Starting phenix.real_space_refine
on Wed Sep 17 04:44:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bpv_44791/09_2025/9bpv_44791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bpv_44791/09_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_44791/09_2025/9bpv_44791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bpv_44791/09_2025/9bpv_44791.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bpv_44791/09_2025/9bpv_44791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bpv_44791/09_2025/9bpv_44791.cif"
  }
  resolution = 3.0
  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=   0.003
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): 0.01s

  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: 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: 1.29, per 1000 atoms: 0.29
  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: 0.36
  Conformation dependent library (CDL) restraints added in 176.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.17
  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: 0.68

  Time building geometry restraints manager: 0.50 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:             0.950
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.370
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.360
-------------------------------------------------------------------------------
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 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:  0.62 (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
 ARG   0.005   0.001   ARG C  22 
 TYR   0.009   0.001   TYR A  59 
 PHE   0.006   0.001   PHE C  43 
 TRP   0.009   0.001   TRP B  91 
 HIS   0.006   0.001   HIS C  95 

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

*********************** 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  : 0.135 
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: 0.5990
  time to fit residues: 53.8939
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  : 0.171 
-------------------------------------------------------------------------------
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 24 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.3649 r_free = 0.3649 target = 0.150428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.125525 restraints weight = 5015.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 1.99
r_work: 0.3173 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3026 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.1252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4544  Z= 0.167
  Angle     :  0.641  11.256   6188  Z= 0.309
  Chirality :  0.043   0.200    684
  Planarity :  0.005   0.046    790
  Dihedral  :  5.202  44.934    632
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  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 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:  0.77 (0.37), residues: 534
  helix:  1.62 (0.49), residues: 124
  sheet:  0.90 (0.39), residues: 176
  loop : -0.36 (0.40), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 147 
 TYR   0.012   0.001   TYR B  20 
 PHE   0.030   0.002   PHE C  43 
 TRP   0.011   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 4534)
  covalent geometry    : angle       0.60908 ( 6166)
  SS BOND              : bond        0.00515 (    8)
  SS BOND              : angle       0.97493 (   16)
  hydrogen bonds       : bond        0.04383 (  180)
  hydrogen bonds       : angle       4.59276 (  504)
  link_NAG-ASN         : bond        0.00447 (    2)
  link_NAG-ASN         : angle       6.34042 (    6)

*********************** 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
  88 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7942 (tp)
REVERT: A  160 LYS cc_start: 0.8284 (tttt) cc_final: 0.7959 (ttmp)
REVERT: A  182 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8004 (mp0)
REVERT: B  117 GLU cc_start: 0.7242 (pt0) cc_final: 0.7039 (mm-30)
REVERT: B  172 GLU cc_start: 0.5538 (mt-10) cc_final: 0.4886 (tt0)
REVERT: B  191 LYS cc_start: 0.8766 (pttp) cc_final: 0.8215 (mmmt)
REVERT: C   64 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8207 (mt-10)
  outliers start: 16
  outliers final: 6
  residues processed: 83
  average time/residue: 0.5535
  time to fit residues: 47.6531
Evaluate side-chains
  76 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
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 19 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3526 r_free = 0.3526 target = 0.140381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.114235 restraints weight = 5124.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 2.14
r_work: 0.3160 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3014 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4544  Z= 0.172
  Angle     :  0.617  10.896   6188  Z= 0.301
  Chirality :  0.043   0.174    684
  Planarity :  0.005   0.037    790
  Dihedral  :  4.335  15.937    630
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 19.92 %
    Favored  : 76.42 %
  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:  0.58 (0.37), residues: 534
  helix:  1.26 (0.47), residues: 131
  sheet:  0.73 (0.38), residues: 181
  loop : -0.36 (0.42), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  88 
 TYR   0.009   0.001   TYR A 140 
 PHE   0.011   0.002   PHE B 142 
 TRP   0.013   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 4534)
  covalent geometry    : angle       0.60016 ( 6166)
  SS BOND              : bond        0.00510 (    8)
  SS BOND              : angle       1.05823 (   16)
  hydrogen bonds       : bond        0.04082 (  180)
  hydrogen bonds       : angle       4.34821 (  504)
  link_NAG-ASN         : bond        0.00362 (    2)
  link_NAG-ASN         : angle       4.45082 (    6)

