Starting phenix.real_space_refine
on Thu Jul  2 01:03:27 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7eng_31210/07_2026/7eng_31210.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7eng_31210/07_2026/7eng_31210.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7eng_31210/07_2026/7eng_31210.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7eng_31210/07_2026/7eng_31210.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7eng_31210/07_2026/7eng_31210.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7eng_31210/07_2026/7eng_31210.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7eng_31210/07_2026/7eng_31210.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7eng_31210/07_2026/7eng_31210.map"
  }
  resolution = 3.59
  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=   1.000
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      22      5.16       5
     C    3127      2.51       5
     N     826      2.21       5
     O     979      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4954
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "L"
      Number of atoms: 1689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1689
          Classifications: {'peptide': 219}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "H"
      Number of atoms: 1694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1694
          Classifications: {'peptide': 226}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213}
    Chain: "B"
      Number of atoms: 1543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1543
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    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 chiralities: 2
  Time building chain proxies: 1.19, per 1000 atoms: 0.24
  Number of scatterers: 4954
  At special positions: 0
  Unit cell: (93.7251, 87.2613, 108.807, 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      22     16.00
     O     979      8.00
     N     826      7.00
     C    3127      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS L 140 " - pdb=" SG  CYS L 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 103 " - pdb=" SG  CYS H 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 150 " - pdb=" SG  CYS H 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.04

  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: 0.33
  Conformation dependent library (CDL) restraints added in 141.0 milliseconds
  

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1186

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 12 sheets defined
      11.7% alpha, 31.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'L' and resid 85 through 89
      removed outlier: 3.519A  pdb=" N   ASP L  88 " --> pdb=" O   GLN L  85 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   VAL L  89 " --> pdb=" O   ALA L  86 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 85 through 89'
    Processing helix  chain 'L' and resid 127 through 132
    Processing helix  chain 'L' and resid 188 through 194
      removed outlier: 3.553A  pdb=" N   TYR L 192 " --> pdb=" O   SER L 188 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   LYS L 194 " --> pdb=" O   ALA L 190 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 4.200A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 4.084A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 166 through 168
      No H-bonds generated for 'chain 'H' and resid 166 through 168'
    Processing helix  chain 'H' and resid 197 through 199
      No H-bonds generated for 'chain 'H' and resid 197 through 199'
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 349 through 353
    Processing helix  chain 'B' and resid 365 through 371
    Processing helix  chain 'B' and resid 383 through 387
      removed outlier: 3.772A  pdb=" N   LEU B 387 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.575A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'L' and resid 59 through 60
      removed outlier: 3.611A  pdb=" N   TYR L  55 " --> pdb=" O   THR L  59 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   LEU L  52 " --> pdb=" O   GLN L  43 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   GLN L  43 " --> pdb=" O   LEU L  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 120 through 121
    Processing sheet with id=AA4, first strand: chain 'L' and resid 151 through 156
      removed outlier: 3.875A  pdb=" N   LYS L 151 " --> pdb=" O   THR L 203 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   TYR L 198 " --> pdb=" O   PHE L 215 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   VAL L 202 " --> pdb=" O   VAL L 211 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL L 211 " --> pdb=" O   VAL L 202 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AA7, first strand: chain 'H' and resid 59 through 60
      removed outlier: 4.028A  pdb=" N   GLY H  44 " --> pdb=" O   ALA H  40 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   ALA H  40 " --> pdb=" O   GLY H  44 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   TYR H 112 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 130 through 134
      removed outlier: 6.323A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   VAL H 191 " --> pdb=" O   HIS H 174 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 130 through 134
      removed outlier: 6.323A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 161 through 164
      removed outlier: 4.051A  pdb=" N   TYR H 204 " --> pdb=" O   VAL H 221 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.612A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 452 through 454

    158 hydrogen bonds defined for protein.
