Starting phenix.real_space_refine
on Sat May 10 00:44:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bpv_44791/05_2025/9bpv_44791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bpv_44791/05_2025/9bpv_44791.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bpv_44791/05_2025/9bpv_44791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bpv_44791/05_2025/9bpv_44791.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bpv_44791/05_2025/9bpv_44791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bpv_44791/05_2025/9bpv_44791.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      28      5.16       5
     C    2819      2.51       5
     N     749      2.21       5
     O     821      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4417
  Number of models: 1
  Model: ""
    Number of chains: 4
    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: "C"
      Number of atoms: 1206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 1206
          Classifications: {'peptide': 151}
          Link IDs: {'PTRANS': 7, 'TRANS': 143}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 3.35, per 1000 atoms: 0.76
  Number of scatterers: 4417
  At special positions: 0
  Unit cell: (76.68, 91.59, 101.175, 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      28     16.00
     O     821      8.00
     N     749      7.00
     C    2819      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    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=2.03
    Simple disulfide: pdb=" SG  CYS B  66 " - pdb=" SG  CYS B 130 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 175 " - pdb=" SG  CYS B 197 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C   4 " - pdb=" SG  CYS C 103 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  38 " - pdb=" SG  CYS C 136 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 155 " - pdb=" SG  CYS C 162 " 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
    NAG-ASN
      " NAG B 301 " - " ASN B 122 "
      " NAG B 302 " - " ASN B   9 "
  Time building additional restraints: 1.11
  Conformation dependent library (CDL) restraints added in 563.4 milliseconds
  

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1048

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 10 sheets defined
      26.4% alpha, 31.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 106 through 111
      removed outlier: 3.556A  pdb=" N   THR A 111 " --> pdb=" O   PRO A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 149
    Processing helix  chain 'B' and resid 98 through 103
    Processing helix  chain 'C' and resid 5 through 11
      removed outlier: 3.921A  pdb=" N   GLN C   8 " --> pdb=" O   HIS C   5 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   SER C  11 " --> pdb=" O   GLN C   8 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 34
      removed outlier: 4.061A  pdb=" N   LEU C  33 " --> pdb=" O   GLU C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 52
    Processing helix  chain 'C' and resid 55 through 79
      removed outlier: 4.548A  pdb=" N   VAL C  59 " --> pdb=" O   ARG C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 102
      removed outlier: 4.363A  pdb=" N   VAL C  85 " --> pdb=" O   ALA C  81 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   GLN C  88 " --> pdb=" O   ASP C  84 " (cutoff:3.500A)
      Proline residue:  C  89  - end of helix
    Processing helix  chain 'C' and resid 116 through 128
    Processing helix  chain 'C' and resid 133 through 144
    Processing helix  chain 'C' and resid 144 through 151
    Processing helix  chain 'C' and resid 151 through 159
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 32
      removed outlier: 4.311A  pdb=" N   VAL A  27 " --> pdb=" O   GLN A  39 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   GLN A  39 " --> pdb=" O   VAL A  27 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   MET A  29 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
      removed outlier: 5.912A  pdb=" N   ILE A  37 " --> pdb=" O   MET A  29 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   SER A  31 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.058A  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: 5.634A  pdb=" N   GLN A  63 " --> pdb=" O   SER A  58 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   SER A  58 " --> pdb=" O   GLN A  63 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   LYS A  65 " --> pdb=" O   TYR A  56 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   TYR A  56 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
      removed outlier: 5.471A  pdb=" N   MET A  67 " --> pdb=" O   ALA A  54 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   ALA A  54 " --> pdb=" O   MET A  67 " (cutoff:3.500A)
      removed outlier: 4.581A  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: 5.634A  pdb=" N   GLN A  63 " --> pdb=" O   SER A  58 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   SER A  58 " --> pdb=" O   GLN A  63 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   LYS A  65 " --> pdb=" O   TYR A  56 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   TYR A  56 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
      removed outlier: 5.471A  pdb=" N   MET A  67 " --> pdb=" O   ALA A  54 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   ALA A  54 " --> pdb=" O   MET A  67 " (cutoff:3.500A)
      removed outlier: 4.581A  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 'B' and resid 11 through 15
    Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 41
    Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 115
    Processing sheet with id=AA9, first strand: chain 'B' and resid 150 through 152
    Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 152

    191 hydrogen bonds defined for protein.
