Starting phenix.real_space_refine
on Wed Feb 12 08:20:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8okd_16926/02_2025/8okd_16926.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8okd_16926/02_2025/8okd_16926.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8okd_16926/02_2025/8okd_16926.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8okd_16926/02_2025/8okd_16926.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8okd_16926/02_2025/8okd_16926.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8okd_16926/02_2025/8okd_16926.cif"
  }
  resolution = 3.1
  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=   0.001 sd=   0.058
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: 5
    Type Number    sf(0)   Gaussians
     P     138      5.49       5
     S      30      5.16       5
     C    4392      2.51       5
     N    1358      2.21       5
     O    1830      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7748
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2390
          Classifications: {'peptide': 291}
          Link IDs: {'PTRANS': 11, 'TRANS': 279}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2390
          Classifications: {'peptide': 291}
          Link IDs: {'PTRANS': 11, 'TRANS': 279}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 1484
          Classifications: {'RNA': 70}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 28, 'rna3p_pyr': 31}
          Link IDs: {'rna2p': 10, 'rna3p': 59}
          Chain breaks: 1
    Chain: "X"
      Number of atoms: 1484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 1484
          Classifications: {'RNA': 70}
          Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 27, 'rna3p_pyr': 31}
          Link IDs: {'rna2p': 11, 'rna3p': 58}
          Chain breaks: 1
  Time building chain proxies: 5.21, per 1000 atoms: 0.67
  Number of scatterers: 7748
  At special positions: 0
  Unit cell: (98.9, 162.54, 66.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P     138     15.00
     O    1830      8.00
     N    1358      7.00
     C    4392      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: 2.08
  Conformation dependent library (CDL) restraints added in 563.6 milliseconds
  

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1112

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 7 sheets defined
      37.3% alpha, 21.0% beta
      46 base pairs and 67 stacking pairs defined.
    Time for finding SS restraints: 2.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 60
      removed outlier: 3.782A  pdb=" N   ALA A  59 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 101
      removed outlier: 3.718A  pdb=" N   LYS A  92 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 109
      removed outlier: 3.954A  pdb=" N   SER A 109 " --> pdb=" O   ARG A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 164
    Processing helix  chain 'A' and resid 206 through 212
    Processing helix  chain 'A' and resid 213 through 217
      removed outlier: 3.862A  pdb=" N   VAL A 217 " --> pdb=" O   GLN A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 262
    Processing helix  chain 'A' and resid 277 through 291
      removed outlier: 3.746A  pdb=" N   CYS A 281 " --> pdb=" O   HIS A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 304
      removed outlier: 4.281A  pdb=" N   GLU A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ASN A 304 " --> pdb=" O   ASP A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 308
    Processing helix  chain 'A' and resid 337 through 369
      removed outlier: 3.842A  pdb=" N   LYS A 358 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU A 369 " --> pdb=" O   MET A 365 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 60
      removed outlier: 3.909A  pdb=" N   ALA B  59 " --> pdb=" O   ASP B  56 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   HIS B  60 " --> pdb=" O   PHE B  57 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 56 through 60'
    Processing helix  chain 'B' and resid 88 through 100
      removed outlier: 3.827A  pdb=" N   LYS B  92 " --> pdb=" O   THR B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 109
      removed outlier: 4.038A  pdb=" N   SER B 109 " --> pdb=" O   ARG B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 166
      removed outlier: 3.660A  pdb=" N   ARG B 166 " --> pdb=" O   HIS B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 190
    Processing helix  chain 'B' and resid 205 through 214
    Processing helix  chain 'B' and resid 215 through 217
      No H-bonds generated for 'chain 'B' and resid 215 through 217'
    Processing helix  chain 'B' and resid 259 through 263
    Processing helix  chain 'B' and resid 277 through 291