    399 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: 0.53

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 805
        1.31 -     1.44: 1466
        1.44 -     1.57: 2781
        1.57 -     1.70: 0
        1.70 -     1.83: 25
  Bond restraints: 5077
  Sorted by residual:
  bond pdb=" C7  NAG A   1 "
       pdb=" N2  NAG A   1 "
    ideal  model  delta    sigma   weight residual
    1.346  1.455 -0.109 2.00e-02 2.50e+03 2.96e+01
  bond pdb=" C7  NAG A   2 "
       pdb=" N2  NAG A   2 "
    ideal  model  delta    sigma   weight residual
    1.346  1.449 -0.103 2.00e-02 2.50e+03 2.67e+01
  bond pdb=" C1  NAG A   2 "
       pdb=" O5  NAG A   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.504 -0.098 2.00e-02 2.50e+03 2.41e+01
  bond pdb=" C1  NAG A   1 "
       pdb=" O5  NAG A   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.490 -0.084 2.00e-02 2.50e+03 1.78e+01
  bond pdb=" C5  NAG A   2 "
       pdb=" O5  NAG A   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.474 -0.061 2.00e-02 2.50e+03 9.38e+00
  ... (remaining 5072 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 6673
        2.02 -     4.03: 199
        4.03 -     6.05: 35
        6.05 -     8.07: 4
        8.07 -    10.08: 2
  Bond angle restraints: 6913
  Sorted by residual:
  angle pdb=" C   SER H 140 "
        pdb=" N   THR H 141 "
        pdb=" CA  THR H 141 "
      ideal   model   delta    sigma   weight residual
     122.42  112.34   10.08 1.33e+00 5.65e-01 5.75e+01
  angle pdb=" N   PRO H 133 "
        pdb=" CA  PRO H 133 "
        pdb=" C   PRO H 133 "
      ideal   model   delta    sigma   weight residual
     111.38  117.90   -6.52 1.59e+00 3.96e-01 1.68e+01
  angle pdb=" N   SER H 137 "
        pdb=" CA  SER H 137 "
        pdb=" C   SER H 137 "
      ideal   model   delta    sigma   weight residual
     111.28  107.11    4.17 1.09e+00 8.42e-01 1.47e+01
  angle pdb=" CB  GLN L   6 "
        pdb=" CG  GLN L   6 "
        pdb=" CD  GLN L   6 "
      ideal   model   delta    sigma   weight residual
     112.60  106.33    6.27 1.70e+00 3.46e-01 1.36e+01
  angle pdb=" N   LYS H 139 "
        pdb=" CA  LYS H 139 "
        pdb=" C   LYS H 139 "
      ideal   model   delta    sigma   weight residual
     113.97  109.49    4.48 1.28e+00 6.10e-01 1.22e+01
  ... (remaining 6908 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 2714
       17.96 -    35.92: 232
       35.92 -    53.88: 38
       53.88 -    71.84: 7
       71.84 -    89.79: 6
  Dihedral angle restraints: 2997
    sinusoidal: 1135
      harmonic: 1862
  Sorted by residual:
  dihedral pdb=" CA  PRO B 337 "
           pdb=" C   PRO B 337 "
           pdb=" N   PHE B 338 "
           pdb=" CA  PHE B 338 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.69   26.31     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CB  CYS L 140 "
           pdb=" SG  CYS L 140 "
           pdb=" SG  CYS L 200 "
           pdb=" CB  CYS L 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   51.38   41.62     1      1.00e+01 1.00e-02 2.42e+01
  dihedral pdb=" CA  SER L  33 "
           pdb=" C   SER L  33 "
           pdb=" N   ASN L  34 "
           pdb=" CA  ASN L  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.12   22.88     0      5.00e+00 4.00e-02 2.09e+01
  ... (remaining 2994 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 710
       0.092 -    0.183: 54
       0.183 -    0.274: 2
       0.274 -    0.366: 1
       0.366 -    0.457: 1
  Chirality restraints: 768
  Sorted by residual:
  chirality pdb=" C1  NAG A   1 "
            pdb=" ND2 ASN B 343 "
            pdb=" C2  NAG A   1 "
            pdb=" O5  NAG A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.94   -0.46 2.00e-01 2.50e+01 5.23e+00
  chirality pdb=" CA  LEU H 134 "
            pdb=" N   LEU H 134 "
            pdb=" C   LEU H 134 "
            pdb=" CB  LEU H 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.87   -0.36 2.00e-01 2.50e+01 3.32e+00
  chirality pdb=" CB  THR H 100 "
            pdb=" CA  THR H 100 "
            pdb=" OG1 THR H 100 "
            pdb=" CG2 THR H 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 765 not shown)

  Planarity restraints: 891
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE H 132 "    0.015 2.00e-02 2.50e+03   2.95e-02 8.73e+00
        pdb=" C   PHE H 132 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   PHE H 132 "    0.019 2.00e-02 2.50e+03
        pdb=" N   PRO H 133 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO L  49 "    0.034 5.00e-02 4.00e+02   5.13e-02 4.21e+00
        pdb=" N   PRO L  50 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO L  50 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO L  50 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET L   4 "   -0.008 2.00e-02 2.50e+03   1.53e-02 2.34e+00
        pdb=" C   MET L   4 "    0.026 2.00e-02 2.50e+03