    504 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.08

  Time building geometry restraints manager: 1.31 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: 1380
        1.34 -     1.46: 773
        1.46 -     1.58: 2343
        1.58 -     1.70: 0
        1.70 -     1.82: 38
  Bond restraints: 4534
  Sorted by residual:
  bond pdb=" N   PHE C  43 "
       pdb=" CA  PHE C  43 "
    ideal  model  delta    sigma   weight residual
    1.462  1.494 -0.032 8.50e-03 1.38e+04 1.45e+01
  bond pdb=" N   VAL A 191 "
       pdb=" CA  VAL A 191 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.037 1.14e-02 7.69e+03 1.08e+01
  bond pdb=" N   VAL A  89 "
       pdb=" CA  VAL A  89 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 1.14e-02 7.69e+03 1.04e+01
  bond pdb=" N   VAL C  59 "
       pdb=" CA  VAL C  59 "
    ideal  model  delta    sigma   weight residual
    1.460  1.498 -0.038 1.21e-02 6.83e+03 9.85e+00
  bond pdb=" N   ILE B 118 "
       pdb=" CA  ILE B 118 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.25e-02 6.40e+03 9.75e+00
  ... (remaining 4529 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 5594
        1.64 -     3.28: 520
        3.28 -     4.92: 45
        4.92 -     6.56: 3
        6.56 -     8.20: 4
  Bond angle restraints: 6166
  Sorted by residual:
  angle pdb=" N   LYS B  58 "
        pdb=" CA  LYS B  58 "
        pdb=" C   LYS B  58 "
      ideal   model   delta    sigma   weight residual
     113.97  105.77    8.20 1.28e+00 6.10e-01 4.11e+01
  angle pdb=" C   GLU B 116 "
        pdb=" N   GLU B 117 "
        pdb=" CA  GLU B 117 "
      ideal   model   delta    sigma   weight residual
     122.08  127.61   -5.53 1.47e+00 4.63e-01 1.41e+01
  angle pdb=" CA  GLY A 193 "
        pdb=" C   GLY A 193 "
        pdb=" O   GLY A 193 "
      ideal   model   delta    sigma   weight residual
     121.18  117.99    3.19 8.80e-01 1.29e+00 1.31e+01
  angle pdb=" N   LEU B  60 "
        pdb=" CA  LEU B  60 "
        pdb=" C   LEU B  60 "
      ideal   model   delta    sigma   weight residual
     113.19  108.99    4.20 1.19e+00 7.06e-01 1.24e+01
  angle pdb=" CA  THR B  57 "
        pdb=" CB  THR B  57 "
        pdb=" OG1 THR B  57 "
      ideal   model   delta    sigma   weight residual
     109.60  104.67    4.93 1.50e+00 4.44e-01 1.08e+01
  ... (remaining 6161 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 2437
       17.14 -    34.29: 248
       34.29 -    51.43: 70
       51.43 -    68.58: 33
       68.58 -    85.72: 6
  Dihedral angle restraints: 2794
    sinusoidal: 1189
      harmonic: 1605
  Sorted by residual:
  dihedral pdb=" CB  CYS B 175 "
           pdb=" SG  CYS B 175 "
           pdb=" SG  CYS B 197 "
           pdb=" CB  CYS B 197 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   57.98   35.02     1      1.00e+01 1.00e-02 1.74e+01
  dihedral pdb=" CB  CYS B  66 "
           pdb=" SG  CYS B  66 "
           pdb=" SG  CYS B 130 "
           pdb=" CB  CYS B 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  124.92  -31.92     1      1.00e+01 1.00e-02 1.45e+01
  dihedral pdb=" CB  CYS C  38 "
           pdb=" SG  CYS C  38 "
           pdb=" SG  CYS C 136 "
           pdb=" CB  CYS C 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.68   31.68     1      1.00e+01 1.00e-02 1.43e+01
  ... (remaining 2791 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.129: 654
       0.129 -    0.258: 29
       0.258 -    0.387: 0
       0.387 -    0.516: 0
       0.516 -    0.645: 1
  Chirality restraints: 684
  Sorted by residual:
  chirality pdb=" CG  LEU C  42 "
            pdb=" CB  LEU C  42 "
            pdb=" CD1 LEU C  42 "
            pdb=" CD2 LEU C  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.94   -0.65 2.00e-01 2.50e+01 1.04e+01
  chirality pdb=" CA  ARG A  28 "
            pdb=" N   ARG A  28 "
            pdb=" C   ARG A  28 "
            pdb=" CB  ARG A  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  ILE C  96 "
            pdb=" N   ILE C  96 "
            pdb=" C   ILE C  96 "
            pdb=" CB  ILE C  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.41e-01
  ... (remaining 681 not shown)

  Planarity restraints: 792
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  39 "    0.234 9.50e-02 1.11e+02   1.05e-01 6.76e+00
        pdb=" NE  ARG C  39 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  39 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  39 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  39 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 151 "   -0.229 9.50e-02 1.11e+02   1.03e-01 6.47e+00
