27
  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: 0.30
  Conformation dependent library (CDL) restraints added in 92.0 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: 0.13
  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: 0.38

  Time building geometry restraints manager: 0.32 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:             8.160
  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:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.640
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.000
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.41), residues: 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
 ARG   0.004   0.000   ARG H  67 
 TYR   0.030   0.004   TYR L  92 
 PHE   0.013   0.003   PHE H  64 
 TRP   0.027   0.008   TRP H  50 
 HIS   0.002   0.001   HIS H  65 

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

*********************** 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  : 0.097 
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: 0.0909
  time to fit residues: 8.6791
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  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0770
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.3980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0980
   chunk 25 optimal weight:    0.1980
   chunk 19 optimal weight:    0.3980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0470
   chunk 37 optimal weight:    0.0770
   overall best weight:    0.0994

-------------------------------------------------------------------------------
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 = 0.3738 r_free = 0.3738 target = 0.106038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.096058 restraints weight = 7321.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.098743 restraints weight = 3961.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.100564 restraints weight = 2485.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.101793 restraints weight = 1705.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.102661 restraints weight = 1254.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3127  Z= 0.136
  Angle     :  0.666   8.586   4287  Z= 0.350
  Chirality :  0.048   0.141    470
  Planarity :  0.005   0.036    560
  Dihedral  :  4.888  22.717    502
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 13.77 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.41), residues: 411
  helix: -3.56 (0.69), residues: 27
  sheet:  0.71 (0.41), residues: 150
  loop :  0.91 (0.40), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  24 
 TYR   0.022   0.002   TYR L  92 
 PHE   0.013   0.002   PHE B 497 
 TRP   0.009   0.001   TRP B 436 
 HIS   0.002   0.002   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3118)
  covalent geometry    : angle       0.64050 ( 4267)
  SS BOND              : bond        0.00870 (    7)
  SS BOND              : angle       3.14043 (   14)
  hydrogen bonds       : bond        0.03725 (  116)
  hydrogen bonds       : angle       6.76232 (  285)
  link_BETA1-4         : bond        0.00786 (    1)
  link_BETA1-4         : angle       1.74351 (    3)
  link_NAG-ASN         : bond        0.00294 (    1)
  link_NAG-ASN         : angle       0.59223 (    3)

*********************** 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
  65 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   90 ASP cc_start: 0.7448 (m-30) cc_final: 0.7248 (m-30)
REVERT: L   37 TYR cc_start: 0.8576 (m-10) cc_final: 0.7974 (m-80)
REVERT: B  398 ASP cc_start: 0.8390 (m-30) cc_final: 0.7956 (m-30)
  outliers start: 9
  outliers final: 7
  residues processed: 64
  average time/residue: 0.0728
  time to fit residues: 5.5495
Evaluate side-chains
  54 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
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  415 THR
Chi-restraints excluded: chain B residue  442 ASP
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 26 optimal weight:    0.4980
   chunk 10 optimal weight:    0.1980
   chunk 38 optimal weight:    0.0970
   chunk 8 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.4778

-------------------------------------------------------------------------------
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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.100810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.091064 restraints weight = 7306.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.093466 restraints weight = 4244.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.095140 restraints weight = 2807.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.096290 restraints weight = 2007.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.097127 restraints weight = 1511.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   3127  Z= 0.260
  Angle     :  0.697   8.288   4287  Z= 0.375
  Chirality :  0.048   0.134    470
  Planarity :  0.005   0.036    560
  Dihedral  :  5.093  26.148    502
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 12.55 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.39), residues: 411
  helix: -3.10 (1.00), residues: 20
  sheet:  0.28 (0.40), residues: 152
  loop :  0.49 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  62 
 TYR   0.044   0.002   TYR L  92 
 PHE   0.012   0.002   PHE B 347 
 TRP   0.015   0.002   TRP L  36 
 HIS   0.005   0.004   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00583 ( 3118)
  covalent geometry    : angle       0.68174 ( 4267)
  SS BOND              : bond        0.00294 (    7)
  SS BOND              : angle       2.51433 (   14)
  hydrogen bonds       : bond        0.04181 (  116)
  hydrogen bonds       : angle       6.37443 (  285)
  link_BETA1-4         : bond        0.00596 (    1)
  link_BETA1-4         : angle       1.85047 (    3)
  link_NAG-ASN         : bond        0.00345 (    1)
  link_NAG-ASN         : angle       0.53639 (    3)

