Starting phenix.real_space_refine
on Wed Sep 17 04:38:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bpu_44790/09_2025/9bpu_44790.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bpu_44790/09_2025/9bpu_44790.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bpu_44790/09_2025/9bpu_44790.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bpu_44790/09_2025/9bpu_44790.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bpu_44790/09_2025/9bpu_44790.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bpu_44790/09_2025/9bpu_44790.cif"
  }
  resolution = 3.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      27      5.16       5
     C    2744      2.51       5
     N     743      2.21       5
     O     804      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4318
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 1068
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1068
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 10, 'TRANS': 127}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1613
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 12, 'TRANS': 182}
    Chain: "B"
      Number of atoms: 1570
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1570
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 19, 'TRANS': 176}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.36, per 1000 atoms: 0.31
  Number of scatterers: 4318
  At special positions: 0
  Unit cell: (67.284, 96.12, 104.664, 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      27     16.00
     O     804      8.00
     N     743      7.00
     C    2744      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  27 " - pdb=" SG  CYS C 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  62 " - pdb=" SG  CYS C 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  76 " - pdb=" SG  CYS C 178 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  66 " - pdb=" SG  CYS A  74 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 188 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  54 " - pdb=" SG  CYS B  62 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 175 " - pdb=" SG  CYS B 197 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG D   1 " - " ASN B   9 "
      " NAG E   1 " - " ASN B 122 "
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 171.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1016

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 12 sheets defined
      23.4% alpha, 41.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'C' and resid 28 through 33
      removed outlier: 4.146A  pdb=" N   HIS C  31 " --> pdb=" O   LEU C  28 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ARG C  33 " --> pdb=" O   SER C  30 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 36 through 58
    Processing helix  chain 'C' and resid 74 through 99
      removed outlier: 3.565A  pdb=" N   SER C  99 " --> pdb=" O   GLY C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 127
    Processing helix  chain 'C' and resid 149 through 167
      removed outlier: 3.690A  pdb=" N   ARG C 153 " --> pdb=" O   SER C 149 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   LEU C 162 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   ARG C 163 " --> pdb=" O   PHE C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 176
    Processing helix  chain 'A' and resid 106 through 111
    Processing helix  chain 'A' and resid 144 through 149
    Processing helix  chain 'B' and resid 99 through 103
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 32
      removed outlier: 4.297A  pdb=" N   VAL A  27 " --> pdb=" O   GLN A  39 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   GLN A  39 " --> pdb=" O   VAL A  27 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   MET A  29 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   ILE A  37 " --> pdb=" O   MET A  29 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   SER A  31 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   LYS A  35 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 69
      removed outlier: 6.715A  pdb=" N   ALA A  54 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   MET A  67 " --> pdb=" O   PHE A  52 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   PHE A  52 " --> pdb=" O   MET A  67 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   THR A  86 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 69
      removed outlier: 6.715A  pdb=" N   ALA A  54 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   MET A  67 " --> pdb=" O   PHE A  52 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   PHE A  52 " --> pdb=" O   MET A  67 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   THR A  86 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 123
    Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 169
    Processing sheet with id=AA6, first strand: chain 'A' and resid 167 through 169
    Processing sheet with id=AA7, first strand: chain 'B' and resid 11 through 15
    Processing sheet with id=AA8, first strand: chain 'B' and resid 34 through 41
    Processing sheet with id=AA9, first strand: chain 'B' and resid 34 through 41
    Processing sheet with id=AB1, first strand: chain 'B' and resid 109 through 114
      removed outlier: 3.594A  pdb=" N   ASN B 122 " --> pdb=" O   VAL B 111 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 151 through 152
    Processing sheet with id=AB3, first strand: chain 'B' and resid 151 through 152

    222 hydrogen bonds defined for protein.
