Starting phenix.real_space_refine
on Thu Jul 24 11:14:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p8v_13255/07_2025/7p8v_13255.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p8v_13255/07_2025/7p8v_13255.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p8v_13255/07_2025/7p8v_13255.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p8v_13255/07_2025/7p8v_13255.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p8v_13255/07_2025/7p8v_13255.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p8v_13255/07_2025/7p8v_13255.cif"
  }
  resolution = 3.6
  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=   0.001
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: 6
    Type Number    sf(0)   Gaussians
     P      41      5.49       5
     Mg      2      5.21       5
     S      16      5.16       5
     C    3625      2.51       5
     N    1108      2.21       5
     O    1196      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5988
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2601
          Classifications: {'peptide': 331}
          Link IDs: {'PTRANS': 13, 'TRANS': 317}
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2601
          Classifications: {'peptide': 331}
          Link IDs: {'PTRANS': 13, 'TRANS': 317}
    Chain: "C"
      Number of atoms: 458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 458
          Classifications: {'DNA': 22}
          Link IDs: {'rna3p': 21}
    Chain: "D"
      Number of atoms: 264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 264
          Classifications: {'DNA': 13}
          Link IDs: {'rna3p': 12}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.96, per 1000 atoms: 0.66
  Number of scatterers: 5988
  At special positions: 0
  Unit cell: (81.605, 73.015, 109.093, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      16     16.00
     P      41     15.00
     Mg      2     11.99
     O    1196      8.00
     N    1108      7.00
     C    3625      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 1.47
  Conformation dependent library (CDL) restraints added in 676.0 milliseconds
  

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1244

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 9 sheets defined
      39.9% alpha, 21.1% beta
      12 base pairs and 30 stacking pairs defined.
    Time for finding SS restraints: 1.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 20
      removed outlier: 3.748A  pdb=" N   GLU A  18 " --> pdb=" O   ILE A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 38
    Processing helix  chain 'A' and resid 64 through 72
      removed outlier: 3.754A  pdb=" N   LEU A  72 " --> pdb=" O   LEU A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 88
    Processing helix  chain 'A' and resid 96 through 105
      removed outlier: 4.126A  pdb=" N   ALA A 100 " --> pdb=" O   GLY A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 159
      removed outlier: 3.620A  pdb=" N   LYS A 159 " --> pdb=" O   PRO A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 182
      removed outlier: 4.029A  pdb=" N   GLU A 167 " --> pdb=" O   THR A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 223
      removed outlier: 7.471A  pdb=" N   THR A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
      removed outlier: 9.636A  pdb=" N   ALA A 219 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   PHE A 220 " --> pdb=" O   CYS A 216 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU A 221 " --> pdb=" O   GLY A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 314 through 330
    Processing helix  chain 'B' and resid 7 through 20
      removed outlier: 3.780A  pdb=" N   GLU B  18 " --> pdb=" O   ILE B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 36
    Processing helix  chain 'B' and resid 64 through 73
      removed outlier: 4.151A  pdb=" N   ALA B  69 " --> pdb=" O   LYS B  65 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   LEU B  70 " --> pdb=" O   ASP B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 88
    Processing helix  chain 'B' and resid 98 through 105
      removed outlier: 3.632A  pdb=" N   ILE B 102 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 160
    Processing helix  chain 'B' and resid 163 through 182
    Processing helix  chain 'B' and resid 208 through 217
      removed outlier: 3.514A  pdb=" N   LEU B 212 " --> pdb=" O   LYS B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 223
    Processing helix  chain 'B' and resid 265 through 279
    Processing helix  chain 'B' and resid 295 through 297
      No H-bonds generated for 'chain 'B' and resid 295 through 297'
    Processing helix  chain 'B' and resid 314 through 330
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5
    Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 137
      removed outlier: 3.726A  pdb=" N   ALA A 120 " --> pdb=" O   ALA A 137 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   ALA A 125 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
      removed outlier: 5.509A  pdb=" N   LEU A 108 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU A 148 " --> pdb=" O   ARG A 107 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLU A 146 " --> pdb=" O   THR A 109 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   HIS A 191 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   ILE A 195 " --> pdb=" O   HIS A 191 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77
    Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 231
      removed outlier: 3.671A  pdb=" N   GLY A 238 " --> pdb=" O   ILE A 227 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   TYR A 255 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 8.083A  pdb=" N   LEU A 292 " --> pdb=" O   TYR A 255 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   TYR A 257 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 300
    Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 113
      removed outlier: 3.633A  pdb=" N   ARG B  55 " --> pdb=" O   ASP B  45 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ARG B 197 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   HIS B 191 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   ILE B 195 " --> pdb=" O   HIS B 191 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 126
      removed outlier: 3.644A  pdb=" N   ALA B 120 " --> pdb=" O   ALA B 137 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 224 through 230
      removed outlier: 3.714A  pdb=" N   GLY B 238 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   TYR B 255 " --> pdb=" O   LEU B 290 " (cutoff:3.500A)
      removed outlier: 8.424A  pdb=" N   LEU B 292 " --> pdb=" O   TYR B 255 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   TYR B 257 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   CYS B 256 " --> pdb=" O   MET B 263 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 299 through 300