*********************** 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
  60 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 47
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
REVERT: L   74 LEU cc_start: 0.8670 (tt) cc_final: 0.8378 (tt)
REVERT: B  369 TYR cc_start: 0.7001 (t80) cc_final: 0.6716 (t80)
  outliers start: 13
  outliers final: 10
  residues processed: 56
  average time/residue: 0.0774
  time to fit residues: 5.0914
Evaluate side-chains
  53 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
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   48 LEU
Chi-restraints excluded: chain L residue   92 TYR
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  480 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0980
   chunk 9 optimal weight:    0.1980
   chunk 2 optimal weight:    0.8980
   chunk 0 optimal weight:    0.1980
   chunk 8 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0980
   chunk 1 optimal weight:    0.6980
   chunk 21 optimal weight:    0.4980
   chunk 33 optimal weight:    0.0980
   overall best weight:    0.1380

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.101011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.091610 restraints weight = 7183.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.094055 restraints weight = 4075.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.095719 restraints weight = 2644.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.096834 restraints weight = 1858.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.097677 restraints weight = 1399.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.3804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3127  Z= 0.127
  Angle     :  0.624   7.386   4287  Z= 0.334
  Chirality :  0.047   0.135    470
  Planarity :  0.004   0.037    560
  Dihedral  :  4.736  24.787    502
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 14.57 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.39), residues: 411
  helix: -2.86 (1.07), residues: 20
  sheet:  0.23 (0.39), residues: 148
  loop :  0.50 (0.38), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  55 
 TYR   0.029   0.001   TYR L  92 
 PHE   0.019   0.001   PHE B 392 
 TRP   0.010   0.001   TRP B 436 
 HIS   0.002   0.001   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3118)
  covalent geometry    : angle       0.60803 ( 4267)
  SS BOND              : bond        0.00179 (    7)
  SS BOND              : angle       2.50086 (   14)
  hydrogen bonds       : bond        0.03472 (  116)
  hydrogen bonds       : angle       6.08502 (  285)
  link_BETA1-4         : bond        0.00463 (    1)
  link_BETA1-4         : angle       1.37121 (    3)
  link_NAG-ASN         : bond        0.00376 (    1)
  link_NAG-ASN         : angle       0.21870 (    3)

*********************** 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
  57 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: H   90 ASP cc_start: 0.7694 (m-30) cc_final: 0.7371 (m-30)
REVERT: L   37 TYR cc_start: 0.8802 (m-10) cc_final: 0.8026 (m-80)
REVERT: B  369 TYR cc_start: 0.7003 (t80) cc_final: 0.6574 (t80)
  outliers start: 10
  outliers final: 8
  residues processed: 56
  average time/residue: 0.0714
  time to fit residues: 4.7545
Evaluate side-chains
  48 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   92 TYR
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  480 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 16 optimal weight:    0.1980
   chunk 12 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 20 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.098902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.089559 restraints weight = 7259.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.091779 restraints weight = 4375.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.093294 restraints weight = 2968.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.094334 restraints weight = 2173.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.095110 restraints weight = 1689.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.4210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   3127  Z= 0.283
  Angle     :  0.718   7.633   4287  Z= 0.383
  Chirality :  0.048   0.134    470
  Planarity :  0.005   0.053    560
  Dihedral  :  5.192  25.509    502
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 13.36 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.40), residues: 411
  helix: -3.08 (1.02), residues: 20
  sheet: -0.10 (0.39), residues: 156
  loop :  0.37 (0.40), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG L  55 
 TYR   0.041   0.002   TYR L  92 
 PHE   0.014   0.002   PHE B 392 
 TRP   0.016   0.002   TRP L  36 
 HIS   0.006   0.004   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00648 ( 3118)
  covalent geometry    : angle       0.71251 ( 4267)
  SS BOND              : bond        0.00698 (    7)
  SS BOND              : angle       1.55151 (   14)
  hydrogen bonds       : bond        0.04251 (  116)
  hydrogen bonds       : angle       6.16656 (  285)
  link_BETA1-4         : bond        0.00585 (    1)
  link_BETA1-4         : angle       1.65068 (    3)
  link_NAG-ASN         : bond        0.00245 (    1)
  link_NAG-ASN         : angle       0.46411 (    3)