        pdb=" O   MET L   4 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   THR L   5 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 888 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 515
        2.74 -     3.28: 4860
        3.28 -     3.82: 7939
        3.82 -     4.36: 9396
        4.36 -     4.90: 16619
  Nonbonded interactions: 39329
  Sorted by model distance:
  nonbonded pdb=" O   THR B 393 "
            pdb=" OG1 THR B 523 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OG  SER B 349 "
            pdb=" O   LEU B 452 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OG1 THR H  28 "
            pdb=" OG  SER H  31 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" NE2 GLN B 474 "
            pdb=" O   THR B 478 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" OG  SER L  33 "
            pdb=" N   SER B 349 "
     model   vdw
     2.255 3.120
  ... (remaining 39324 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:             4.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.310
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
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   0.109   5085  Z= 0.322
  Angle     :  0.844  10.940   6931  Z= 0.461
  Chirality :  0.053   0.457    768
  Planarity :  0.005   0.051    890
  Dihedral  : 14.203  89.794   1793
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  0.91 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -2.69 (0.32), residues: 634
  helix: -3.42 (0.70), residues: 41
  sheet: -1.32 (0.31), residues: 254
  loop : -1.92 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 355 
 TYR   0.022   0.002   TYR L  31 
 PHE   0.018   0.002   PHE L 215 
 TRP   0.013   0.002   TRP L  56 
 HIS   0.005   0.001   HIS L  95 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00664 /  0.32 ( 5077)
  covalent geometry    : angle       0.82509 /  0.46 ( 6913)
  SS BOND              : bond        0.00795 /  0.38 (    6)
  SS BOND              : angle       2.14287 /  1.06 (   12)
  hydrogen bonds       : bond        0.17659 / 11.83 (  143)
  hydrogen bonds       : angle       8.71255 /  6.05 (  399)
  link_BETA1-4         : bond        0.00700 /  0.37 (    1)
  link_BETA1-4         : angle       3.25111 /  1.93 (    3)
  link_NAG-ASN         : bond        0.00409 /  0.22 (    1)
  link_NAG-ASN         : angle       6.85152 /  4.00 (    3)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   30 LEU cc_start: 0.8286 (tt) cc_final: 0.8060 (tp)
REVERT: H   53 TYR cc_start: 0.7338 (p90) cc_final: 0.7068 (p90)
REVERT: H   60 TYR cc_start: 0.8269 (m-80) cc_final: 0.7968 (m-80)
REVERT: H  161 THR cc_start: 0.7024 (p) cc_final: 0.6816 (p)
REVERT: B  467 ASP cc_start: 0.7461 (p0) cc_final: 0.6930 (p0)
  outliers start: 2
  outliers final: 1
  residues processed: 84
  average time/residue: 0.0852
  time to fit residues: 9.0233
Evaluate side-chains
  65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.4980
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0970
   chunk 16 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.5578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L 130 GLN
L 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.215285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.185658 restraints weight = 6197.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.183577 restraints weight = 10551.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.184890 restraints weight = 8835.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.184662 restraints weight = 6135.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.185032 restraints weight = 5269.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.4179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.1300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5085  Z= 0.139
  Angle     :  0.658   7.384   6931  Z= 0.337
  Chirality :  0.047   0.349    768
  Planarity :  0.005   0.052    890
  Dihedral  :  5.411  28.300    700
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  9.07 %
    Favored  : 90.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -2.30 (0.32), residues: 634
  helix: -3.24 (0.74), residues: 34
  sheet: -1.06 (0.32), residues: 252
  loop : -1.69 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 355 
 TYR   0.013   0.002   TYR L  31 
 PHE   0.014   0.001   PHE L 215 
 TRP   0.009   0.001   TRP B 436 
 HIS   0.003   0.001   HIS L 204 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.14 ( 5077)
  covalent geometry    : angle       0.64130 /  0.33 ( 6913)
  SS BOND              : bond        0.00471 /  0.21 (    6)
  SS BOND              : angle       1.40354 /  0.77 (   12)
  hydrogen bonds       : bond        0.03610 /  2.49 (  143)
  hydrogen bonds       : angle       7.26256 /  5.02 (  399)
  link_BETA1-4         : bond        0.00675 /  0.36 (    1)
  link_BETA1-4         : angle       4.72997 /  2.70 (    3)
  link_NAG-ASN         : bond        0.00660 /  0.35 (    1)