    576 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: 0.63

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1328
        1.34 -     1.45: 732
        1.45 -     1.57: 2336
        1.57 -     1.69: 1
        1.69 -     1.81: 37
  Bond restraints: 4434
  Sorted by residual:
  bond pdb=" N   MET B 131 "
       pdb=" CA  MET B 131 "
    ideal  model  delta    sigma   weight residual
    1.453  1.489 -0.035 9.20e-03 1.18e+04 1.48e+01
  bond pdb=" N   TYR B  39 "
       pdb=" CA  TYR B  39 "
    ideal  model  delta    sigma   weight residual
    1.454  1.491 -0.037 1.23e-02 6.61e+03 8.83e+00
  bond pdb=" N   SER B 190 "
       pdb=" CA  SER B 190 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.09e-02 8.42e+03 8.60e+00
  bond pdb=" N   VAL A 122 "
       pdb=" CA  VAL A 122 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.20e-02 6.94e+03 8.14e+00
  bond pdb=" N   TYR B 125 "
       pdb=" CA  TYR B 125 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.23e-02 6.61e+03 7.99e+00
  ... (remaining 4429 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 5733
        1.73 -     3.45: 251
        3.45 -     5.18: 39
        5.18 -     6.90: 7
        6.90 -     8.63: 2
  Bond angle restraints: 6032
  Sorted by residual:
  angle pdb=" C   ALA A 124 "
        pdb=" CA  ALA A 124 "
        pdb=" CB  ALA A 124 "
      ideal   model   delta    sigma   weight residual
     117.23  111.85    5.38 1.36e+00 5.41e-01 1.57e+01
  angle pdb=" CA  GLN B 126 "
        pdb=" C   GLN B 126 "
        pdb=" O   GLN B 126 "
      ideal   model   delta    sigma   weight residual
     122.51  118.14    4.37 1.34e+00 5.57e-01 1.06e+01
  angle pdb=" CA  ASP B  71 "
        pdb=" C   ASP B  71 "
        pdb=" O   ASP B  71 "
      ideal   model   delta    sigma   weight residual
     121.58  118.05    3.53 1.12e+00 7.97e-01 9.95e+00
  angle pdb=" CA  GLN B   8 "
        pdb=" C   GLN B   8 "
        pdb=" O   GLN B   8 "
      ideal   model   delta    sigma   weight residual
     120.70  117.54    3.16 1.03e+00 9.43e-01 9.43e+00
  angle pdb=" CA  GLY A  48 "
        pdb=" C   GLY A  48 "
        pdb=" O   GLY A  48 "
      ideal   model   delta    sigma   weight residual
     122.33  118.28    4.05 1.32e+00 5.74e-01 9.42e+00
  ... (remaining 6027 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.12: 2479
       22.12 -    44.25: 233
       44.25 -    66.37: 45
       66.37 -    88.49: 9
       88.49 -   110.62: 6
  Dihedral angle restraints: 2772
    sinusoidal: 1210
      harmonic: 1562
  Sorted by residual:
  dihedral pdb=" CB  CYS C  62 "
           pdb=" SG  CYS C  62 "
           pdb=" SG  CYS C 152 "
           pdb=" CB  CYS C 152 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   61.02   31.98     1      1.00e+01 1.00e-02 1.46e+01
  dihedral pdb=" O4  BMA E   3 "
           pdb=" C4  BMA E   3 "
           pdb=" C5  BMA E   3 "
           pdb=" O5  BMA E   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  178.09  110.62     1      3.00e+01 1.11e-03 1.44e+01
  dihedral pdb=" C3  BMA E   3 "
           pdb=" C4  BMA E   3 "
           pdb=" C5  BMA E   3 "
           pdb=" O5  BMA E   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.62  -61.13  108.75     1      3.00e+01 1.11e-03 1.41e+01
  ... (remaining 2769 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 530
       0.054 -    0.107: 101
       0.107 -    0.161: 31
       0.161 -    0.214: 5
       0.214 -    0.268: 2
  Chirality restraints: 669
  Sorted by residual:
  chirality pdb=" C5  BMA E   3 "
            pdb=" C4  BMA E   3 "
            pdb=" C6  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B 122 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN B   9 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 9.52e-01
  ... (remaining 666 not shown)

  Planarity restraints: 775
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  42 "    0.035 5.00e-02 4.00e+02   5.13e-02 4.21e+00
        pdb=" N   PRO A  43 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B  50 "   -0.009 2.00e-02 2.50e+03   1.78e-02 3.17e+00
        pdb=" CD  GLU B  50 "    0.031 2.00e-02 2.50e+03
        pdb=" OE1 GLU B  50 "   -0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU B  50 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 100 "   -0.016 2.00e-02 2.50e+03   8.96e-03 2.01e+00
        pdb=" CG  TRP A 100 "    0.022 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 100 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 100 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 100 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 100 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 100 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 100 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 100 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 100 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 772 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 523