        pdb=" NE  ARG C 151 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 151 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 151 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 151 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  88 "    0.214 9.50e-02 1.11e+02   9.59e-02 5.63e+00
        pdb=" NE  ARG A  88 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  88 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  88 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  88 "    0.008 2.00e-02 2.50e+03
  ... (remaining 789 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 334
        2.74 -     3.28: 4160
        3.28 -     3.82: 7244
        3.82 -     4.36: 8868
        4.36 -     4.90: 15059
  Nonbonded interactions: 35665
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  39 "
            pdb=" O   LYS B  68 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OD2 ASP B  71 "
            pdb=" NH1 ARG C 147 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" NH2 ARG A 130 "
            pdb=" O   GLN B 163 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" O   VAL A 108 "
            pdb=" OH  TYR A 149 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OH  TYR B 125 "
            pdb=" OG1 THR B 180 "
     model   vdw
     2.293 3.040
  ... (remaining 35660 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:             0.620
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.560
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:11.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
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   0.039   4544  Z= 0.513
  Angle     :  0.933   8.912   6188  Z= 0.648
  Chirality :  0.063   0.645    684
  Planarity :  0.009   0.105    790
  Dihedral  : 16.577  85.720   1722
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 20.33 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.37), residues: 534
  helix:  1.47 (0.50), residues: 117
  sheet:  0.83 (0.39), residues: 181
  loop : -0.41 (0.40), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  91 
 HIS   0.006   0.001   HIS C  95 
 PHE   0.006   0.001   PHE C  43 
 TYR   0.009   0.001   TYR A  59 
 ARG   0.005   0.001   ARG C  22 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00748 (    2)
  link_NAG-ASN         : angle       4.53958 (    6)
  hydrogen bonds       : bond        0.15483 (  180)
  hydrogen bonds       : angle       6.07637 (  504)
  SS BOND              : bond        0.00540 (    8)
  SS BOND              : angle       1.08592 (   16)
  covalent geometry    : bond        0.00699 ( 4534)
  covalent geometry    : angle       0.92215 ( 6166)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A  160 LYS cc_start: 0.8039 (tttt) cc_final: 0.7760 (ttmt)
REVERT: A  182 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7729 (mp0)
REVERT: B  117 GLU cc_start: 0.6923 (pt0) cc_final: 0.6610 (pt0)
REVERT: B  172 GLU cc_start: 0.5330 (mt-10) cc_final: 0.4660 (tt0)
REVERT: B  191 LYS cc_start: 0.8053 (pttp) cc_final: 0.7798 (pttp)
REVERT: C   64 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7354 (mt-10)
  outliers start: 3
  outliers final: 2
  residues processed: 87
  average time/residue: 1.1229
  time to fit residues: 101.3715
Evaluate side-chains
  74 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain C residue   42 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 149 ASN
C 126 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.145086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.118464 restraints weight = 5037.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.17
r_work: 0.3155 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.1145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4544  Z= 0.143
  Angle     :  0.630  12.718   6188  Z= 0.301
  Chirality :  0.042   0.175    684
  Planarity :  0.005   0.046    790
  Dihedral  :  5.210  47.995    632
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 19.51 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.37), residues: 534
  helix:  1.46 (0.48), residues: 131
  sheet:  0.85 (0.38), residues: 181
  loop : -0.28 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A  97 
 PHE   0.030   0.002   PHE C  43 
 TYR   0.012   0.001   TYR B  20 
 ARG   0.007   0.001   ARG C 147 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00414 (    2)
  link_NAG-ASN         : angle       6.57954 (    6)
  hydrogen bonds       : bond        0.04333 (  180)
  hydrogen bonds       : angle       4.56178 (  504)