*********************** 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
  82 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LYS cc_start: 0.8300 (tttt) cc_final: 0.7970 (ttmp)
REVERT: A  182 GLU cc_start: 0.8526 (mt-10) cc_final: 0.7986 (mp0)
REVERT: A  206 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7816 (tm-30)
REVERT: B   59 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7056 (tp30)
REVERT: B  117 GLU cc_start: 0.7354 (pt0) cc_final: 0.7050 (mm-30)
REVERT: B  166 LEU cc_start: 0.8863 (mt) cc_final: 0.8491 (mp)
REVERT: B  172 GLU cc_start: 0.5642 (mt-10) cc_final: 0.5076 (tt0)
REVERT: B  191 LYS cc_start: 0.8757 (pttp) cc_final: 0.8174 (mmmt)
REVERT: C   43 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.5622 (t80)
REVERT: C   64 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8261 (mt-10)
  outliers start: 18
  outliers final: 8
  residues processed: 76
  average time/residue: 0.5518
  time to fit residues: 43.5037
Evaluate side-chains
  74 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  199 ASN
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   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 24 optimal weight:    4.9990
   chunk 23 optimal weight:    0.0270
   chunk 46 optimal weight:    0.0870
   chunk 38 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.4416

-------------------------------------------------------------------------------
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 = 0.3553 r_free = 0.3553 target = 0.142574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.116925 restraints weight = 5031.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.11
r_work: 0.3200 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4544  Z= 0.110
  Angle     :  0.556  10.657   6188  Z= 0.271
  Chirality :  0.041   0.227    684
  Planarity :  0.004   0.033    790
  Dihedral  :  4.113  16.023    630
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 20.33 %
    Favored  : 76.42 %
  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:  0.80 (0.37), residues: 534
  helix:  1.63 (0.48), residues: 124
  sheet:  0.85 (0.39), residues: 179
  loop : -0.27 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 147 
 TYR   0.013   0.001   TYR B  20 
 PHE   0.008   0.001   PHE B 142 
 TRP   0.015   0.001   TRP A 100 
 HIS   0.003   0.000   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 4534)
  covalent geometry    : angle       0.54251 ( 6166)
  SS BOND              : bond        0.00313 (    8)
  SS BOND              : angle       0.80579 (   16)
  hydrogen bonds       : bond        0.03462 (  180)
  hydrogen bonds       : angle       4.12127 (  504)
  link_NAG-ASN         : bond        0.00207 (    2)
  link_NAG-ASN         : angle       3.80555 (    6)

*********************** 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
  90 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LYS cc_start: 0.8321 (tttt) cc_final: 0.8002 (ttmp)
REVERT: A  182 GLU cc_start: 0.8501 (mt-10) cc_final: 0.7963 (mp0)
REVERT: B  117 GLU cc_start: 0.7348 (pt0) cc_final: 0.7022 (mm-30)
REVERT: B  166 LEU cc_start: 0.8815 (mt) cc_final: 0.8449 (mp)
REVERT: B  191 LYS cc_start: 0.8743 (pttp) cc_final: 0.8178 (mmmt)
REVERT: C   43 PHE cc_start: 0.6687 (OUTLIER) cc_final: 0.5367 (t80)
REVERT: C   64 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8138 (mt-10)
  outliers start: 16
  outliers final: 8
  residues processed: 85
  average time/residue: 0.5461
  time to fit residues: 48.1424
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  : 0.185 
-------------------------------------------------------------------------------
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   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 21 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 17 optimal weight:    0.2980
   overall best weight:    0.8386

-------------------------------------------------------------------------------
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 = 0.3602 r_free = 0.3602 target = 0.146785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.121613 restraints weight = 5071.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 2.08
r_work: 0.3073 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2061

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= 0.145
  Angle     :  0.587  10.919   6188  Z= 0.287
  Chirality :  0.042   0.177    684
  Planarity :  0.004   0.036    790
  Dihedral  :  4.178  14.716    630
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 21.54 %
    Favored  : 74.39 %
  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:  0.77 (0.37), residues: 534
  helix:  1.57 (0.48), residues: 124
  sheet:  0.80 (0.39), residues: 181
  loop : -0.26 (0.42), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 147 
 TYR   0.013   0.001   TYR B  20 
 PHE   0.009   0.001   PHE C  43 
 TRP   0.009   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 4534)
  covalent geometry    : angle       0.57479 ( 6166)
  SS BOND              : bond        0.00401 (    8)
  SS BOND              : angle       0.94054 (   16)
  hydrogen bonds       : bond        0.03616 (  180)
  hydrogen bonds       : angle       4.14311 (  504)
  link_NAG-ASN         : bond        0.00249 (    2)
  link_NAG-ASN         : angle       3.67375 (    6)