      removed outlier: 3.731A  pdb=" N   CYS B 281 " --> pdb=" O   HIS B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 304
      removed outlier: 4.333A  pdb=" N   GLU B 301 " --> pdb=" O   GLU B 297 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ASN B 304 " --> pdb=" O   ASP B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 369
      removed outlier: 3.801A  pdb=" N   LYS B 358 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   LEU B 369 " --> pdb=" O   MET B 365 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113
      removed outlier: 3.762A  pdb=" N   SER A 129 " --> pdb=" O   HIS A 112 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ILE A 128 " --> pdb=" O   LEU A  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113
      removed outlier: 3.762A  pdb=" N   SER A 129 " --> pdb=" O   HIS A 112 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ILE A 128 " --> pdb=" O   LEU A  67 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 123
      removed outlier: 7.098A  pdb=" N   SER A 122 " --> pdb=" O   LEU A 324 " (cutoff:3.500A)
      removed outlier: 8.216A  pdb=" N   ASP A 326 " --> pdb=" O   SER A 122 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   THR A 194 " --> pdb=" O   TYR A 325 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER A 243 " --> pdb=" O   THR A 270 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 221
      removed outlier: 3.531A  pdb=" N   GLY A 218 " --> pdb=" O   ILE A 241 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ILE A 241 " --> pdb=" O   GLY A 218 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   HIS A 220 " --> pdb=" O   ARG A 239 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ARG A 239 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 134
      removed outlier: 7.798A  pdb=" N   HIS B  64 " --> pdb=" O   PRO B 179 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ALA B  66 " --> pdb=" O   TRP B 177 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   TRP B 177 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ARG B  68 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 122 through 123
      removed outlier: 6.824A  pdb=" N   SER B 122 " --> pdb=" O   LEU B 324 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   ASP B 326 " --> pdb=" O   SER B 122 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   THR B 194 " --> pdb=" O   TYR B 325 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL B 269 " --> pdb=" O   TYR B 195 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 220 through 221

    190 hydrogen bonds defined for protein.
    507 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      120 hydrogen bonds
      212 hydrogen bond angles
      0 basepair planarities
      46 basepair parallelities
      67 stacking parallelities
  Total time for adding SS restraints: 2.50

  Time building geometry restraints manager: 2.37 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: 1941
        1.34 -     1.46: 2451
        1.46 -     1.57: 3492
        1.57 -     1.69: 274
        1.69 -     1.81: 48
  Bond restraints: 8206
  Sorted by residual:
  bond pdb=" C   GLU A 260 "
       pdb=" N   PRO A 261 "
    ideal  model  delta    sigma   weight residual
    1.334  1.345 -0.011 8.40e-03 1.42e+04 1.75e+00
  bond pdb=" C   GLU B 260 "
       pdb=" N   PRO B 261 "
    ideal  model  delta    sigma   weight residual
    1.334  1.344 -0.011 8.40e-03 1.42e+04 1.68e+00
  bond pdb=" CB  LYS A 307 "
       pdb=" CG  LYS A 307 "
    ideal  model  delta    sigma   weight residual
    1.520  1.544 -0.024 3.00e-02 1.11e+03 6.35e-01
  bond pdb=" CG1 ILE A  69 "
       pdb=" CD1 ILE A  69 "
    ideal  model  delta    sigma   weight residual
    1.513  1.485  0.028 3.90e-02 6.57e+02 5.31e-01
  bond pdb=" C3'   U X  20 "
       pdb=" O3'   U X  20 "
    ideal  model  delta    sigma   weight residual
    1.417  1.428 -0.011 1.50e-02 4.44e+03 5.18e-01
  ... (remaining 8201 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 11572
        1.66 -     3.31: 167
        3.31 -     4.97: 21
        4.97 -     6.63: 3
        6.63 -     8.28: 3
  Bond angle restraints: 11766
  Sorted by residual:
  angle pdb=" N   GLY A 233 "
        pdb=" CA  GLY A 233 "
        pdb=" C   GLY A 233 "
      ideal   model   delta    sigma   weight residual
     113.18  121.06   -7.88 2.37e+00 1.78e-01 1.10e+01
  angle pdb=" CB  MET B 283 "
        pdb=" CG  MET B 283 "
        pdb=" SD  MET B 283 "
      ideal   model   delta    sigma   weight residual
     112.70  120.98   -8.28 3.00e+00 1.11e-01 7.63e+00
  angle pdb=" CA  LYS A 307 "
        pdb=" CB  LYS A 307 "
        pdb=" CG  LYS A 307 "
      ideal   model   delta    sigma   weight residual
     114.10  119.38   -5.28 2.00e+00 2.50e-01 6.98e+00
  angle pdb=" C   ALA B 118 "