        2.75 -     3.29: 4033
        3.29 -     3.83: 7185
        3.83 -     4.36: 8209
        4.36 -     4.90: 14499
  Nonbonded interactions: 34449
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 138 "
            pdb=" O   GLN B 160 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OG  SER B  84 "
            pdb=" O   SER B  87 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OG1 THR A  53 "
            pdb=" OE1 GLU A  92 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" NE2 GLN A 157 "
            pdb=" OE1 GLN A 190 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" NH2 ARG C  47 "
            pdb=" OD2 ASP B  98 "
     model   vdw
     2.336 3.120
  ... (remaining 34444 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.290
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.087   4446  Z= 0.347
  Angle     :  0.781   8.626   6061  Z= 0.455
  Chirality :  0.051   0.268    669
  Planarity :  0.004   0.051    773
  Dihedral  : 17.752 110.615   1735
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 24.79 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.38), residues: 521
  helix:  1.86 (0.49), residues: 119
  sheet: -0.54 (0.36), residues: 203
  loop : -0.42 (0.45), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  88 
 TYR   0.012   0.001   TYR B 125 
 PHE   0.007   0.001   PHE B 153 
 TRP   0.022   0.002   TRP A 100 
 HIS   0.007   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 ( 4434)
  covalent geometry    : angle       0.77914 ( 6032)
  SS BOND              : bond        0.00252 (    7)
  SS BOND              : angle       0.59973 (   14)
  hydrogen bonds       : bond        0.13976 (  180)
  hydrogen bonds       : angle       6.77233 (  576)
  link_BETA1-4         : bond        0.00291 (    3)
  link_BETA1-4         : angle       1.67583 (    9)
  link_NAG-ASN         : bond        0.00234 (    2)
  link_NAG-ASN         : angle       1.22201 (    6)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 LEU cc_start: 0.8178 (mt) cc_final: 0.7926 (mt)
  outliers start: 3
  outliers final: 2
  residues processed: 98
  average time/residue: 0.0688
  time to fit residues: 8.4735
Evaluate side-chains
  88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain B residue  134 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    9.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0870
   chunk 50 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.1362

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

Flipped N/Q/H residues before XYZ refinement:
A 168 GLN
B 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.174132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.145323 restraints weight = 5447.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 2.43
r_work: 0.3634 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.0925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4446  Z= 0.173
  Angle     :  0.624   7.079   6061  Z= 0.306
  Chirality :  0.042   0.134    669
  Planarity :  0.004   0.034    773
  Dihedral  :  9.717  67.881    690
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 21.37 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.37), residues: 521
  helix:  1.96 (0.48), residues: 117
  sheet: -0.46 (0.36), residues: 201
  loop : -0.34 (0.44), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  88 
 TYR   0.015   0.001   TYR B 138 
 PHE   0.018   0.002   PHE A  62 
 TRP   0.016   0.002   TRP A 100 
 HIS   0.004   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 4434)
  covalent geometry    : angle       0.61756 ( 6032)
  SS BOND              : bond        0.00268 (    7)
  SS BOND              : angle       0.68139 (   14)
  hydrogen bonds       : bond        0.03700 (  180)
  hydrogen bonds       : angle       4.99990 (  576)
  link_BETA1-4         : bond        0.00378 (    3)
  link_BETA1-4         : angle       2.28394 (    9)
  link_NAG-ASN         : bond        0.00413 (    2)
  link_NAG-ASN         : angle       0.92090 (    6)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8443 (t0) cc_final: 0.8203 (t0)
REVERT: B   40 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7492 (tt0)
  outliers start: 22
  outliers final: 12
  residues processed: 99
  average time/residue: 0.0728
  time to fit residues: 9.1341
Evaluate side-chains
  88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   88 LYS
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain B residue  199 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B 167 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.172786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.144097 restraints weight = 5411.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 2.42