*********************** 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
  89 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 MET cc_start: 0.9042 (tpt) cc_final: 0.8830 (tpt)
REVERT: A  160 LYS cc_start: 0.8343 (tttt) cc_final: 0.8006 (ttmp)
REVERT: A  165 GLU cc_start: 0.8016 (tp30) cc_final: 0.7804 (tp30)
REVERT: A  182 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7964 (mp0)
REVERT: A  206 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7778 (tm-30)
REVERT: B   68 LYS cc_start: 0.8268 (mmpt) cc_final: 0.7861 (mmpt)
REVERT: B  138 TYR cc_start: 0.8981 (p90) cc_final: 0.8758 (p90)
REVERT: B  166 LEU cc_start: 0.8825 (mt) cc_final: 0.8477 (mp)
REVERT: B  191 LYS cc_start: 0.8769 (pttp) cc_final: 0.8205 (mmmt)
REVERT: C   43 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.5466 (t80)
REVERT: C   64 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8148 (mt-10)
  outliers start: 20
  outliers final: 10
  residues processed: 84
  average time/residue: 0.5424
  time to fit residues: 47.2128
Evaluate side-chains
  81 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  141 GLU
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   42 LEU
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 23 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0370
   overall best weight:    0.6858

-------------------------------------------------------------------------------
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 = 0.3600 r_free = 0.3600 target = 0.146682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.122460 restraints weight = 5096.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 2.00
r_work: 0.3089 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4544  Z= 0.129
  Angle     :  0.572  10.782   6188  Z= 0.279
  Chirality :  0.041   0.171    684
  Planarity :  0.004   0.034    790
  Dihedral  :  4.162  15.143    630
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 22.36 %
    Favored  : 74.39 %
  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:  0.80 (0.37), residues: 534
  helix:  1.65 (0.49), residues: 124
  sheet:  0.82 (0.39), residues: 178
  loop : -0.26 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  88 
 TYR   0.013   0.001   TYR B  20 
 PHE   0.009   0.001   PHE C  43 
 TRP   0.018   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4534)
  covalent geometry    : angle       0.56145 ( 6166)
  SS BOND              : bond        0.00344 (    8)
  SS BOND              : angle       0.88407 (   16)
  hydrogen bonds       : bond        0.03499 (  180)
  hydrogen bonds       : angle       4.05958 (  504)
  link_NAG-ASN         : bond        0.00170 (    2)
  link_NAG-ASN         : angle       3.36663 (    6)

*********************** 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
  87 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 MET cc_start: 0.9056 (tpt) cc_final: 0.8855 (tpt)
REVERT: A  160 LYS cc_start: 0.8377 (tttt) cc_final: 0.8065 (ttmp)
REVERT: A  165 GLU cc_start: 0.7979 (tp30) cc_final: 0.7777 (tp30)
REVERT: A  178 LEU cc_start: 0.8743 (mt) cc_final: 0.8529 (mp)
REVERT: A  182 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8002 (mp0)
REVERT: A  206 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7792 (tm-30)
REVERT: B   68 LYS cc_start: 0.8307 (mmpt) cc_final: 0.7890 (mmpt)
REVERT: B  166 LEU cc_start: 0.8844 (mt) cc_final: 0.8498 (mp)
REVERT: B  191 LYS cc_start: 0.8720 (pttp) cc_final: 0.8213 (mmmt)
REVERT: C   43 PHE cc_start: 0.6759 (OUTLIER) cc_final: 0.5314 (t80)
REVERT: C   64 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8110 (mt-10)
  outliers start: 16
  outliers final: 10
  residues processed: 82
  average time/residue: 0.5343
  time to fit residues: 45.4855
Evaluate side-chains
  80 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  142 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   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 49 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 = 0.3562 r_free = 0.3562 target = 0.143593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.118422 restraints weight = 5023.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 2.05
r_work: 0.3037 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   4544  Z= 0.206
  Angle     :  0.622   8.144   6188  Z= 0.310
  Chirality :  0.044   0.181    684
  Planarity :  0.005   0.035    790
  Dihedral  :  4.362  16.250    628
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 22.97 %
    Favored  : 74.39 %
  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:  0.55 (0.37), residues: 534
  helix:  1.57 (0.49), residues: 120
  sheet:  0.57 (0.37), residues: 188
  loop : -0.39 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 147 
 TYR   0.013   0.001   TYR B  20 
 PHE   0.018   0.002   PHE C  43 
 TRP   0.016   0.002   TRP A 100 
 HIS   0.003   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 4534)
  covalent geometry    : angle       0.61058 ( 6166)
  SS BOND              : bond        0.00433 (    8)
  SS BOND              : angle       1.21755 (   16)
  hydrogen bonds       : bond        0.04025 (  180)
  hydrogen bonds       : angle       4.29820 (  504)
  link_NAG-ASN         : bond        0.00354 (    2)
  link_NAG-ASN         : angle       3.41455 (    6)