  SS BOND              : bond        0.00446 (    8)
  SS BOND              : angle       0.86317 (   16)
  covalent geometry    : bond        0.00331 ( 4534)
  covalent geometry    : angle       0.59507 ( 6166)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 GLU cc_start: 0.8201 (tt0) cc_final: 0.7804 (pt0)
REVERT: A  123 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7871 (tp)
REVERT: A  160 LYS cc_start: 0.8269 (tttt) cc_final: 0.7927 (ttmp)
REVERT: A  182 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7961 (mp0)
REVERT: B  117 GLU cc_start: 0.7264 (pt0) cc_final: 0.7001 (mm-30)
REVERT: B  172 GLU cc_start: 0.5471 (mt-10) cc_final: 0.4866 (tt0)
REVERT: B  191 LYS cc_start: 0.8768 (pttp) cc_final: 0.8535 (pttp)
REVERT: C   64 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8153 (mt-10)
  outliers start: 14
  outliers final: 6
  residues processed: 80
  average time/residue: 0.9870
  time to fit residues: 82.4107
Evaluate side-chains
  75 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  130 CYS
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue  123 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0000
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.6584

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

Flipped N/Q/H residues before XYZ refinement:
A  30 ASN
A  97 HIS
** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 149 ASN
C 126 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.149197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.124817 restraints weight = 5045.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.98
r_work: 0.3198 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4544  Z= 0.128
  Angle     :  0.575  10.409   6188  Z= 0.278
  Chirality :  0.041   0.172    684
  Planarity :  0.004   0.036    790
  Dihedral  :  4.166  16.632    630
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 19.11 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.37), residues: 534
  helix:  1.44 (0.48), residues: 131
  sheet:  0.90 (0.39), residues: 179
  loop : -0.29 (0.41), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 100 
 HIS   0.003   0.000   HIS A  97 
 PHE   0.009   0.001   PHE B 142 
 TYR   0.007   0.001   TYR A 140 
 ARG   0.004   0.000   ARG C 147 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00285 (    2)
  link_NAG-ASN         : angle       4.41718 (    6)
  hydrogen bonds       : bond        0.03765 (  180)
  hydrogen bonds       : angle       4.23730 (  504)
  SS BOND              : bond        0.00404 (    8)
  SS BOND              : angle       0.84509 (   16)
  covalent geometry    : bond        0.00297 ( 4534)
  covalent geometry    : angle       0.55739 ( 6166)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7903 (tp)
REVERT: A  160 LYS cc_start: 0.8304 (tttt) cc_final: 0.8004 (ttmp)
REVERT: A  182 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8032 (mp0)
REVERT: A  206 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7798 (tm-30)
REVERT: B  117 GLU cc_start: 0.7250 (pt0) cc_final: 0.7047 (mm-30)
REVERT: B  138 TYR cc_start: 0.8903 (p90) cc_final: 0.8596 (p90)
REVERT: B  166 LEU cc_start: 0.8852 (mt) cc_final: 0.8543 (mp)
REVERT: B  172 GLU cc_start: 0.5594 (mt-10) cc_final: 0.5108 (tt0)
REVERT: B  191 LYS cc_start: 0.8754 (pttp) cc_final: 0.8528 (pttp)
REVERT: C   43 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.5427 (t80)
REVERT: C   64 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8200 (mt-10)
  outliers start: 16
  outliers final: 7
  residues processed: 81
  average time/residue: 1.1717
  time to fit residues: 98.6590
Evaluate side-chains
  75 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  130 CYS
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   43 PHE
Chi-restraints excluded: chain C residue  123 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 41 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 149 ASN
B 160 GLN
C 126 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.147978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.122555 restraints weight = 5028.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 2.07
r_work: 0.3074 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2927 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.1736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4544  Z= 0.138
  Angle     :  0.568  10.426   6188  Z= 0.276
  Chirality :  0.041   0.167    684
  Planarity :  0.004   0.035    790
  Dihedral  :  4.121  16.543    630