*********************** 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
  59 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 44
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
REVERT: H   90 ASP cc_start: 0.7784 (m-30) cc_final: 0.7321 (m-30)
REVERT: L  102 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7006 (mp10)
REVERT: B  369 TYR cc_start: 0.6908 (t80) cc_final: 0.6503 (t80)
  outliers start: 15
  outliers final: 12
  residues processed: 55
  average time/residue: 0.0691
  time to fit residues: 4.4533
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  : 0.102 
-------------------------------------------------------------------------------
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 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   50 TYR
Chi-restraints excluded: chain L residue   92 TYR
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  480 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    0.4980
   chunk 5 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0050
   chunk 9 optimal weight:    0.4980
   chunk 28 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0870
   chunk 21 optimal weight:    0.3980
   overall best weight:    0.2972

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.098148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.088239 restraints weight = 7355.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.090697 restraints weight = 4225.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.092384 restraints weight = 2771.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.093537 restraints weight = 1973.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.094375 restraints weight = 1500.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.4428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3127  Z= 0.178
  Angle     :  0.628   6.630   4287  Z= 0.333
  Chirality :  0.046   0.139    470
  Planarity :  0.004   0.042    560
  Dihedral  :  4.932  27.835    502
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 14.57 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.40), residues: 411
  helix: -2.96 (1.05), residues: 20
  sheet: -0.06 (0.40), residues: 152
  loop :  0.23 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  55 
 TYR   0.032   0.002   TYR L  92 
 PHE   0.013   0.001   PHE B 392 
 TRP   0.011   0.001   TRP B 436 
 HIS   0.003   0.002   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 3118)
  covalent geometry    : angle       0.62417 ( 4267)
  SS BOND              : bond        0.00517 (    7)
  SS BOND              : angle       1.23592 (   14)
  hydrogen bonds       : bond        0.03676 (  116)
  hydrogen bonds       : angle       6.07628 (  285)
  link_BETA1-4         : bond        0.00447 (    1)
  link_BETA1-4         : angle       1.39862 (    3)
  link_NAG-ASN         : bond        0.00280 (    1)
  link_NAG-ASN         : angle       0.23463 (    3)

*********************** 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
  55 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: H   90 ASP cc_start: 0.7799 (m-30) cc_final: 0.7294 (m-30)
REVERT: B  369 TYR cc_start: 0.7103 (t80) cc_final: 0.6450 (t80)
  outliers start: 12
  outliers final: 11
  residues processed: 51
  average time/residue: 0.0739
  time to fit residues: 4.4432
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  : 0.102 
-------------------------------------------------------------------------------
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   20 THR
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   50 TYR
Chi-restraints excluded: chain L residue   92 TYR
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    0.0980
   chunk 1 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 16 optimal weight:    0.3980
   chunk 15 optimal weight:    0.0870
   chunk 23 optimal weight:    0.2980
   chunk 32 optimal weight:    0.3980
   chunk 35 optimal weight:    0.4980
   chunk 11 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 24 optimal weight:    0.4980
   overall best weight:    0.2558

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.098624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.088644 restraints weight = 7435.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.091101 restraints weight = 4250.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.092794 restraints weight = 2786.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.093997 restraints weight = 1988.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.094732 restraints weight = 1501.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.4619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3127  Z= 0.159
  Angle     :  0.608   7.553   4287  Z= 0.321
  Chirality :  0.046   0.138    470
  Planarity :  0.005   0.041    560
  Dihedral  :  4.774  29.263    502
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 14.98 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.41), residues: 411
  helix: -2.97 (1.02), residues: 20
  sheet: -0.10 (0.40), residues: 156
  loop :  0.23 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  55 
 TYR   0.030   0.001   TYR L  92 
 PHE   0.010   0.001   PHE B 392 
 TRP   0.012   0.001   TRP B 436 
 HIS   0.003   0.002   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 3118)
  covalent geometry    : angle       0.60551 ( 4267)
  SS BOND              : bond        0.00496 (    7)
  SS BOND              : angle       1.07873 (   14)
  hydrogen bonds       : bond        0.03464 (  116)
  hydrogen bonds       : angle       6.01389 (  285)
  link_BETA1-4         : bond        0.00463 (    1)
  link_BETA1-4         : angle       1.29670 (    3)
  link_NAG-ASN         : bond        0.00282 (    1)
  link_NAG-ASN         : angle       0.29073 (    3)