    262 hydrogen bonds defined for protein.
    747 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      29 hydrogen bonds
      58 hydrogen bond angles
      0 basepair planarities
      12 basepair parallelities
      30 stacking parallelities
  Total time for adding SS restraints: 1.71

  Time building geometry restraints manager: 1.65 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 951
        1.31 -     1.44: 1701
        1.44 -     1.56: 3415
        1.56 -     1.69: 78
        1.69 -     1.82: 24
  Bond restraints: 6169
  Sorted by residual:
  bond pdb=" N3B ANP A 701 "
       pdb=" PG  ANP A 701 "
    ideal  model  delta    sigma   weight residual
    1.795  1.620  0.175 2.00e-02 2.50e+03 7.66e+01
  bond pdb=" N3B ANP B 702 "
       pdb=" PG  ANP B 702 "
    ideal  model  delta    sigma   weight residual
    1.795  1.620  0.175 2.00e-02 2.50e+03 7.64e+01
  bond pdb=" O3A ANP B 702 "
       pdb=" PB  ANP B 702 "
    ideal  model  delta    sigma   weight residual
    1.700  1.579  0.121 2.00e-02 2.50e+03 3.64e+01
  bond pdb=" O3A ANP A 701 "
       pdb=" PB  ANP A 701 "
    ideal  model  delta    sigma   weight residual
    1.700  1.589  0.111 2.00e-02 2.50e+03 3.08e+01
  bond pdb=" O3G ANP A 701 "
       pdb=" PG  ANP A 701 "
    ideal  model  delta    sigma   weight residual
    1.528  1.424  0.104 2.00e-02 2.50e+03 2.73e+01
  ... (remaining 6164 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 7056
        2.56 -     5.12: 1429
        5.12 -     7.68: 34
        7.68 -    10.24: 3
       10.24 -    12.80: 3
  Bond angle restraints: 8525
  Sorted by residual:
  angle pdb=" CA  GLY B 127 "
        pdb=" C   GLY B 127 "
        pdb=" O   GLY B 127 "
      ideal   model   delta    sigma   weight residual
     122.52  117.40    5.12 7.90e-01 1.60e+00 4.19e+01
  angle pdb=" C   GLN A 117 "
        pdb=" CA  GLN A 117 "
        pdb=" CB  GLN A 117 "
      ideal   model   delta    sigma   weight residual
     109.54  120.67  -11.13 1.84e+00 2.95e-01 3.66e+01
  angle pdb=" CA  GLY A 127 "
        pdb=" C   GLY A 127 "
        pdb=" O   GLY A 127 "
      ideal   model   delta    sigma   weight residual
     122.52  118.13    4.39 7.90e-01 1.60e+00 3.09e+01
  angle pdb=" CA  GLY A 217 "
        pdb=" C   GLY A 217 "
        pdb=" O   GLY A 217 "
      ideal   model   delta    sigma   weight residual
     122.39  117.41    4.98 9.30e-01 1.16e+00 2.87e+01
  angle pdb=" CA  PRO A   7 "
        pdb=" C   PRO A   7 "
        pdb=" O   PRO A   7 "
      ideal   model   delta    sigma   weight residual
     120.90  117.14    3.76 7.20e-01 1.93e+00 2.73e+01
  ... (remaining 8520 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.54: 3336
       29.54 -    59.07: 312
       59.07 -    88.60: 19
       88.60 -   118.14: 1
      118.14 -   147.67: 2
  Dihedral angle restraints: 3670
    sinusoidal: 1752
      harmonic: 1918
  Sorted by residual:
  dihedral pdb=" C   GLN A 117 "
           pdb=" N   GLN A 117 "
           pdb=" CA  GLN A 117 "
           pdb=" CB  GLN A 117 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.60   12.00     0      2.50e+00 1.60e-01 2.30e+01
  dihedral pdb=" O1B ANP A 701 "
           pdb=" N3B ANP A 701 "
           pdb=" PB  ANP A 701 "
           pdb=" PG  ANP A 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      35.15 -177.18 -147.67     1      3.00e+01 1.11e-03 1.97e+01
  dihedral pdb=" O1A ANP B 702 "
           pdb=" O3A ANP B 702 "
           pdb=" PA  ANP B 702 "
           pdb=" PB  ANP B 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  -46.03  129.14     1      3.00e+01 1.11e-03 1.74e+01
  ... (remaining 3667 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 354
       0.061 -    0.121: 368
       0.121 -    0.182: 186
       0.182 -    0.242: 52
       0.242 -    0.303: 6
  Chirality restraints: 966
  Sorted by residual:
  chirality pdb=" CA  GLN A 117 "
            pdb=" N   GLN A 117 "
            pdb=" C   GLN A 117 "
            pdb=" CB  GLN A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CA  LEU B 234 "
            pdb=" N   LEU B 234 "
            pdb=" C   LEU B 234 "
            pdb=" CB  LEU B 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.27e+00
  chirality pdb=" C3' ANP A 701 "
            pdb=" C2' ANP A 701 "
            pdb=" C4' ANP A 701 "
            pdb=" O3' ANP A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.64    0.29 2.00e-01 2.50e+01 2.07e+00
  ... (remaining 963 not shown)