r_work: 0.3614 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3453 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4446  Z= 0.170
  Angle     :  0.608   7.090   6061  Z= 0.295
  Chirality :  0.042   0.135    669
  Planarity :  0.004   0.032    773
  Dihedral  :  7.817  56.403    690
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 19.66 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.38), residues: 521
  helix:  2.30 (0.48), residues: 111
  sheet: -0.51 (0.36), residues: 201
  loop : -0.28 (0.44), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  60 
 TYR   0.012   0.001   TYR B  99 
 PHE   0.013   0.001   PHE A  62 
 TRP   0.014   0.001   TRP A 152 
 HIS   0.005   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 4434)
  covalent geometry    : angle       0.60199 ( 6032)
  SS BOND              : bond        0.00231 (    7)
  SS BOND              : angle       0.66128 (   14)
  hydrogen bonds       : bond        0.03472 (  180)
  hydrogen bonds       : angle       4.81545 (  576)
  link_BETA1-4         : bond        0.00421 (    3)
  link_BETA1-4         : angle       2.20228 (    9)
  link_NAG-ASN         : bond        0.00398 (    2)
  link_NAG-ASN         : angle       0.88002 (    6)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8511 (t0) cc_final: 0.7993 (t0)
REVERT: A   88 ARG cc_start: 0.8589 (ttp-170) cc_final: 0.8004 (ttp-170)
REVERT: B   40 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7422 (tt0)
  outliers start: 25
  outliers final: 15
  residues processed: 95
  average time/residue: 0.0772
  time to fit residues: 9.3141
Evaluate side-chains
  96 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   57 TRP
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  199 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 43 optimal weight:    9.9990
   chunk 0 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B 167 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.172393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.143869 restraints weight = 5349.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 2.41
r_work: 0.3610 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3451 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4446  Z= 0.165
  Angle     :  0.597   7.266   6061  Z= 0.292
  Chirality :  0.041   0.137    669
  Planarity :  0.004   0.032    773
  Dihedral  :  7.191  55.680    690
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 19.02 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.38), residues: 521
  helix:  1.91 (0.48), residues: 117
  sheet: -0.55 (0.37), residues: 201
  loop : -0.26 (0.45), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  60 
 TYR   0.011   0.001   TYR B 138 
 PHE   0.010   0.001   PHE A  62 
 TRP   0.014   0.001   TRP A 152 
 HIS   0.003   0.001   HIS A  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 4434)
  covalent geometry    : angle       0.59141 ( 6032)
  SS BOND              : bond        0.00326 (    7)
  SS BOND              : angle       0.88298 (   14)
  hydrogen bonds       : bond        0.03322 (  180)
  hydrogen bonds       : angle       4.71560 (  576)
  link_BETA1-4         : bond        0.00309 (    3)
  link_BETA1-4         : angle       1.95363 (    9)
  link_NAG-ASN         : bond        0.00423 (    2)
  link_NAG-ASN         : angle       0.81258 (    6)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 81
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8524 (t0) cc_final: 0.7964 (t0)
REVERT: B   59 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6188 (pt0)
  outliers start: 26
  outliers final: 19
  residues processed: 99
  average time/residue: 0.0703
  time to fit residues: 8.9670
Evaluate side-chains
  103 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   57 TRP
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   88 LYS
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain B residue  199 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 4 optimal weight:   10.0000
   chunk 25 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.174010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.145614 restraints weight = 5380.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 2.41
r_work: 0.3619 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3458 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4446  Z= 0.147
  Angle     :  0.588   7.237   6061  Z= 0.287
  Chirality :  0.041   0.140    669
  Planarity :  0.004   0.032    773
  Dihedral  :  6.977  55.447    690
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 17.74 %