*********************** 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
  57 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: H   90 ASP cc_start: 0.7850 (m-30) cc_final: 0.7417 (m-30)
REVERT: L  102 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.6820 (mp10)
  outliers start: 14
  outliers final: 12
  residues processed: 55
  average time/residue: 0.0874
  time to fit residues: 5.5617
Evaluate side-chains
  54 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
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   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   20 THR
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   92 TYR
Chi-restraints excluded: chain L residue  102 GLN
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0980
   chunk 14 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0970
   chunk 19 optimal weight:    0.0970
   chunk 13 optimal weight:    0.6980
   chunk 18 optimal weight:    0.3980
   chunk 9 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.1776

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.099921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.089932 restraints weight = 7351.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.092459 restraints weight = 4201.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.094151 restraints weight = 2734.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.095260 restraints weight = 1944.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.096092 restraints weight = 1481.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.4775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3127  Z= 0.130
  Angle     :  0.590   7.474   4287  Z= 0.310
  Chirality :  0.045   0.139    470
  Planarity :  0.004   0.038    560
  Dihedral  :  4.605  29.575    502
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 14.98 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.41), residues: 411
  helix: -2.96 (1.01), residues: 20
  sheet: -0.07 (0.40), residues: 156
  loop :  0.26 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  78 
 TYR   0.027   0.001   TYR L  92 
 PHE   0.009   0.001   PHE H  27 
 TRP   0.011   0.001   TRP B 436 
 HIS   0.002   0.001   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3118)
  covalent geometry    : angle       0.58799 ( 4267)
  SS BOND              : bond        0.00420 (    7)
  SS BOND              : angle       1.01136 (   14)
  hydrogen bonds       : bond        0.03301 (  116)
  hydrogen bonds       : angle       5.94868 (  285)
  link_BETA1-4         : bond        0.00462 (    1)
  link_BETA1-4         : angle       1.21556 (    3)
  link_NAG-ASN         : bond        0.00277 (    1)
  link_NAG-ASN         : angle       0.32816 (    3)

*********************** 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: 13
    poor density    : 43
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: H   90 ASP cc_start: 0.7870 (m-30) cc_final: 0.7489 (m-30)
REVERT: L  102 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.6774 (mp10)
REVERT: B  398 ASP cc_start: 0.8508 (m-30) cc_final: 0.8137 (m-30)
  outliers start: 13
  outliers final: 10
  residues processed: 54
  average time/residue: 0.0980
  time to fit residues: 6.0647
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  : 0.113 
-------------------------------------------------------------------------------
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   21 LEU
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   92 TYR
Chi-restraints excluded: chain L residue  102 GLN
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    0.0470
   chunk 32 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0970
   chunk 20 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 21 optimal weight:    0.1980
   chunk 12 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0070
   overall best weight:    0.1894

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 487 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.100115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.090224 restraints weight = 7325.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.092726 restraints weight = 4143.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.094370 restraints weight = 2686.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.095549 restraints weight = 1919.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.096388 restraints weight = 1437.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.4843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3127  Z= 0.134
  Angle     :  0.599   7.558   4287  Z= 0.313
  Chirality :  0.045   0.140    470
  Planarity :  0.004   0.038    560
  Dihedral  :  4.537  29.721    502
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 16.19 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.42), residues: 411
  helix: -2.92 (1.03), residues: 20
  sheet: -0.02 (0.40), residues: 156
  loop :  0.36 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 408 
 TYR   0.026   0.001   TYR L  92 
 PHE   0.011   0.001   PHE B 377 
 TRP   0.011   0.001   TRP B 436 
 HIS   0.002   0.001   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3118)
  covalent geometry    : angle       0.59697 ( 4267)
  SS BOND              : bond        0.00396 (    7)
  SS BOND              : angle       0.90730 (   14)
  hydrogen bonds       : bond        0.03318 (  116)
  hydrogen bonds       : angle       5.87532 (  285)
  link_BETA1-4         : bond        0.00473 (    1)
  link_BETA1-4         : angle       1.18298 (    3)
  link_NAG-ASN         : bond        0.00257 (    1)
  link_NAG-ASN         : angle       0.37048 (    3)