*********************** 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
  79 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7785 (tp)
REVERT: A  160 LYS cc_start: 0.8302 (tttt) cc_final: 0.7949 (ttmp)
REVERT: A  178 LEU cc_start: 0.8758 (mt) cc_final: 0.8546 (mp)
REVERT: A  182 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7937 (mp0)
REVERT: A  206 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7800 (tm-30)
REVERT: B   68 LYS cc_start: 0.8369 (mmpt) cc_final: 0.7961 (mmpt)
REVERT: B  166 LEU cc_start: 0.8841 (mt) cc_final: 0.8500 (mp)
REVERT: B  191 LYS cc_start: 0.8764 (pttp) cc_final: 0.8175 (mmmt)
REVERT: C   43 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6058 (t80)
REVERT: C   64 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8201 (mt-10)
  outliers start: 13
  outliers final: 9
  residues processed: 74
  average time/residue: 0.5715
  time to fit residues: 43.7526
Evaluate side-chains
  74 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
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  142 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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3583 r_free = 0.3583 target = 0.145334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.120484 restraints weight = 5012.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 2.05
r_work: 0.3065 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4544  Z= 0.143
  Angle     :  0.577   8.880   6188  Z= 0.286
  Chirality :  0.041   0.155    684
  Planarity :  0.004   0.032    790
  Dihedral  :  4.259  15.957    628
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 23.17 %
    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 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:  0.67 (0.37), residues: 534
  helix:  1.61 (0.49), residues: 120
  sheet:  0.74 (0.38), residues: 180
  loop : -0.35 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 147 
 TYR   0.014   0.001   TYR B  20 
 PHE   0.012   0.001   PHE C  43 
 TRP   0.020   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4534)
  covalent geometry    : angle       0.56799 ( 6166)
  SS BOND              : bond        0.00380 (    8)
  SS BOND              : angle       1.09152 (   16)
  hydrogen bonds       : bond        0.03640 (  180)
  hydrogen bonds       : angle       4.20632 (  504)
  link_NAG-ASN         : bond        0.00186 (    2)
  link_NAG-ASN         : angle       3.03603 (    6)

*********************** 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
  78 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LYS cc_start: 0.8284 (tttt) cc_final: 0.7968 (ttmp)
REVERT: A  182 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7952 (mp0)
REVERT: B   68 LYS cc_start: 0.8435 (mmpt) cc_final: 0.8013 (mmpt)
REVERT: B  138 TYR cc_start: 0.8986 (p90) cc_final: 0.8762 (p90)
REVERT: B  166 LEU cc_start: 0.8848 (mt) cc_final: 0.8495 (mp)
REVERT: B  191 LYS cc_start: 0.8762 (pttp) cc_final: 0.8218 (mmmt)
REVERT: C   43 PHE cc_start: 0.7058 (OUTLIER) cc_final: 0.5784 (t80)
REVERT: C   64 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8171 (mt-10)
  outliers start: 15
  outliers final: 9
  residues processed: 75
  average time/residue: 0.5871
  time to fit residues: 45.6352
Evaluate side-chains
  70 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  142 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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 29 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3581 r_free = 0.3581 target = 0.145187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.120357 restraints weight = 5077.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 2.05
r_work: 0.3059 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4544  Z= 0.139
  Angle     :  0.574   8.628   6188  Z= 0.285
  Chirality :  0.041   0.153    684
  Planarity :  0.004   0.033    790
  Dihedral  :  4.215  15.676    628
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 24.19 %
    Favored  : 73.37 %
  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:  0.68 (0.37), residues: 534
  helix:  1.64 (0.49), residues: 120
  sheet:  0.72 (0.38), residues: 178
  loop : -0.33 (0.41), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 147 
 TYR   0.015   0.001   TYR B  20 
 PHE   0.011   0.001   PHE C  43 
 TRP   0.023   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4534)
  covalent geometry    : angle       0.56533 ( 6166)
  SS BOND              : bond        0.00344 (    8)
  SS BOND              : angle       1.09173 (   16)
  hydrogen bonds       : bond        0.03602 (  180)
  hydrogen bonds       : angle       4.23325 (  504)
  link_NAG-ASN         : bond        0.00177 (    2)
  link_NAG-ASN         : angle       2.84457 (    6)