  Planarity restraints: 983
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 208 "   -0.019 2.00e-02 2.50e+03   3.93e-02 1.54e+01
        pdb=" C   LYS A 208 "    0.068 2.00e-02 2.50e+03
        pdb=" O   LYS A 208 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   GLU A 209 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 163 "   -0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" C   THR A 163 "    0.055 2.00e-02 2.50e+03
        pdb=" O   THR A 163 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLU A 164 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 185 "    0.014 2.00e-02 2.50e+03   2.93e-02 8.56e+00
        pdb=" C   VAL B 185 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   VAL B 185 "    0.019 2.00e-02 2.50e+03
        pdb=" N   THR B 186 "    0.018 2.00e-02 2.50e+03
  ... (remaining 980 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 829
        2.81 -     3.33: 5816
        3.33 -     3.85: 9502
        3.85 -     4.38: 12614
        4.38 -     4.90: 19284
  Nonbonded interactions: 48045
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A  33 "
            pdb="MG    MG A 702 "
     model   vdw
     2.287 2.170
  nonbonded pdb="MG    MG B 701 "
            pdb=" O2B ANP B 702 "
     model   vdw
     2.320 2.170
  nonbonded pdb=" OD1 ASN B  33 "
            pdb="MG    MG B 701 "
     model   vdw
     2.337 2.170
  nonbonded pdb=" O3G ANP A 701 "
            pdb="MG    MG A 702 "
     model   vdw
     2.341 2.170
  nonbonded pdb=" O1A ANP A 701 "
            pdb="MG    MG A 702 "
     model   vdw
     2.374 2.170
  ... (remaining 48040 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 1 through 331)
  selection = (chain 'B' and resid 1 through 331)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.690
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.930
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.010
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
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      :  0.013   0.175   6169  Z= 0.987
  Angle     :  1.812  12.797   8525  Z= 1.349
  Chirality :  0.102   0.303    966
  Planarity :  0.009   0.040    983
  Dihedral  : 20.306 147.672   2426
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  7.85 %
    Favored  : 91.79 %
  Cbeta Deviations :  0.16 %
  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: -0.42 (0.31), residues: 658
  helix:  1.02 (0.32), residues: 250
  sheet: -0.83 (0.39), residues: 150
  loop : -1.15 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.004   TRP A 229 
 HIS   0.011   0.003   HIS B 170 
 PHE   0.031   0.005   PHE A 168 
 TYR   0.017   0.004   TYR A 257 
 ARG   0.013   0.002   ARG B 211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21398 (  291)
  hydrogen bonds       : angle       8.14779 (  805)
  covalent geometry    : bond        0.01349 ( 6169)
  covalent geometry    : angle       1.81227 ( 8525)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 THR cc_start: 0.9100 (m) cc_final: 0.8815 (p)
REVERT: A  169 ASN cc_start: 0.8237 (m110) cc_final: 0.7878 (m110)
REVERT: A  173 GLU cc_start: 0.7886 (tp30) cc_final: 0.7614 (tp30)
REVERT: A  229 TRP cc_start: 0.8208 (t-100) cc_final: 0.7829 (t-100)
REVERT: A  231 HIS cc_start: 0.6665 (t70) cc_final: 0.6349 (t70)
REVERT: B   22 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7728 (mtm-85)
REVERT: B  274 GLN cc_start: 0.7801 (mt0) cc_final: 0.7304 (tt0)
  outliers start: 2
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1984
  time to fit residues: 20.0399
Evaluate side-chains
  51 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 35 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 117 GLN
A 188 ASN
B 122 GLN
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 308 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.129099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.102104 restraints weight = 9445.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.104734 restraints weight = 5672.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.105702 restraints weight = 3838.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6169  Z= 0.156
  Angle     :  0.595   7.426   8525  Z= 0.325
  Chirality :  0.042   0.152    966
  Planarity :  0.005   0.043    983
  Dihedral  : 21.045 140.613   1176
  Min Nonbonded Distance : 1.795