    Favored  : 76.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.38), residues: 521
  helix:  1.94 (0.48), residues: 117
  sheet: -0.58 (0.37), residues: 201
  loop : -0.25 (0.45), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  60 
 TYR   0.011   0.001   TYR B 138 
 PHE   0.009   0.001   PHE B 153 
 TRP   0.013   0.001   TRP A 152 
 HIS   0.003   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 4434)
  covalent geometry    : angle       0.58360 ( 6032)
  SS BOND              : bond        0.00394 (    7)
  SS BOND              : angle       0.83701 (   14)
  hydrogen bonds       : bond        0.03150 (  180)
  hydrogen bonds       : angle       4.63520 (  576)
  link_BETA1-4         : bond        0.00350 (    3)
  link_BETA1-4         : angle       1.68330 (    9)
  link_NAG-ASN         : bond        0.00318 (    2)
  link_NAG-ASN         : angle       0.74701 (    6)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 88
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8491 (t0) cc_final: 0.8040 (t0)
REVERT: A   88 ARG cc_start: 0.8557 (ttp-170) cc_final: 0.7974 (ttp-170)
REVERT: B   59 GLU cc_start: 0.6674 (mt-10) cc_final: 0.6206 (pt0)
  outliers start: 29
  outliers final: 19
  residues processed: 106
  average time/residue: 0.0758
  time to fit residues: 10.1433
Evaluate side-chains
  97 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   57 TRP
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   88 LYS
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain B residue  199 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 34 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 3 optimal weight:    9.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
B  70 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.171780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.143113 restraints weight = 5477.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 2.43
r_work: 0.3599 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3437 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4446  Z= 0.180
  Angle     :  0.612   7.133   6061  Z= 0.298
  Chirality :  0.042   0.139    669
  Planarity :  0.004   0.034    773
  Dihedral  :  7.046  55.614    690
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 19.44 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.38), residues: 521
  helix:  1.88 (0.48), residues: 117
  sheet: -0.62 (0.36), residues: 201
  loop : -0.30 (0.45), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  90 
 TYR   0.011   0.001   TYR B 138 
 PHE   0.010   0.001   PHE B 153 
 TRP   0.020   0.002   TRP A 100 
 HIS   0.003   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 4434)
  covalent geometry    : angle       0.60789 ( 6032)
  SS BOND              : bond        0.00429 (    7)
  SS BOND              : angle       0.86186 (   14)
  hydrogen bonds       : bond        0.03302 (  180)
  hydrogen bonds       : angle       4.71958 (  576)
  link_BETA1-4         : bond        0.00354 (    3)
  link_BETA1-4         : angle       1.65832 (    9)
  link_NAG-ASN         : bond        0.00460 (    2)
  link_NAG-ASN         : angle       0.94698 (    6)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 86
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8514 (t0) cc_final: 0.8060 (t0)
REVERT: B   59 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6301 (pt0)
  outliers start: 25
  outliers final: 23
  residues processed: 101
  average time/residue: 0.0780
  time to fit residues: 9.8791
Evaluate side-chains
  108 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   57 TRP
Chi-restraints excluded: chain C residue   98 ARG
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   88 LYS
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain B residue  199 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 42 optimal weight:    0.4980
   chunk 38 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.173223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.144825 restraints weight = 5492.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 2.43
r_work: 0.3622 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3460 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4446  Z= 0.134
  Angle     :  0.587   7.405   6061  Z= 0.285
  Chirality :  0.041   0.145    669
  Planarity :  0.004   0.032    773
  Dihedral  :  6.871  55.153    690
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 19.87 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.38), residues: 521
  helix:  1.98 (0.47), residues: 122
  sheet: -0.53 (0.36), residues: 201
  loop : -0.30 (0.46), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  60 
 TYR   0.011   0.001   TYR B 138 
 PHE   0.008   0.001   PHE B 142 
 TRP   0.018   0.001   TRP A 100 