*********************** 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
  74 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LYS cc_start: 0.8252 (tttt) cc_final: 0.7928 (ttmp)
REVERT: A  182 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7945 (mp0)
REVERT: A  206 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7828 (tm-30)
REVERT: B   68 LYS cc_start: 0.8444 (mmpt) cc_final: 0.8027 (mmpt)
REVERT: B  166 LEU cc_start: 0.8823 (mt) cc_final: 0.8472 (mp)
REVERT: B  191 LYS cc_start: 0.8772 (pttp) cc_final: 0.8202 (mmmt)
REVERT: C   43 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.5734 (t80)
REVERT: C   64 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8094 (mt-10)
  outliers start: 12
  outliers final: 8
  residues processed: 71
  average time/residue: 0.6434
  time to fit residues: 47.2263
Evaluate side-chains
  67 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  199 ASN
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   85 VAL
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 31 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   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
C 126 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.145832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.120743 restraints weight = 5043.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 2.08
r_work: 0.3066 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   4544  Z= 0.150
  Angle     :  0.630  13.856   6188  Z= 0.312
  Chirality :  0.043   0.346    684
  Planarity :  0.004   0.032    790
  Dihedral  :  4.207  15.549    628
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 23.78 %
    Favored  : 73.58 %
  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:  0.66 (0.37), residues: 534
  helix:  1.67 (0.49), residues: 120
  sheet:  0.67 (0.38), residues: 178
  loop : -0.34 (0.41), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  45 
 TYR   0.014   0.001   TYR B  20 
 PHE   0.012   0.001   PHE C  43 
 TRP   0.021   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 4534)
  covalent geometry    : angle       0.60812 ( 6166)
  SS BOND              : bond        0.00974 (    8)
  SS BOND              : angle       2.85648 (   16)
  hydrogen bonds       : bond        0.03628 (  180)
  hydrogen bonds       : angle       4.31792 (  504)
  link_NAG-ASN         : bond        0.00170 (    2)
  link_NAG-ASN         : angle       2.70682 (    6)

********************** 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
  75 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LYS cc_start: 0.8262 (tttt) cc_final: 0.7928 (ttmp)
REVERT: A  182 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7925 (mp0)
REVERT: A  206 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7832 (tm-30)
REVERT: B   68 LYS cc_start: 0.8500 (mmpt) cc_final: 0.8105 (mmpt)
REVERT: B  166 LEU cc_start: 0.8816 (mt) cc_final: 0.8462 (mp)
REVERT: B  191 LYS cc_start: 0.8728 (pttp) cc_final: 0.8172 (mmmt)
REVERT: C   43 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.5789 (t80)
REVERT: C   64 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8112 (mt-10)
  outliers start: 13
  outliers final: 9
  residues processed: 69
  average time/residue: 0.6378
  time to fit residues: 45.4404
Evaluate side-chains
  68 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  199 ASN
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   85 VAL
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 26 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0270
   chunk 38 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.6638

-------------------------------------------------------------------------------
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 = 0.3587 r_free = 0.3587 target = 0.145567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.121355 restraints weight = 5130.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.00
r_work: 0.3090 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   4544  Z= 0.141
  Angle     :  0.622  14.386   6188  Z= 0.308
  Chirality :  0.043   0.335    684
  Planarity :  0.004   0.032    790
  Dihedral  :  4.159  15.417    628
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 24.39 %
    Favored  : 73.58 %
  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:  0.72 (0.37), residues: 534
  helix:  1.74 (0.49), residues: 120
  sheet:  0.71 (0.39), residues: 176
  loop : -0.30 (0.41), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  45 
 TYR   0.015   0.001   TYR B  20 
 PHE   0.010   0.001   PHE C  43 
 TRP   0.021   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 4534)
  covalent geometry    : angle       0.60169 ( 6166)
  SS BOND              : bond        0.00860 (    8)
  SS BOND              : angle       2.80346 (   16)
  hydrogen bonds       : bond        0.03575 (  180)
  hydrogen bonds       : angle       4.27823 (  504)
  link_NAG-ASN         : bond        0.00145 (    2)
  link_NAG-ASN         : angle       2.51313 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1703.45 seconds
wall clock time: 29 minutes 46.05 seconds (1786.05 seconds total)