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.96 %
    Favored  : 85.40 %
  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: -0.00 (0.33), residues: 658
  helix:  1.24 (0.32), residues: 256
  sheet: -0.55 (0.38), residues: 172
  loop : -0.85 (0.41), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 229 
 HIS   0.004   0.001   HIS B 319 
 PHE   0.015   0.002   PHE A 183 
 TYR   0.010   0.001   TYR B 124 
 ARG   0.004   0.001   ARG B  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04708 (  291)
  hydrogen bonds       : angle       5.73335 (  805)
  covalent geometry    : bond        0.00361 ( 6169)
  covalent geometry    : angle       0.59507 ( 8525)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 6
  residues processed: 67
  average time/residue: 0.1567
  time to fit residues: 14.7873
Evaluate side-chains
  46 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  256 CYS
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain B residue   94 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 39 optimal weight:    0.2980
   chunk 48 optimal weight:    0.7980
   chunk 61 optimal weight:    7.9990
   chunk 22 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.129227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.102691 restraints weight = 9646.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.105080 restraints weight = 5975.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.105684 restraints weight = 3845.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6169  Z= 0.126
  Angle     :  0.528   6.529   8525  Z= 0.289
  Chirality :  0.041   0.146    966
  Planarity :  0.004   0.039    983
  Dihedral  : 20.778 137.558   1172
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.51 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.21 (0.33), residues: 658
  helix:  0.92 (0.32), residues: 270
  sheet: -0.39 (0.40), residues: 160
  loop : -1.12 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 229 
 HIS   0.004   0.001   HIS B 308 
 PHE   0.013   0.002   PHE A 168 
 TYR   0.008   0.001   TYR B 323 
 ARG   0.004   0.000   ARG A 162 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03879 (  291)
  hydrogen bonds       : angle       5.31434 (  805)
  covalent geometry    : bond        0.00281 ( 6169)
  covalent geometry    : angle       0.52755 ( 8525)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
REVERT: A  173 GLU cc_start: 0.7589 (tp30) cc_final: 0.7281 (tp30)
  outliers start: 14
  outliers final: 9
  residues processed: 61
  average time/residue: 0.2576
  time to fit residues: 20.6829
Evaluate side-chains
  51 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  256 CYS
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  323 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 52 optimal weight:    0.4980
   chunk 56 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 66 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    1.0584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.126996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.100239 restraints weight = 9817.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.101464 restraints weight = 6364.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.103525 restraints weight = 4514.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6169  Z= 0.148
  Angle     :  0.526   6.315   8525  Z= 0.287
  Chirality :  0.041   0.149    966
  Planarity :  0.004   0.040    983
  Dihedral  : 20.650 140.531   1172
  Min Nonbonded Distance : 1.854