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 20.12 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.37), residues: 534
  helix:  1.63 (0.48), residues: 124
  sheet:  0.91 (0.39), residues: 181
  loop : -0.27 (0.42), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A  97 
 PHE   0.009   0.001   PHE C  43 
 TYR   0.012   0.001   TYR B  20 
 ARG   0.004   0.000   ARG C 147 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00259 (    2)
  link_NAG-ASN         : angle       3.71612 (    6)
  hydrogen bonds       : bond        0.03637 (  180)
  hydrogen bonds       : angle       4.15076 (  504)
  SS BOND              : bond        0.00418 (    8)
  SS BOND              : angle       0.90464 (   16)
  covalent geometry    : bond        0.00323 ( 4534)
  covalent geometry    : angle       0.55486 ( 6166)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7832 (tp)
REVERT: A  160 LYS cc_start: 0.8307 (tttt) cc_final: 0.7979 (ttmp)
REVERT: A  182 GLU cc_start: 0.8510 (mt-10) cc_final: 0.7968 (mp0)
REVERT: B  117 GLU cc_start: 0.7307 (pt0) cc_final: 0.7052 (mm-30)
REVERT: B  166 LEU cc_start: 0.8830 (mt) cc_final: 0.8450 (mp)
REVERT: B  191 LYS cc_start: 0.8724 (pttp) cc_final: 0.8171 (mmmt)
REVERT: C   43 PHE cc_start: 0.6795 (OUTLIER) cc_final: 0.5455 (t80)
REVERT: C   64 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8197 (mt-10)
  outliers start: 16
  outliers final: 8
  residues processed: 78
  average time/residue: 1.1224
  time to fit residues: 91.1220
Evaluate side-chains
  76 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  130 CYS
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   43 PHE
Chi-restraints excluded: chain C residue  123 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 51 optimal weight:    0.3980
   chunk 27 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 18 optimal weight:    0.3980
   chunk 2 optimal weight:    4.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
A 157 GLN
B 149 ASN
C 126 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.140002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.113575 restraints weight = 5121.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.16
r_work: 0.3148 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4544  Z= 0.176
  Angle     :  0.606  11.037   6188  Z= 0.299
  Chirality :  0.043   0.219    684
  Planarity :  0.004   0.033    790
  Dihedral  :  4.282  15.199    630
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 21.75 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.37), residues: 534
  helix:  1.44 (0.48), residues: 124
  sheet:  0.80 (0.38), residues: 183
  loop : -0.41 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 100 
 HIS   0.004   0.001   HIS A  97 
 PHE   0.011   0.002   PHE C  43 
 TYR   0.013   0.001   TYR B  20 
 ARG   0.006   0.001   ARG C 147 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00323 (    2)
  link_NAG-ASN         : angle       3.60503 (    6)
  hydrogen bonds       : bond        0.03879 (  180)
  hydrogen bonds       : angle       4.22172 (  504)
  SS BOND              : bond        0.00452 (    8)
  SS BOND              : angle       1.08933 (   16)
  covalent geometry    : bond        0.00418 ( 4534)
  covalent geometry    : angle       0.59412 ( 6166)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 LYS cc_start: 0.8723 (ttpp) cc_final: 0.8413 (tttt)
REVERT: A  160 LYS cc_start: 0.8316 (tttt) cc_final: 0.7967 (ttmp)
REVERT: A  182 GLU cc_start: 0.8556 (mt-10) cc_final: 0.7991 (mp0)
REVERT: A  206 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7790 (tm-30)
REVERT: B  166 LEU cc_start: 0.8847 (mt) cc_final: 0.8485 (mp)
REVERT: B  191 LYS cc_start: 0.8757 (pttp) cc_final: 0.8147 (mmmt)
REVERT: C   43 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.5370 (t80)
REVERT: C   64 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8195 (mt-10)
  outliers start: 18
  outliers final: 8
  residues processed: 81
  average time/residue: 1.0921
  time to fit residues: 92.1852
Evaluate side-chains
  75 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   65 MET
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  130 CYS
Chi-restraints excluded: chain C residue   43 PHE
Chi-restraints excluded: chain C residue  123 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0980
   chunk 50 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 6 optimal weight:    0.4980
   chunk 8 optimal weight:    0.0980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
B 149 ASN