  link_NAG-ASN         : angle       4.80286 /  2.62 (    3)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   53 TYR cc_start: 0.7239 (p90) cc_final: 0.6996 (p90)
REVERT: H   60 TYR cc_start: 0.8197 (m-80) cc_final: 0.7996 (m-80)
REVERT: H   90 ASP cc_start: 0.8480 (m-30) cc_final: 0.8275 (m-30)
REVERT: B  383 SER cc_start: 0.8192 (t) cc_final: 0.7984 (p)
  outliers start: 3
  outliers final: 3
  residues processed: 77
  average time/residue: 0.0938
  time to fit residues: 9.0288
Evaluate side-chains
  65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain H residue  102 ASP
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   chunk 40 optimal weight:    0.2980
   chunk 10 optimal weight:    0.5980
   chunk 54 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 35 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    1.1182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.208947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.176679 restraints weight = 5946.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.171914 restraints weight = 10736.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.175102 restraints weight = 9534.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.174249 restraints weight = 6075.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.174069 restraints weight = 6712.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.4089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   5085  Z= 0.190
  Angle     :  0.649   7.542   6931  Z= 0.333
  Chirality :  0.047   0.366    768
  Planarity :  0.004   0.038    890
  Dihedral  :  5.320  26.956    699
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 12.89 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -2.13 (0.32), residues: 634
  helix: -3.13 (0.76), residues: 35
  sheet: -0.87 (0.32), residues: 247
  loop : -1.62 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 357 
 TYR   0.022   0.002   TYR H 155 
 PHE   0.021   0.002   PHE H 156 
 TRP   0.009   0.001   TRP B 436 
 HIS   0.004   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00451 /  0.19 ( 5077)
  covalent geometry    : angle       0.63310 /  0.33 ( 6913)
  SS BOND              : bond        0.00914 /  0.46 (    6)
  SS BOND              : angle       1.69123 /  0.91 (   12)
  hydrogen bonds       : bond        0.03574 /  2.41 (  143)
  hydrogen bonds       : angle       7.11584 /  4.93 (  399)
  link_BETA1-4         : bond        0.01088 /  0.57 (    1)
  link_BETA1-4         : angle       4.03120 /  2.31 (    3)
  link_NAG-ASN         : bond        0.00441 /  0.23 (    1)
  link_NAG-ASN         : angle       4.78769 /  2.64 (    3)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  146 TYR cc_start: 0.8385 (t80) cc_final: 0.8010 (t80)
REVERT: H   53 TYR cc_start: 0.7378 (p90) cc_final: 0.7091 (p90)
REVERT: H   60 TYR cc_start: 0.8212 (m-80) cc_final: 0.7973 (m-80)
REVERT: H   83 MET cc_start: 0.7221 (mtt) cc_final: 0.7013 (mtt)
REVERT: H   90 ASP cc_start: 0.8497 (m-30) cc_final: 0.8264 (m-30)
REVERT: B  383 SER cc_start: 0.8266 (t) cc_final: 0.8026 (p)
  outliers start: 6
  outliers final: 5
  residues processed: 75
  average time/residue: 0.0818
  time to fit residues: 7.7557
Evaluate side-chains
  67 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue  102 ASP
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 8 optimal weight:    5.9990
   chunk 31 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.8180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.210796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.183572 restraints weight = 5887.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.180100 restraints weight = 8952.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.180694 restraints weight = 8358.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.179525 restraints weight = 5770.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.180451 restraints weight = 5346.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5085  Z= 0.152
  Angle     :  0.612   7.648   6931  Z= 0.312
  Chirality :  0.045   0.325    768
  Planarity :  0.004   0.035    890
  Dihedral  :  5.105  26.312    699
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 13.43 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -2.07 (0.32), residues: 634
  helix: -3.15 (0.67), residues: 41
  sheet: -0.71 (0.33), residues: 239
  loop : -1.62 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  60 
 TYR   0.021   0.002   TYR H 155 
 PHE   0.013   0.001   PHE L 124 
 TRP   0.009   0.001   TRP B 436 
 HIS   0.005   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.15 ( 5077)
  covalent geometry    : angle       0.59917 /  0.31 ( 6913)
  SS BOND              : bond        0.00821 /  0.41 (    6)
  SS BOND              : angle       1.41146 /  0.79 (   12)
  hydrogen bonds       : bond        0.03222 /  2.15 (  143)
  hydrogen bonds       : angle       6.87934 /  4.76 (  399)
  link_BETA1-4         : bond        0.00988 /  0.52 (    1)