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.42 %
    Favored  : 80.66 %
  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: -0.25 (0.34), residues: 658
  helix:  0.91 (0.33), residues: 272
  sheet: -0.69 (0.40), residues: 168
  loop : -0.94 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 229 
 HIS   0.004   0.001   HIS B 308 
 PHE   0.019   0.002   PHE A 168 
 TYR   0.009   0.001   TYR B 291 
 ARG   0.010   0.000   ARG A 162 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03880 (  291)
  hydrogen bonds       : angle       5.17617 (  805)
  covalent geometry    : bond        0.00344 ( 6169)
  covalent geometry    : angle       0.52572 ( 8525)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 47
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
REVERT: A  173 GLU cc_start: 0.7667 (tp30) cc_final: 0.7371 (tp30)
  outliers start: 16
  outliers final: 13
  residues processed: 59
  average time/residue: 0.2982
  time to fit residues: 24.2976
Evaluate side-chains
  55 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  256 CYS
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  323 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 62 optimal weight:    0.3980
   chunk 32 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.127571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.100105 restraints weight = 9618.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.102895 restraints weight = 5534.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.104778 restraints weight = 3836.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6169  Z= 0.121
  Angle     :  0.500   6.515   8525  Z= 0.270
  Chirality :  0.040   0.144    966
  Planarity :  0.004   0.040    983
  Dihedral  : 20.492 140.706   1172
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 16.06 %
    Favored  : 80.47 %
  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: -0.16 (0.34), residues: 658
  helix:  0.92 (0.33), residues: 272
  sheet: -0.51 (0.41), residues: 164
  loop : -0.92 (0.43), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 229 
 HIS   0.003   0.001   HIS B 308 
 PHE   0.013   0.002   PHE A 168 
 TYR   0.008   0.001   TYR B 257 
 ARG   0.003   0.000   ARG B  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03489 (  291)
  hydrogen bonds       : angle       5.05588 (  805)
  covalent geometry    : bond        0.00277 ( 6169)
  covalent geometry    : angle       0.50021 ( 8525)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 45
  time to evaluate  : 0.666 
Fit side-chains
   revert: symmetry clash
REVERT: A  173 GLU cc_start: 0.7499 (tp30) cc_final: 0.7173 (tp30)
  outliers start: 19
  outliers final: 15
  residues processed: 58
  average time/residue: 0.1990
  time to fit residues: 15.6477
Evaluate side-chains
  57 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  256 CYS
Chi-restraints excluded: chain A residue  262 MET
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  323 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0050
   chunk 27 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 68 optimal weight:    8.9990
   chunk 13 optimal weight:   20.0000
   chunk 29 optimal weight:    4.9990
   overall best weight:    1.7400

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

Flipped N/Q/H residues before XYZ refinement:
B 122 GLN
** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.124151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.096363 restraints weight = 9655.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.099317 restraints weight = 5427.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.101309 restraints weight = 3702.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   6169  Z= 0.209
  Angle     :  0.566   6.071   8525  Z= 0.307
  Chirality :  0.043   0.155    966
  Planarity :  0.004   0.042    983
  Dihedral  : 20.609 147.496   1172
  Min Nonbonded Distance : 1.778