C 126 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.144056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.119104 restraints weight = 5014.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 2.05
r_work: 0.3085 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2936 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4544  Z= 0.108
  Angle     :  0.547   6.033   6188  Z= 0.271
  Chirality :  0.041   0.181    684
  Planarity :  0.004   0.029    790
  Dihedral  :  4.059  15.304    628
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 23.17 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.37), residues: 534
  helix:  1.81 (0.49), residues: 120
  sheet:  0.97 (0.39), residues: 175
  loop : -0.36 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 100 
 HIS   0.004   0.001   HIS A  97 
 PHE   0.010   0.001   PHE C  43 
 TYR   0.014   0.001   TYR B  20 
 ARG   0.004   0.000   ARG C 147 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00158 (    2)
  link_NAG-ASN         : angle       3.17253 (    6)
  hydrogen bonds       : bond        0.03389 (  180)
  hydrogen bonds       : angle       4.06699 (  504)
  SS BOND              : bond        0.00293 (    8)
  SS BOND              : angle       0.82426 (   16)
  covalent geometry    : bond        0.00249 ( 4534)
  covalent geometry    : angle       0.53692 ( 6166)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LYS cc_start: 0.8356 (tttt) cc_final: 0.8028 (ttmp)
REVERT: A  182 GLU cc_start: 0.8523 (mt-10) cc_final: 0.7958 (mp0)
REVERT: A  206 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7749 (tm-30)
REVERT: B   65 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7603 (tpt)
REVERT: B  166 LEU cc_start: 0.8809 (mt) cc_final: 0.8460 (mp)
REVERT: B  191 LYS cc_start: 0.8756 (pttp) cc_final: 0.8184 (mmmt)
REVERT: C   43 PHE cc_start: 0.6694 (OUTLIER) cc_final: 0.5266 (t80)
REVERT: C   64 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8135 (mt-10)
  outliers start: 11
  outliers final: 5
  residues processed: 78
  average time/residue: 1.1143
  time to fit residues: 90.6142
Evaluate side-chains
  77 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   65 MET
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  130 CYS
Chi-restraints excluded: chain C residue   43 PHE
Chi-restraints excluded: chain C residue  123 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0570
   chunk 40 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
C 126 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.146249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.121038 restraints weight = 5004.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.06
r_work: 0.3104 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4544  Z= 0.123
  Angle     :  0.559   6.835   6188  Z= 0.275
  Chirality :  0.041   0.158    684
  Planarity :  0.004   0.028    790
  Dihedral  :  4.045  15.213    628
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 23.37 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.37), residues: 534
  helix:  1.86 (0.49), residues: 120
  sheet:  0.95 (0.39), residues: 175
  loop : -0.35 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A  97 
 PHE   0.009   0.001   PHE C  43 
 TYR   0.015   0.001   TYR B  20 
 ARG   0.003   0.000   ARG C 147 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00168 (    2)
  link_NAG-ASN         : angle       3.00523 (    6)
  hydrogen bonds       : bond        0.03426 (  180)
  hydrogen bonds       : angle       4.04209 (  504)
  SS BOND              : bond        0.00308 (    8)
  SS BOND              : angle       0.87656 (   16)
  covalent geometry    : bond        0.00287 ( 4534)
  covalent geometry    : angle       0.54986 ( 6166)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LYS cc_start: 0.8336 (tttt) cc_final: 0.8029 (ttmp)
REVERT: A  182 GLU cc_start: 0.8495 (mt-10) cc_final: 0.7967 (mp0)
REVERT: A  206 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7778 (tm-30)
REVERT: B  138 TYR cc_start: 0.9016 (p90) cc_final: 0.8795 (p90)
REVERT: B  166 LEU cc_start: 0.8818 (mt) cc_final: 0.8475 (mp)
REVERT: B  191 LYS cc_start: 0.8727 (pttp) cc_final: 0.8196 (mmmt)
REVERT: C   43 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.5387 (t80)
REVERT: C   64 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8095 (mt-10)
  outliers start: 12
  outliers final: 7
  residues processed: 82
  average time/residue: 1.2801
  time to fit residues: 109.4159
Evaluate side-chains
  78 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  130 CYS
Chi-restraints excluded: chain C residue   43 PHE