  link_BETA1-4         : angle       3.90739 /  2.24 (    3)
  link_NAG-ASN         : bond        0.00336 /  0.18 (    1)
  link_NAG-ASN         : angle       3.72523 /  2.04 (    3)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   53 TYR cc_start: 0.7301 (p90) cc_final: 0.7028 (p90)
REVERT: H   60 TYR cc_start: 0.8208 (m-80) cc_final: 0.7978 (m-80)
REVERT: H   90 ASP cc_start: 0.8478 (m-30) cc_final: 0.8277 (m-30)
REVERT: H  156 PHE cc_start: 0.7777 (t80) cc_final: 0.7571 (t80)
REVERT: B  383 SER cc_start: 0.8292 (t) cc_final: 0.8042 (p)
REVERT: B  408 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6313 (ptm160)
  outliers start: 15
  outliers final: 8
  residues processed: 80
  average time/residue: 0.0779
  time to fit residues: 7.9266
Evaluate side-chains
  69 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain H residue  161 THR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  408 ARG
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 20 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0030
   chunk 1 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.7790

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.214835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.184077 restraints weight = 6148.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.181067 restraints weight = 11771.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.183259 restraints weight = 9372.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.182868 restraints weight = 5844.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.183025 restraints weight = 5980.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.4146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5085  Z= 0.148
  Angle     :  0.614   8.773   6931  Z= 0.313
  Chirality :  0.045   0.311    768
  Planarity :  0.004   0.033    890
  Dihedral  :  4.962  25.316    699
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.43 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.98 (0.32), residues: 634
  helix: -3.09 (0.66), residues: 41
  sheet: -0.68 (0.33), residues: 239
  loop : -1.54 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  60 
 TYR   0.019   0.001   TYR H 155 
 PHE   0.011   0.001   PHE L 124 
 TRP   0.009   0.001   TRP B 436 
 HIS   0.007   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.15 ( 5077)
  covalent geometry    : angle       0.60257 /  0.31 ( 6913)
  SS BOND              : bond        0.00745 /  0.36 (    6)
  SS BOND              : angle       1.55061 /  0.91 (   12)
  hydrogen bonds       : bond        0.03153 /  2.11 (  143)
  hydrogen bonds       : angle       6.71138 /  4.65 (  399)
  link_BETA1-4         : bond        0.00974 /  0.51 (    1)
  link_BETA1-4         : angle       3.65855 /  2.09 (    3)
  link_NAG-ASN         : bond        0.00361 /  0.19 (    1)
  link_NAG-ASN         : angle       3.47577 /  1.90 (    3)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   53 TYR cc_start: 0.7285 (p90) cc_final: 0.7009 (p90)
REVERT: B  383 SER cc_start: 0.8260 (t) cc_final: 0.8033 (p)
REVERT: B  408 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6543 (ptm160)
  outliers start: 12
  outliers final: 9
  residues processed: 69
  average time/residue: 0.0809
  time to fit residues: 7.1417
Evaluate side-chains
  68 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  110 VAL
Chi-restraints excluded: chain H residue  161 THR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  408 ARG
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 39 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.6986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.210092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.178641 restraints weight = 6207.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.170022 restraints weight = 9245.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.165801 restraints weight = 6852.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.165642 restraints weight = 6622.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.165769 restraints weight = 5508.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   5085  Z= 0.261
  Angle     :  0.684   7.845   6931  Z= 0.350
  Chirality :  0.048   0.376    768
  Planarity :  0.005   0.038    890
  Dihedral  :  5.315  27.471    699
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.97 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -2.11 (0.32), residues: 634
  helix: -3.01 (0.69), residues: 41
  sheet: -0.74 (0.33), residues: 236
  loop : -1.67 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  60 
 TYR   0.019   0.002   TYR L  55 
 PHE   0.020   0.002   PHE H 156 
 TRP   0.010   0.002   TRP B 436 
 HIS   0.007   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00627 /  0.26 ( 5077)
  covalent geometry    : angle       0.66972 /  0.35 ( 6913)
  SS BOND              : bond        0.00986 /  0.49 (    6)
  SS BOND              : angle       1.95967 /  1.03 (   12)