        pdb=" N   LYS B 119 "
        pdb=" CA  LYS B 119 "
      ideal   model   delta    sigma   weight residual
     120.90  124.51   -3.61 1.41e+00 5.03e-01 6.55e+00
  angle pdb=" CA  LEU B 303 "
        pdb=" CB  LEU B 303 "
        pdb=" CG  LEU B 303 "
      ideal   model   delta    sigma   weight residual
     116.30  124.17   -7.87 3.50e+00 8.16e-02 5.05e+00
  ... (remaining 11761 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.81: 4606
       32.81 -    65.63: 431
       65.63 -    98.44: 58
       98.44 -   131.25: 2
      131.25 -   164.07: 1
  Dihedral angle restraints: 5098
    sinusoidal: 3384
      harmonic: 1714
  Sorted by residual:
  dihedral pdb=" O4'   C X  48 "
           pdb=" C1'   C X  48 "
           pdb=" N1    C X  48 "
           pdb=" C2    C X  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -54.00 -106.00     1      1.50e+01 4.44e-03 5.44e+01
  dihedral pdb=" O4'   C C  48 "
           pdb=" C1'   C C  48 "
           pdb=" N1    C C  48 "
           pdb=" C2    C C  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -57.34 -102.66     1      1.50e+01 4.44e-03 5.20e+01
  dihedral pdb=" O4'   U X  20 "
           pdb=" C1'   U X  20 "
           pdb=" N1    U X  20 "
           pdb=" C2    U X  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -78.93  -81.07     1      1.50e+01 4.44e-03 3.60e+01
  ... (remaining 5095 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1177
       0.042 -    0.083: 169
       0.083 -    0.125: 54
       0.125 -    0.167: 5
       0.167 -    0.208: 1
  Chirality restraints: 1406
  Sorted by residual:
  chirality pdb=" C1'   U C  39 "
            pdb=" O4'   U C  39 "
            pdb=" C2'   U C  39 "
            pdb=" N1    U C  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.26    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  ILE A 128 "
            pdb=" N   ILE A 128 "
            pdb=" C   ILE A 128 "
            pdb=" CB  ILE A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 6.00e-01
  chirality pdb=" CA  PHE A 320 "
            pdb=" N   PHE A 320 "
            pdb=" C   PHE A 320 "
            pdb=" CB  PHE A 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.07e-01
  ... (remaining 1403 not shown)

  Planarity restraints: 996
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 267 "   -0.010 2.00e-02 2.50e+03   1.50e-02 3.94e+00
        pdb=" CG  PHE A 267 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 267 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 267 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 267 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 267 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 267 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 295 "   -0.024 5.00e-02 4.00e+02   3.65e-02 2.13e+00
        pdb=" N   PRO B 296 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B 296 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 296 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 124 "    0.007 2.00e-02 2.50e+03   1.04e-02 1.88e+00
        pdb=" CG  PHE A 124 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 124 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 124 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 124 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 124 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 124 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 993 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 947
        2.75 -     3.28: 7297
        3.28 -     3.82: 13914
        3.82 -     4.36: 16028
        4.36 -     4.90: 24623
  Nonbonded interactions: 62809
  Sorted by model distance:
  nonbonded pdb=" O2'   A C   7 "
            pdb=" O2    C C  48 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O2'   A X   7 "
            pdb=" O2    C X  48 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O2'   A C  57 "
            pdb=" OP2   U C  59 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" ND2 ASN B 224 "
            pdb=" O   LEU B 302 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" O   GLY A 115 "
            pdb=" NE2 GLN A 126 "
     model   vdw
     2.306 3.120
  ... (remaining 62804 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'X'
}

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=0.00 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:             0.720
  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:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     22.780
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5958
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      :  0.003   0.028   8206  Z= 0.180
  Angle     :  0.509   8.284  11766  Z= 0.267
  Chirality :  0.034   0.208   1406
  Planarity :  0.003   0.036    996