Chi-restraints excluded: chain C residue  123 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    0.3980
   chunk 14 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 31 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
C 126 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.145811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.121356 restraints weight = 5030.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.00
r_work: 0.3127 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4544  Z= 0.123
  Angle     :  0.551   6.589   6188  Z= 0.272
  Chirality :  0.041   0.145    684
  Planarity :  0.004   0.028    790
  Dihedral  :  4.065  16.954    628
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 23.58 %
    Favored  : 73.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.37), residues: 534
  helix:  1.87 (0.50), residues: 120
  sheet:  0.94 (0.38), residues: 175
  loop : -0.34 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A  97 
 PHE   0.010   0.001   PHE C  43 
 TYR   0.014   0.001   TYR B  20 
 ARG   0.004   0.000   ARG C 147 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00139 (    2)
  link_NAG-ASN         : angle       2.81321 (    6)
  hydrogen bonds       : bond        0.03401 (  180)
  hydrogen bonds       : angle       4.00865 (  504)
  SS BOND              : bond        0.00301 (    8)
  SS BOND              : angle       0.87162 (   16)
  covalent geometry    : bond        0.00288 ( 4534)
  covalent geometry    : angle       0.54335 ( 6166)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 LYS cc_start: 0.8749 (ttpp) cc_final: 0.8421 (tttt)
REVERT: A  160 LYS cc_start: 0.8343 (tttt) cc_final: 0.8032 (ttmp)
REVERT: A  182 GLU cc_start: 0.8498 (mt-10) cc_final: 0.7974 (mp0)
REVERT: B   59 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7498 (tt0)
REVERT: B  138 TYR cc_start: 0.8988 (p90) cc_final: 0.8760 (p90)
REVERT: B  166 LEU cc_start: 0.8828 (mt) cc_final: 0.8478 (mp)
REVERT: B  191 LYS cc_start: 0.8730 (pttp) cc_final: 0.8199 (mmmt)
REVERT: C   43 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.5404 (t80)
REVERT: C   64 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8094 (mt-10)
  outliers start: 12
  outliers final: 7
  residues processed: 78
  average time/residue: 1.1067
  time to fit residues: 89.8136
Evaluate side-chains
  78 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  199 ASN
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  130 CYS
Chi-restraints excluded: chain C residue   43 PHE
Chi-restraints excluded: chain C residue  123 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 35 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 5 optimal weight:    0.4980
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
C 126 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.145618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.120374 restraints weight = 5020.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 2.05
r_work: 0.3059 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4544  Z= 0.153
  Angle     :  0.582   7.862   6188  Z= 0.287
  Chirality :  0.042   0.162    684
  Planarity :  0.004   0.028    790
  Dihedral  :  4.181  15.786    628
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 23.58 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.37), residues: 534
  helix:  1.76 (0.49), residues: 120
  sheet:  0.82 (0.38), residues: 175
  loop : -0.36 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 100 
 HIS   0.003   0.001   HIS A  97 
 PHE   0.012   0.001   PHE C  43 
 TYR   0.015   0.001   TYR B  20 
 ARG   0.004   0.000   ARG C 147 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00208 (    2)
  link_NAG-ASN         : angle       2.76214 (    6)
  hydrogen bonds       : bond        0.03649 (  180)
  hydrogen bonds       : angle       4.13079 (  504)
  SS BOND              : bond        0.00335 (    8)
  SS BOND              : angle       1.01535 (   16)
  covalent geometry    : bond        0.00366 ( 4534)
  covalent geometry    : angle       0.57381 ( 6166)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 LYS cc_start: 0.8800 (ttpp) cc_final: 0.8487 (tttt)
REVERT: A  160 LYS cc_start: 0.8260 (tttt) cc_final: 0.7938 (ttmp)
REVERT: A  182 GLU cc_start: 0.8505 (mt-10) cc_final: 0.7924 (mp0)
REVERT: A  206 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7800 (tm-30)
REVERT: B   59 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7549 (tt0)
REVERT: B  166 LEU cc_start: 0.8818 (mt) cc_final: 0.8461 (mp)
REVERT: B  191 LYS cc_start: 0.8729 (pttp) cc_final: 0.8192 (mmmt)