  hydrogen bonds       : bond        0.03516 /  2.35 (  143)
  hydrogen bonds       : angle       6.88097 /  4.77 (  399)
  link_BETA1-4         : bond        0.00877 /  0.46 (    1)
  link_BETA1-4         : angle       3.61086 /  2.06 (    3)
  link_NAG-ASN         : bond        0.00000 /  0.00 (    1)
  link_NAG-ASN         : angle       4.31219 /  2.39 (    3)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L    4 MET cc_start: 0.8555 (mmm) cc_final: 0.7867 (mmm)
REVERT: L   27 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8489 (mp10)
REVERT: H   53 TYR cc_start: 0.7349 (p90) cc_final: 0.7101 (p90)
REVERT: H   90 ASP cc_start: 0.8593 (m-30) cc_final: 0.8235 (m-30)
REVERT: B  383 SER cc_start: 0.8360 (t) cc_final: 0.8080 (p)
  outliers start: 15
  outliers final: 12
  residues processed: 74
  average time/residue: 0.0765
  time to fit residues: 7.3751
Evaluate side-chains
  71 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   27 GLN
Chi-restraints excluded: chain L residue   34 ASN
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain H residue  110 VAL
Chi-restraints excluded: chain H residue  161 THR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 43 optimal weight:    0.0870
   chunk 24 optimal weight:    0.6980
   chunk 35 optimal weight:    9.9990
   chunk 0 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 8 optimal weight:    4.9990
   chunk 30 optimal weight:    0.5980
   chunk 32 optimal weight:    0.4980
   chunk 54 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.4758

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.211744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.183613 restraints weight = 5919.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.181550 restraints weight = 10984.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.181881 restraints weight = 9499.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.181488 restraints weight = 6676.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.181639 restraints weight = 6509.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.4170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5085  Z= 0.121
  Angle     :  0.596   7.267   6931  Z= 0.302
  Chirality :  0.045   0.323    768
  Planarity :  0.004   0.036    890
  Dihedral  :  4.909  25.814    699
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 16.33 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.95 (0.33), residues: 634
  helix: -2.93 (0.68), residues: 41
  sheet: -0.66 (0.33), residues: 239
  loop : -1.54 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  60 
 TYR   0.015   0.001   TYR H 155 
 PHE   0.015   0.001   PHE L 124 
 TRP   0.010   0.001   TRP B 436 
 HIS   0.008   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 5077)
  covalent geometry    : angle       0.58249 /  0.30 ( 6913)
  SS BOND              : bond        0.00657 /  0.32 (    6)
  SS BOND              : angle       1.49110 /  0.83 (   12)
  hydrogen bonds       : bond        0.03012 /  1.99 (  143)
  hydrogen bonds       : angle       6.62117 /  4.59 (  399)
  link_BETA1-4         : bond        0.01045 /  0.55 (    1)
  link_BETA1-4         : angle       3.52022 /  2.04 (    3)
  link_NAG-ASN         : bond        0.00987 /  0.52 (    1)
  link_NAG-ASN         : angle       4.21289 /  2.29 (    3)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   53 TYR cc_start: 0.7232 (p90) cc_final: 0.6992 (p90)
REVERT: H   90 ASP cc_start: 0.8447 (m-30) cc_final: 0.8086 (m-30)
REVERT: H  156 PHE cc_start: 0.7508 (t80) cc_final: 0.7296 (t80)
REVERT: B  383 SER cc_start: 0.8366 (t) cc_final: 0.8094 (p)
REVERT: B  408 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6455 (ptm160)
  outliers start: 14
  outliers final: 11
  residues processed: 71
  average time/residue: 0.0938
  time to fit residues: 8.4444
Evaluate side-chains
  66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain H residue  110 VAL
Chi-restraints excluded: chain H residue  161 THR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  408 ARG
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 10 optimal weight:    0.4980
   chunk 6 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L 158 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.209299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.179146 restraints weight = 5981.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.177844 restraints weight = 9992.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.179026 restraints weight = 9313.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.177855 restraints weight = 6871.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.179220 restraints weight = 6314.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.4141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5085  Z= 0.175
  Angle     :  0.625   7.874   6931  Z= 0.317
  Chirality :  0.046   0.315    768
  Planarity :  0.004   0.034    890