  Dihedral  : 21.865 164.067   3986
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 35.94 %
    Favored  : 63.67 %
  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: -0.76 (0.35), residues: 570
  helix:  1.83 (0.43), residues: 146
  sheet: -0.83 (0.51), residues: 100
  loop : -1.57 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 352 
 HIS   0.002   0.001   HIS A 360 
 PHE   0.034   0.002   PHE A 267 
 TYR   0.007   0.001   TYR A 160 
 ARG   0.002   0.000   ARG B 193 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.613 
Fit side-chains
REVERT: A  119 LYS cc_start: 0.6643 (pttt) cc_final: 0.6378 (ptmm)
REVERT: A  228 MET cc_start: 0.6839 (mtm) cc_final: 0.6537 (mtp)
REVERT: A  313 GLN cc_start: 0.5796 (tp-100) cc_final: 0.5578 (mt0)
REVERT: A  316 MET cc_start: 0.5871 (ptp) cc_final: 0.5106 (ptt)
REVERT: A  320 PHE cc_start: 0.6789 (p90) cc_final: 0.5657 (p90)
REVERT: A  328 LYS cc_start: 0.5720 (ttmm) cc_final: 0.5416 (ttpt)
REVERT: A  331 ASN cc_start: 0.7059 (m-40) cc_final: 0.6816 (m-40)
REVERT: B  210 ASP cc_start: 0.6151 (t0) cc_final: 0.5945 (t0)
REVERT: B  247 GLN cc_start: 0.6086 (pt0) cc_final: 0.5367 (pm20)
REVERT: B  282 MET cc_start: 0.5447 (tpp) cc_final: 0.5172 (mtt)
REVERT: B  347 HIS cc_start: 0.5805 (t70) cc_final: 0.5526 (t-170)
  outliers start: 2
  outliers final: 1
  residues processed: 100
  average time/residue: 0.2431
  time to fit residues: 31.2997
Evaluate side-chains
  65 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    7.9990
   chunk 54 optimal weight:    0.4980
   chunk 30 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 56 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 65 optimal weight:   10.0000
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 126 GLN
A 238 GLN
A 247 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.197158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.162492 restraints weight = 8731.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.4033 rms_B_bonded: 1.44
r_work: 0.3819 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3671 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8206  Z= 0.175
  Angle     :  0.532   8.542  11766  Z= 0.276
  Chirality :  0.035   0.194   1406
  Planarity :  0.004   0.034    996
  Dihedral  : 21.066 162.652   2821
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 32.81 %
    Favored  : 64.06 %
  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: -0.61 (0.35), residues: 570
  helix:  1.83 (0.42), residues: 146
  sheet: -0.48 (0.50), residues: 90
  loop : -1.49 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 352 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.021   0.002   PHE A 320 
 TYR   0.008   0.001   TYR A 197 
 ARG   0.004   0.001   ARG B 133 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.596 
Fit side-chains
REVERT: A  304 ASN cc_start: 0.6927 (m-40) cc_final: 0.5988 (t0)
REVERT: A  316 MET cc_start: 0.5927 (ptp) cc_final: 0.5631 (ptt)
REVERT: B  247 GLN cc_start: 0.5854 (pt0) cc_final: 0.5593 (pm20)
REVERT: B  282 MET cc_start: 0.6263 (tpp) cc_final: 0.5958 (mtt)
REVERT: B  303 LEU cc_start: 0.7443 (pp) cc_final: 0.6862 (mt)
  outliers start: 16
  outliers final: 9
  residues processed: 76
  average time/residue: 0.1887
  time to fit residues: 20.0659
Evaluate side-chains
  66 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  361 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 52 optimal weight:    0.0970
   chunk 0 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 43 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 16 optimal weight:    0.0010
   chunk 57 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    2.2190

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

Flipped N/Q/H residues before XYZ refinement:
A  84 ASN
A 126 GLN
A 247 GLN
B  64 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.190663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.156493 restraints weight = 8863.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3981 rms_B_bonded: 1.33
r_work: 0.3753 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3608 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8206  Z= 0.283
  Angle     :  0.617   8.514  11766  Z= 0.320
  Chirality :  0.040   0.254   1406
  Planarity :  0.004   0.037    996
  Dihedral  : 21.130 158.403   2818
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 28.91 %
    Favored  : 65.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.99 (0.34), residues: 570
  helix:  1.03 (0.40), residues: 158
  sheet: -0.55 (0.50), residues: 90
  loop : -1.62 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 177 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.028   0.002   PHE A 320 
 TYR   0.013   0.002   TYR B 276 