*********************** 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
  54 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: H   90 ASP cc_start: 0.7870 (m-30) cc_final: 0.7489 (m-30)
REVERT: L  102 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.6751 (mp10)
  outliers start: 12
  outliers final: 10
  residues processed: 51
  average time/residue: 0.0820
  time to fit residues: 4.8855
Evaluate side-chains
  53 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
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   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   92 TYR
Chi-restraints excluded: chain L residue  102 GLN
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    0.0870
   chunk 3 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0570
   chunk 5 optimal weight:    0.3980
   chunk 8 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0980
   chunk 14 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0870
   chunk 15 optimal weight:    0.0970
   chunk 23 optimal weight:    0.0870
   overall best weight:    0.0830

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.101902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.091981 restraints weight = 7204.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.094489 restraints weight = 4116.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.096091 restraints weight = 2676.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.097298 restraints weight = 1926.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.098081 restraints weight = 1447.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.4927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3127  Z= 0.108
  Angle     :  0.583   7.325   4287  Z= 0.304
  Chirality :  0.045   0.143    470
  Planarity :  0.004   0.037    560
  Dihedral  :  4.373  29.057    502
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 16.60 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.42), residues: 411
  helix: -2.59 (1.49), residues: 12
  sheet: -0.00 (0.41), residues: 157
  loop :  0.52 (0.42), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 408 
 TYR   0.022   0.001   TYR L  92 
 PHE   0.023   0.001   PHE B 392 
 TRP   0.011   0.001   TRP B 436 
 HIS   0.001   0.000   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 3118)
  covalent geometry    : angle       0.58188 ( 4267)
  SS BOND              : bond        0.00361 (    7)
  SS BOND              : angle       0.85890 (   14)
  hydrogen bonds       : bond        0.03152 (  116)
  hydrogen bonds       : angle       5.88285 (  285)
  link_BETA1-4         : bond        0.00400 (    1)
  link_BETA1-4         : angle       1.12459 (    3)
  link_NAG-ASN         : bond        0.00279 (    1)
  link_NAG-ASN         : angle       0.38254 (    3)

********************** 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
  53 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: H   90 ASP cc_start: 0.7727 (m-30) cc_final: 0.7406 (m-30)
REVERT: L  102 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.6607 (mp10)
REVERT: B  408 ARG cc_start: 0.7051 (ttp80) cc_final: 0.6765 (tmt-80)
  outliers start: 10
  outliers final: 7
  residues processed: 52
  average time/residue: 0.0830
  time to fit residues: 5.0297
Evaluate side-chains
  48 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
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   48 LEU
Chi-restraints excluded: chain L residue   92 TYR
Chi-restraints excluded: chain L residue  102 GLN
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  415 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0170
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0770
   chunk 3 optimal weight:    0.1980
   chunk 29 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0970
   chunk 0 optimal weight:    0.9990
   chunk 2 optimal weight:    0.4980
   overall best weight:    0.1774

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** 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 = 0.3647 r_free = 0.3647 target = 0.100806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.090861 restraints weight = 7265.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.093340 restraints weight = 4146.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.094928 restraints weight = 2708.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.096106 restraints weight = 1957.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.096963 restraints weight = 1490.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.5039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3127  Z= 0.130
  Angle     :  0.582   7.190   4287  Z= 0.304
  Chirality :  0.044   0.139    470
  Planarity :  0.005   0.038    560
  Dihedral  :  4.371  28.990    502
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 17.41 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.42), residues: 411
  helix: -2.62 (1.49), residues: 12
  sheet:  0.08 (0.41), residues: 157
  loop :  0.47 (0.42), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  78 
 TYR   0.024   0.001   TYR L  92 
 PHE   0.010   0.001   PHE B 377 
 TRP   0.011   0.001   TRP B 436 
 HIS   0.001   0.001   HIS H  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3118)
  covalent geometry    : angle       0.58038 ( 4267)
  SS BOND              : bond        0.00391 (    7)
  SS BOND              : angle       0.85678 (   14)
  hydrogen bonds       : bond        0.03279 (  116)
  hydrogen bonds       : angle       5.86030 (  285)
  link_BETA1-4         : bond        0.00383 (    1)
  link_BETA1-4         : angle       1.13576 (    3)
  link_NAG-ASN         : bond        0.00224 (    1)
  link_NAG-ASN         : angle       0.44943 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 848.98 seconds
wall clock time: 15 minutes 17.56 seconds (917.56 seconds total)