  Dihedral  :  4.992  26.122    699
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.06 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.98 (0.32), residues: 634
  helix: -2.87 (0.69), residues: 41
  sheet: -0.61 (0.33), residues: 234
  loop : -1.62 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 217 
 TYR   0.015   0.002   TYR L  55 
 PHE   0.013   0.001   PHE L 124 
 TRP   0.009   0.001   TRP B 436 
 HIS   0.006   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00416 /  0.17 ( 5077)
  covalent geometry    : angle       0.61093 /  0.31 ( 6913)
  SS BOND              : bond        0.00804 /  0.40 (    6)
  SS BOND              : angle       1.63666 /  0.88 (   12)
  hydrogen bonds       : bond        0.03162 /  2.10 (  143)
  hydrogen bonds       : angle       6.55430 /  4.54 (  399)
  link_BETA1-4         : bond        0.00845 /  0.44 (    1)
  link_BETA1-4         : angle       3.24654 /  1.84 (    3)
  link_NAG-ASN         : bond        0.00310 /  0.16 (    1)
  link_NAG-ASN         : angle       4.45819 /  2.40 (    3)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   27 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8457 (mp10)
REVERT: H   53 TYR cc_start: 0.7248 (p90) cc_final: 0.7016 (p90)
REVERT: H   90 ASP cc_start: 0.8496 (m-30) cc_final: 0.8172 (m-30)
REVERT: B  383 SER cc_start: 0.8327 (t) cc_final: 0.8038 (p)
REVERT: B  408 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6498 (ptm160)
  outliers start: 13
  outliers final: 11
  residues processed: 65
  average time/residue: 0.0790
  time to fit residues: 6.6386
Evaluate side-chains
  66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   27 GLN
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain H residue  110 VAL
Chi-restraints excluded: chain H residue  161 THR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  408 ARG
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 39 optimal weight:    8.9990
   chunk 2 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 14 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 25 optimal weight:    0.3980
   overall best weight:    0.7182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.211237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.182840 restraints weight = 6048.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.182476 restraints weight = 10482.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.184285 restraints weight = 8974.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.183086 restraints weight = 6178.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.183834 restraints weight = 6849.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.4186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5085  Z= 0.142
  Angle     :  0.608   7.248   6931  Z= 0.310
  Chirality :  0.045   0.317    768
  Planarity :  0.004   0.033    890
  Dihedral  :  4.917  25.091    699
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.42 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.93 (0.32), residues: 634
  helix: -2.83 (0.70), residues: 41
  sheet: -0.54 (0.33), residues: 234
  loop : -1.62 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 355 
 TYR   0.030   0.002   TYR B 396 
 PHE   0.028   0.001   PHE H 156 
 TRP   0.009   0.001   TRP B 436 
 HIS   0.007   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.14 ( 5077)
  covalent geometry    : angle       0.59490 /  0.31 ( 6913)
  SS BOND              : bond        0.00656 /  0.32 (    6)
  SS BOND              : angle       1.42247 /  0.80 (   12)
  hydrogen bonds       : bond        0.03090 /  2.07 (  143)
  hydrogen bonds       : angle       6.53205 /  4.55 (  399)
  link_BETA1-4         : bond        0.01056 /  0.56 (    1)
  link_BETA1-4         : angle       3.23854 /  1.83 (    3)
  link_NAG-ASN         : bond        0.00468 /  0.25 (    1)
  link_NAG-ASN         : angle       4.41898 /  2.38 (    3)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   27 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8386 (mp10)
REVERT: H   53 TYR cc_start: 0.7171 (p90) cc_final: 0.6962 (p90)
REVERT: H   90 ASP cc_start: 0.8462 (m-30) cc_final: 0.8154 (m-30)
REVERT: H  220 LYS cc_start: 0.7165 (tmtt) cc_final: 0.6810 (tmtt)
REVERT: B  383 SER cc_start: 0.8315 (t) cc_final: 0.8031 (p)
REVERT: B  408 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6490 (ptm160)
  outliers start: 14
  outliers final: 11
  residues processed: 62
  average time/residue: 0.0816
  time to fit residues: 6.5946
Evaluate side-chains
  64 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   27 GLN
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain H residue  110 VAL
Chi-restraints excluded: chain H residue  161 THR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  408 ARG
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 7 optimal weight:    0.0770
   chunk 41 optimal weight:    9.9990
   chunk 44 optimal weight:    0.4980