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 17.52 %
    Favored  : 78.47 %
  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: -0.32 (0.34), residues: 658
  helix:  0.81 (0.33), residues: 270
  sheet: -0.57 (0.41), residues: 168
  loop : -1.05 (0.44), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 229 
 HIS   0.005   0.001   HIS B 308 
 PHE   0.027   0.003   PHE A 168 
 TYR   0.014   0.002   TYR B 257 
 ARG   0.004   0.000   ARG A  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04333 (  291)
  hydrogen bonds       : angle       5.20731 (  805)
  covalent geometry    : bond        0.00497 ( 6169)
  covalent geometry    : angle       0.56608 ( 8525)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 46
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
REVERT: A  173 GLU cc_start: 0.7722 (tp30) cc_final: 0.7367 (tp30)
  outliers start: 22
  outliers final: 14
  residues processed: 62
  average time/residue: 0.1663
  time to fit residues: 14.3637
Evaluate side-chains
  53 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  256 CYS
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  323 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 63 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 12 optimal weight:    4.9990
   chunk 60 optimal weight:    9.9990
   chunk 19 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 169 ASN
B 117 GLN
B 245 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.127343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.101440 restraints weight = 9598.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.102632 restraints weight = 6265.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.103632 restraints weight = 4737.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.3100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6169  Z= 0.123
  Angle     :  0.512   7.135   8525  Z= 0.275
  Chirality :  0.040   0.141    966
  Planarity :  0.004   0.041    983
  Dihedral  : 20.359 146.372   1172
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 18.25 %
    Favored  : 78.65 %
  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: -0.18 (0.34), residues: 658
  helix:  0.85 (0.33), residues: 272
  sheet: -0.47 (0.41), residues: 168
  loop : -0.91 (0.44), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 229 
 HIS   0.003   0.001   HIS A 308 
 PHE   0.011   0.001   PHE A 168 
 TYR   0.008   0.001   TYR B 257 
 ARG   0.002   0.000   ARG B  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03460 (  291)
  hydrogen bonds       : angle       5.08402 (  805)
  covalent geometry    : bond        0.00288 ( 6169)
  covalent geometry    : angle       0.51221 ( 8525)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 42
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 GLU cc_start: 0.7430 (tp30) cc_final: 0.7076 (tp30)
  outliers start: 17
  outliers final: 14
  residues processed: 54
  average time/residue: 0.1772
  time to fit residues: 13.1753
Evaluate side-chains
  52 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 38
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  256 CYS
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  117 GLN
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  323 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 68 optimal weight:    8.9990
   chunk 62 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 117 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.121065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.091659 restraints weight = 9890.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.094894 restraints weight = 5154.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.097048 restraints weight = 3379.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.3189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6169  Z= 0.120
  Angle     :  0.498   6.284   8525  Z= 0.269
  Chirality :  0.040   0.143    966
  Planarity :  0.003   0.043    983
  Dihedral  : 20.261 145.696   1172
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 18.43 %
    Favored  : 78.47 %
  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: -0.14 (0.34), residues: 658
  helix:  0.88 (0.33), residues: 272
  sheet: -0.42 (0.41), residues: 168
  loop : -0.90 (0.44), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 229 
 HIS   0.003   0.001   HIS A 308 
 PHE   0.013   0.001   PHE A 168 
 TYR   0.008   0.001   TYR B 257 
 ARG   0.003   0.000   ARG B  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03389 (  291)
  hydrogen bonds       : angle       5.02762 (  805)
  covalent geometry    : bond        0.00283 ( 6169)
  covalent geometry    : angle       0.49850 ( 8525)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 41
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
REVERT: A  173 GLU cc_start: 0.7591 (tp30) cc_final: 0.7249 (tp30)
  outliers start: 17
  outliers final: 15
  residues processed: 52
  average time/residue: 0.1755
  time to fit residues: 13.6617
Evaluate side-chains
  51 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 36
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  256 CYS
Chi-restraints excluded: chain A residue  262 MET
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  117 GLN
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  323 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 68 optimal weight:    8.9990
   chunk 0 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B 117 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.120164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.090874 restraints weight = 10022.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.094119 restraints weight = 5176.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.096074 restraints weight = 3383.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.3247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6169  Z= 0.143
  Angle     :  0.510   6.653   8525  Z= 0.275
  Chirality :  0.041   0.146    966
  Planarity :  0.004   0.043    983
  Dihedral  : 20.269 148.208   1172
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 19.34 %
    Favored  : 77.92 %
  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: -0.17 (0.34), residues: 658
  helix:  0.83 (0.33), residues: 272
  sheet: -0.44 (0.41), residues: 168
  loop : -0.88 (0.44), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 229 
 HIS   0.003   0.001   HIS A 308 
 PHE   0.017   0.002   PHE A 168 
 TYR   0.009   0.001   TYR B 257 
 ARG   0.003   0.000   ARG B  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03558 (  291)
  hydrogen bonds       : angle       5.00694 (  805)
  covalent geometry    : bond        0.00337 ( 6169)
  covalent geometry    : angle       0.50967 ( 8525)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 40
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
REVERT: A  173 GLU cc_start: 0.7650 (tp30) cc_final: 0.7291 (tp30)
  outliers start: 15
  outliers final: 13
  residues processed: 49
  average time/residue: 0.2668
  time to fit residues: 18.3001
Evaluate side-chains
  49 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 1.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  256 CYS
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  117 GLN
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  323 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0870
   chunk 42 optimal weight:    0.7980
   chunk 60 optimal weight:    0.2980
   chunk 20 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
B 117 GLN
B 122 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.122387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.092286 restraints weight = 10101.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.095409 restraints weight = 5471.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.097547 restraints weight = 3695.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.3319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6169  Z= 0.113
  Angle     :  0.508   8.934   8525  Z= 0.270
  Chirality :  0.040   0.141    966
  Planarity :  0.003   0.043    983
  Dihedral  : 20.184 148.148   1172
  Min Nonbonded Distance : 1.884