 HIS   0.004   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 4434)
  covalent geometry    : angle       0.58443 ( 6032)
  SS BOND              : bond        0.00311 (    7)
  SS BOND              : angle       0.67866 (   14)
  hydrogen bonds       : bond        0.02966 (  180)
  hydrogen bonds       : angle       4.55904 (  576)
  link_BETA1-4         : bond        0.00368 (    3)
  link_BETA1-4         : angle       1.49717 (    9)
  link_NAG-ASN         : bond        0.00250 (    2)
  link_NAG-ASN         : angle       0.71918 (    6)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8501 (t0) cc_final: 0.8081 (t0)
REVERT: B   59 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6212 (pt0)
REVERT: B   68 LYS cc_start: 0.8292 (tppt) cc_final: 0.7967 (tppp)
  outliers start: 22
  outliers final: 18
  residues processed: 98
  average time/residue: 0.0809
  time to fit residues: 10.0062
Evaluate side-chains
  100 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   57 TRP
Chi-restraints excluded: chain C residue   98 ARG
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain B residue  199 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 3 optimal weight:   10.0000
   chunk 50 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.172919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.144421 restraints weight = 5402.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 2.43
r_work: 0.3620 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3455 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4446  Z= 0.144
  Angle     :  0.602   7.618   6061  Z= 0.294
  Chirality :  0.041   0.145    669
  Planarity :  0.004   0.034    773
  Dihedral  :  6.850  55.136    690
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 20.51 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.38), residues: 521
  helix:  1.99 (0.47), residues: 122
  sheet: -0.62 (0.36), residues: 210
  loop : -0.05 (0.48), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  90 
 TYR   0.011   0.001   TYR B 138 
 PHE   0.008   0.001   PHE B 153 
 TRP   0.014   0.001   TRP A 100 
 HIS   0.003   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 4434)
  covalent geometry    : angle       0.59961 ( 6032)
  SS BOND              : bond        0.00324 (    7)
  SS BOND              : angle       0.63317 (   14)
  hydrogen bonds       : bond        0.02983 (  180)
  hydrogen bonds       : angle       4.53840 (  576)
  link_BETA1-4         : bond        0.00361 (    3)
  link_BETA1-4         : angle       1.51405 (    9)
  link_NAG-ASN         : bond        0.00326 (    2)
  link_NAG-ASN         : angle       0.83185 (    6)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8499 (t0) cc_final: 0.8065 (t0)
REVERT: B   68 LYS cc_start: 0.8275 (tppt) cc_final: 0.7947 (tppp)
  outliers start: 22
  outliers final: 20
  residues processed: 99
  average time/residue: 0.0813
  time to fit residues: 10.0166
Evaluate side-chains
  101 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   57 TRP
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   88 LYS
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain B residue  199 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 14 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.8184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.173467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.144822 restraints weight = 5424.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 2.43
r_work: 0.3629 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3465 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4446  Z= 0.138
  Angle     :  0.592   7.779   6061  Z= 0.289
  Chirality :  0.041   0.147    669
  Planarity :  0.004   0.032    773
  Dihedral  :  6.810  54.987    690
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 20.51 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.38), residues: 521
  helix:  2.40 (0.47), residues: 116
  sheet: -0.61 (0.36), residues: 203
  loop : -0.14 (0.45), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  88 
 TYR   0.011   0.001   TYR B 138 
 PHE   0.008   0.001   PHE B 153 
 TRP   0.012   0.001   TRP A 152 
 HIS   0.003   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 4434)
  covalent geometry    : angle       0.58920 ( 6032)
  SS BOND              : bond        0.00290 (    7)
  SS BOND              : angle       0.60998 (   14)
  hydrogen bonds       : bond        0.02905 (  180)
  hydrogen bonds       : angle       4.51205 (  576)
  link_BETA1-4         : bond        0.00349 (    3)
  link_BETA1-4         : angle       1.45804 (    9)
  link_NAG-ASN         : bond        0.00270 (    2)
  link_NAG-ASN         : angle       0.75919 (    6)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 83