   chunk 55 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 32 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 26 optimal weight:    0.3980
   chunk 47 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   overall best weight:    0.5338

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.212907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.184659 restraints weight = 5956.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.182605 restraints weight = 10544.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.184041 restraints weight = 8244.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.183565 restraints weight = 5673.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.183755 restraints weight = 5167.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.4196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5085  Z= 0.121
  Angle     :  0.584   6.717   6931  Z= 0.298
  Chirality :  0.045   0.269    768
  Planarity :  0.004   0.032    890
  Dihedral  :  4.733  24.679    699
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.42 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.88 (0.32), residues: 634
  helix: -2.70 (0.70), residues: 41
  sheet: -0.48 (0.33), residues: 236
  loop : -1.62 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 217 
 TYR   0.015   0.001   TYR H 155 
 PHE   0.027   0.001   PHE H 156 
 TRP   0.010   0.001   TRP B 436 
 HIS   0.008   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.12 ( 5077)
  covalent geometry    : angle       0.57395 /  0.30 ( 6913)
  SS BOND              : bond        0.00606 /  0.29 (    6)
  SS BOND              : angle       1.27459 /  0.76 (   12)
  hydrogen bonds       : bond        0.02951 /  1.97 (  143)
  hydrogen bonds       : angle       6.35434 /  4.39 (  399)
  link_BETA1-4         : bond        0.00808 /  0.43 (    1)
  link_BETA1-4         : angle       3.00187 /  1.69 (    3)
  link_NAG-ASN         : bond        0.00378 /  0.20 (    1)
  link_NAG-ASN         : angle       3.58319 /  1.93 (    3)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   27 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8425 (mp10)
REVERT: H   53 TYR cc_start: 0.7243 (p90) cc_final: 0.7033 (p90)
REVERT: H   90 ASP cc_start: 0.8515 (m-30) cc_final: 0.8261 (m-30)
REVERT: B  408 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6466 (ptm160)
  outliers start: 14
  outliers final: 12
  residues processed: 68
  average time/residue: 0.0845
  time to fit residues: 7.3202
Evaluate side-chains
  68 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   27 GLN
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain H residue  110 VAL
Chi-restraints excluded: chain H residue  161 THR
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  408 ARG
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 48 optimal weight:    0.0020
   chunk 56 optimal weight:    0.7980
   chunk 9 optimal weight:    0.2980
   chunk 55 optimal weight:    0.0020
   chunk 54 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.3596

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.215024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.179141 restraints weight = 6053.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.175623 restraints weight = 7172.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.177163 restraints weight = 7761.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.178501 restraints weight = 5754.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.178300 restraints weight = 4380.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.4068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   5085  Z= 0.106
  Angle     :  0.564   6.499   6931  Z= 0.287
  Chirality :  0.045   0.301    768
  Planarity :  0.004   0.034    890
  Dihedral  :  4.614  23.733    699
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 17.79 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.78 (0.32), residues: 634
  helix: -2.61 (0.71), residues: 41
  sheet: -0.39 (0.33), residues: 236
  loop : -1.58 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 217 
 TYR   0.027   0.001   TYR B 396 
 PHE   0.010   0.001   PHE L 124 
 TRP   0.009   0.001   TRP B 436 
 HIS   0.007   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.10 ( 5077)
  covalent geometry    : angle       0.55348 /  0.28 ( 6913)
  SS BOND              : bond        0.00556 /  0.27 (    6)
  SS BOND              : angle       1.20625 /  0.72 (   12)
  hydrogen bonds       : bond        0.02802 /  1.87 (  143)
  hydrogen bonds       : angle       6.27740 /  4.33 (  399)
  link_BETA1-4         : bond        0.01009 /  0.53 (    1)
  link_BETA1-4         : angle       2.70463 /  1.59 (    3)
  link_NAG-ASN         : bond        0.00828 /  0.44 (    1)
  link_NAG-ASN         : angle       4.08983 /  2.21 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1030.86 seconds
wall clock time: 18 minutes 32.37 seconds (1112.37 seconds total)