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 19.16 %
    Favored  : 78.10 %
  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: -0.07 (0.34), residues: 658
  helix:  0.91 (0.33), residues: 272
  sheet: -0.34 (0.41), residues: 168
  loop : -0.88 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 229 
 HIS   0.003   0.001   HIS A 308 
 PHE   0.011   0.001   PHE A 168 
 TYR   0.007   0.001   TYR B 257 
 ARG   0.002   0.000   ARG B  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03265 (  291)
  hydrogen bonds       : angle       4.94813 (  805)
  covalent geometry    : bond        0.00260 ( 6169)
  covalent geometry    : angle       0.50761 ( 8525)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 37
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
REVERT: A  173 GLU cc_start: 0.7614 (tp30) cc_final: 0.7294 (tp30)
  outliers start: 15
  outliers final: 13
  residues processed: 47
  average time/residue: 0.2154
  time to fit residues: 13.7714
Evaluate side-chains
  49 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  256 CYS
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  117 GLN
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  323 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 61 optimal weight:    0.0670
   chunk 37 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0970
   chunk 3 optimal weight:    0.7980
   chunk 26 optimal weight:    0.2980
   overall best weight:    0.4516

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

Flipped N/Q/H residues before XYZ refinement:
B 117 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.130567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.099193 restraints weight = 10264.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.102413 restraints weight = 5688.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.104565 restraints weight = 3881.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.3386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6169  Z= 0.104
  Angle     :  0.489   6.214   8525  Z= 0.262
  Chirality :  0.040   0.140    966
  Planarity :  0.003   0.044    983
  Dihedral  : 20.124 148.439   1172
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 18.98 %
    Favored  : 78.10 %
  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:  0.00 (0.34), residues: 658
  helix:  0.97 (0.33), residues: 272
  sheet: -0.27 (0.41), residues: 168
  loop : -0.86 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 229 
 HIS   0.003   0.001   HIS A 308 
 PHE   0.010   0.001   PHE A 168 
 TYR   0.007   0.001   TYR B 257 
 ARG   0.002   0.000   ARG B  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03190 (  291)
  hydrogen bonds       : angle       4.87979 (  805)
  covalent geometry    : bond        0.00235 ( 6169)
  covalent geometry    : angle       0.48874 ( 8525)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2307.35 seconds
wall clock time: 43 minutes 12.46 seconds (2592.46 seconds total)