 ARG   0.004   0.001   ARG B 133 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 54
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 ASN cc_start: 0.6746 (m-40) cc_final: 0.6111 (t0)
REVERT: A  316 MET cc_start: 0.6833 (ptp) cc_final: 0.6477 (ptt)
REVERT: B   64 HIS cc_start: 0.6821 (OUTLIER) cc_final: 0.6258 (t-90)
REVERT: B   82 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.7359 (mt0)
REVERT: B  156 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6599 (pt0)
REVERT: B  260 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6593 (tp30)
REVERT: B  279 VAL cc_start: 0.6869 (OUTLIER) cc_final: 0.6650 (m)
REVERT: B  303 LEU cc_start: 0.7433 (pp) cc_final: 0.6660 (mt)
REVERT: B  350 GLN cc_start: 0.6745 (OUTLIER) cc_final: 0.6312 (mt0)
  outliers start: 29
  outliers final: 14
  residues processed: 75
  average time/residue: 0.1697
  time to fit residues: 18.3009
Evaluate side-chains
  67 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 48
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  350 GLN
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  361 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 47 optimal weight:    0.1980
   chunk 32 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0010
   overall best weight:    1.0190

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

Flipped N/Q/H residues before XYZ refinement:
B  64 HIS
B 266 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.194003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.158190 restraints weight = 8870.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.4002 rms_B_bonded: 1.48
r_work: 0.3789 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3637 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8206  Z= 0.164
  Angle     :  0.520   8.142  11766  Z= 0.271
  Chirality :  0.035   0.211   1406
  Planarity :  0.004   0.039    996
  Dihedral  : 20.900 156.297   2818
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 29.10 %
    Favored  : 66.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.34), residues: 570
  helix:  1.47 (0.42), residues: 146
  sheet: -0.58 (0.49), residues: 90
  loop : -1.47 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 352 
 HIS   0.006   0.001   HIS B  64 
 PHE   0.022   0.001   PHE A 320 
 TYR   0.008   0.001   TYR A 195 
 ARG   0.005   0.000   ARG B 280 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 49
  time to evaluate  : 0.608 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.6356 (mp10)
REVERT: A  275 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7799 (tt)
REVERT: A  304 ASN cc_start: 0.6460 (m-40) cc_final: 0.5770 (t0)
REVERT: A  316 MET cc_start: 0.6602 (ptp) cc_final: 0.6341 (ptt)
REVERT: B   82 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7347 (mp10)
REVERT: B  156 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6492 (pt0)
REVERT: B  279 VAL cc_start: 0.6422 (OUTLIER) cc_final: 0.6215 (m)
REVERT: B  303 LEU cc_start: 0.7266 (pp) cc_final: 0.6565 (mt)
  outliers start: 20
  outliers final: 9
  residues processed: 66
  average time/residue: 0.1572
  time to fit residues: 15.2373
Evaluate side-chains
  60 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 GLN
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  362 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 64 optimal weight:   20.0000
   chunk 51 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 65 optimal weight:   10.0000
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.195665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.160214 restraints weight = 8867.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.4031 rms_B_bonded: 1.46
r_work: 0.3822 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3677 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8206  Z= 0.153
  Angle     :  0.488   7.479  11766  Z= 0.254
  Chirality :  0.034   0.186   1406
  Planarity :  0.003   0.031    996
  Dihedral  : 20.780 153.933   2818
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 28.52 %
    Favored  : 67.38 %
  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: -0.67 (0.34), residues: 570
  helix:  1.55 (0.42), residues: 146
  sheet: -0.43 (0.49), residues: 90
  loop : -1.43 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 352 
 HIS   0.002   0.001   HIS A 162 
 PHE   0.022   0.001   PHE A 320 
 TYR   0.008   0.001   TYR A 195 
 ARG   0.005   0.000   ARG B 280 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 52
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
REVERT: A  282 MET cc_start: 0.6556 (mpp) cc_final: 0.6277 (mtm)
REVERT: A  304 ASN cc_start: 0.6304 (m-40) cc_final: 0.5583 (t0)
REVERT: A  316 MET cc_start: 0.6547 (ptp) cc_final: 0.6240 (ptt)
REVERT: B   82 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7318 (mp10)