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8458 (t0) cc_final: 0.8027 (t0)
REVERT: A   88 ARG cc_start: 0.8590 (ttp-170) cc_final: 0.7994 (ttp-170)
REVERT: A  129 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8388 (mtp)
REVERT: B   59 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6259 (pt0)
REVERT: B   68 LYS cc_start: 0.8271 (tppt) cc_final: 0.7976 (tppp)
  outliers start: 23
  outliers final: 21
  residues processed: 97
  average time/residue: 0.0812
  time to fit residues: 9.9069
Evaluate side-chains
  100 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   57 TRP
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  129 MET
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain B residue  199 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 50 optimal weight:    0.4980
   chunk 18 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 20 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.7782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.173256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.144856 restraints weight = 5363.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3751 rms_B_bonded: 2.41
r_work: 0.3632 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4446  Z= 0.137
  Angle     :  0.602   7.654   6061  Z= 0.296
  Chirality :  0.041   0.148    669
  Planarity :  0.004   0.034    773
  Dihedral  :  6.794  54.947    690
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 21.37 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.38), residues: 521
  helix:  2.42 (0.47), residues: 116
  sheet: -0.59 (0.37), residues: 203
  loop : -0.13 (0.45), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  60 
 TYR   0.011   0.001   TYR B 138 
 PHE   0.007   0.001   PHE B 153 
 TRP   0.016   0.001   TRP A 100 
 HIS   0.003   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 4434)
  covalent geometry    : angle       0.60015 ( 6032)
  SS BOND              : bond        0.00279 (    7)
  SS BOND              : angle       0.59276 (   14)
  hydrogen bonds       : bond        0.02879 (  180)
  hydrogen bonds       : angle       4.48843 (  576)
  link_BETA1-4         : bond        0.00352 (    3)
  link_BETA1-4         : angle       1.44455 (    9)
  link_NAG-ASN         : bond        0.00276 (    2)
  link_NAG-ASN         : angle       0.79111 (    6)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8457 (t0) cc_final: 0.8035 (t0)
REVERT: A   88 ARG cc_start: 0.8589 (ttp-170) cc_final: 0.7971 (ttp-170)
REVERT: A  129 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8376 (mtp)
REVERT: B   68 LYS cc_start: 0.8231 (tppt) cc_final: 0.7947 (tppp)
  outliers start: 22
  outliers final: 19
  residues processed: 93
  average time/residue: 0.0739
  time to fit residues: 8.6715
Evaluate side-chains
  106 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   57 TRP
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  129 MET
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain B residue  199 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 46 optimal weight:    0.0050
   chunk 49 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.6594

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.173940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.146661 restraints weight = 5370.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3763 rms_B_bonded: 2.32
r_work: 0.3642 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3483 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4446  Z= 0.125
  Angle     :  0.589   7.684   6061  Z= 0.289
  Chirality :  0.040   0.151    669
  Planarity :  0.004   0.036    773
  Dihedral  :  6.711  54.684    690
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 22.01 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.38), residues: 521
  helix:  2.48 (0.47), residues: 116
  sheet: -0.56 (0.37), residues: 203
  loop : -0.09 (0.46), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  60 
 TYR   0.011   0.001   TYR B 138 
 PHE   0.007   0.001   PHE B 142 
 TRP   0.014   0.001   TRP A 100 
 HIS   0.003   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4434)
  covalent geometry    : angle       0.58690 ( 6032)
  SS BOND              : bond        0.00245 (    7)
  SS BOND              : angle       0.57297 (   14)
  hydrogen bonds       : bond        0.02770 (  180)
  hydrogen bonds       : angle       4.39981 (  576)
  link_BETA1-4         : bond        0.00354 (    3)
  link_BETA1-4         : angle       1.39700 (    9)
  link_NAG-ASN         : bond        0.00214 (    2)
  link_NAG-ASN         : angle       0.72903 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1429.00 seconds
wall clock time: 25 minutes 7.08 seconds (1507.08 seconds total)