REVERT: C   43 PHE cc_start: 0.7075 (OUTLIER) cc_final: 0.5774 (t80)
REVERT: C   64 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8172 (mt-10)
  outliers start: 13
  outliers final: 6
  residues processed: 69
  average time/residue: 1.1475
  time to fit residues: 82.3996
Evaluate side-chains
  67 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  130 CYS
Chi-restraints excluded: chain C residue   43 PHE
Chi-restraints excluded: chain C residue  123 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 29 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 17 optimal weight:    0.4980
   chunk 27 optimal weight:    1.9990
   chunk 38 optimal weight:    0.3980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
C 126 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.147028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.121801 restraints weight = 4976.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 2.06
r_work: 0.3156 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4544  Z= 0.122
  Angle     :  0.556   7.882   6188  Z= 0.274
  Chirality :  0.041   0.145    684
  Planarity :  0.004   0.028    790
  Dihedral  :  4.096  14.835    628
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 24.39 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.37), residues: 534
  helix:  1.83 (0.50), residues: 120
  sheet:  0.85 (0.38), residues: 173
  loop : -0.34 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 100 
 HIS   0.004   0.001   HIS A  97 
 PHE   0.009   0.001   PHE C  43 
 TYR   0.016   0.001   TYR B  20 
 ARG   0.004   0.000   ARG C 147 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00159 (    2)
  link_NAG-ASN         : angle       2.49727 (    6)
  hydrogen bonds       : bond        0.03393 (  180)
  hydrogen bonds       : angle       4.07648 (  504)
  SS BOND              : bond        0.00296 (    8)
  SS BOND              : angle       0.94009 (   16)
  covalent geometry    : bond        0.00287 ( 4534)
  covalent geometry    : angle       0.54950 ( 6166)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 LYS cc_start: 0.8780 (ttpp) cc_final: 0.8453 (tttt)
REVERT: A  160 LYS cc_start: 0.8333 (tttt) cc_final: 0.8011 (ttmp)
REVERT: A  182 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7944 (mp0)
REVERT: A  206 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7797 (tm-30)
REVERT: B   59 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7578 (tt0)
REVERT: B  166 LEU cc_start: 0.8811 (mt) cc_final: 0.8451 (mp)
REVERT: B  191 LYS cc_start: 0.8722 (pttp) cc_final: 0.8174 (mmmt)
REVERT: C   43 PHE cc_start: 0.6948 (OUTLIER) cc_final: 0.5601 (t80)
REVERT: C   64 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8018 (mt-10)
  outliers start: 9
  outliers final: 6
  residues processed: 69
  average time/residue: 1.0987
  time to fit residues: 78.9843
Evaluate side-chains
  71 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  130 CYS
Chi-restraints excluded: chain C residue   43 PHE
Chi-restraints excluded: chain C residue  123 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 29 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
C 126 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.145168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.119917 restraints weight = 5011.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.07
r_work: 0.3094 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4544  Z= 0.138
  Angle     :  0.569   8.057   6188  Z= 0.280
  Chirality :  0.041   0.151    684
  Planarity :  0.004   0.029    790
  Dihedral  :  4.142  16.006    628
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 23.98 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.37), residues: 534
  helix:  1.81 (0.50), residues: 120
  sheet:  0.84 (0.38), residues: 173
  loop : -0.35 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 100 
 HIS   0.004   0.001   HIS A  97 
 PHE   0.011   0.001   PHE C  43 
 TYR   0.015   0.001   TYR B  20 
 ARG   0.004   0.000   ARG C 147 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00161 (    2)
  link_NAG-ASN         : angle       2.49015 (    6)
  hydrogen bonds       : bond        0.03507 (  180)
  hydrogen bonds       : angle       4.10438 (  504)
  SS BOND              : bond        0.00309 (    8)
  SS BOND              : angle       1.02443 (   16)
  covalent geometry    : bond        0.00330 ( 4534)
  covalent geometry    : angle       0.56212 ( 6166)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3454.07 seconds
wall clock time: 60 minutes 18.17 seconds (3618.17 seconds total)