REVERT: B  156 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6556 (pt0)
REVERT: B  282 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6593 (tpp)
REVERT: B  300 ASP cc_start: 0.6266 (m-30) cc_final: 0.6064 (m-30)
REVERT: B  303 LEU cc_start: 0.7478 (pp) cc_final: 0.6604 (mt)
  outliers start: 21
  outliers final: 12
  residues processed: 66
  average time/residue: 0.1580
  time to fit residues: 15.3519
Evaluate side-chains
  63 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASN
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  318 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 26 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 67 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 69 optimal weight:    7.9990
   chunk 55 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
B  64 HIS
B 347 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.189566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.155097 restraints weight = 8821.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3965 rms_B_bonded: 1.29
r_work: 0.3752 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3605 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8206  Z= 0.342
  Angle     :  0.652   8.658  11766  Z= 0.335
  Chirality :  0.042   0.269   1406
  Planarity :  0.005   0.038    996
  Dihedral  : 21.089 156.035   2818
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 27.73 %
    Favored  : 66.80 %
  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: -1.24 (0.34), residues: 570
  helix:  0.67 (0.40), residues: 158
  sheet: -0.58 (0.49), residues: 90
  loop : -1.73 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 177 
 HIS   0.005   0.001   HIS A 162 
 PHE   0.028   0.002   PHE A 320 
 TYR   0.015   0.002   TYR A 195 
 ARG   0.004   0.001   ARG B 280 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 50
  time to evaluate  : 0.632 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.6520 (mp10)
REVERT: A  198 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.7046 (m-80)
REVERT: A  316 MET cc_start: 0.6864 (ptp) cc_final: 0.6629 (ptt)
REVERT: B   82 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7450 (mp10)
REVERT: B  156 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6550 (pt0)
REVERT: B  282 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6635 (tpp)
REVERT: B  304 ASN cc_start: 0.7020 (m-40) cc_final: 0.6725 (m-40)
REVERT: B  350 GLN cc_start: 0.6687 (OUTLIER) cc_final: 0.6273 (mt0)
  outliers start: 28
  outliers final: 17
  residues processed: 71
  average time/residue: 0.1768
  time to fit residues: 17.7740
Evaluate side-chains
  70 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 47
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 GLN
Chi-restraints excluded: chain A residue   84 ASN
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  198 PHE
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  350 GLN
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  362 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 70 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   chunk 59 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 = 0.4321 r_free = 0.4321 target = 0.188438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.153356 restraints weight = 8854.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3954 rms_B_bonded: 1.35
r_work: 0.3740 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3594 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8206  Z= 0.341
  Angle     :  0.670  11.636  11766  Z= 0.342
  Chirality :  0.042   0.268   1406
  Planarity :  0.005   0.041    996
  Dihedral  : 21.135 156.955   2818
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 26.56 %
    Favored  : 67.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.51 (0.34), residues: 570
  helix:  0.38 (0.40), residues: 160
  sheet: -0.74 (0.48), residues: 90
  loop : -1.88 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 177 
 HIS   0.009   0.001   HIS A 162 
 PHE   0.031   0.002   PHE A 320 
 TYR   0.015   0.002   TYR A 195 
 ARG   0.004   0.001   ARG B 280 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 49
  time to evaluate  : 0.655 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.6523 (mp10)
REVERT: A  131 ASP cc_start: 0.7140 (OUTLIER) cc_final: 0.6882 (t0)
REVERT: A  316 MET cc_start: 0.6827 (ptp) cc_final: 0.6554 (ptt)
REVERT: B   82 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.7504 (mp10)
REVERT: B   92 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8073 (mmtt)
REVERT: B  156 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6575 (pt0)
REVERT: B  282 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6657 (tpp)
REVERT: B  304 ASN cc_start: 0.7013 (m-40) cc_final: 0.6724 (m-40)
REVERT: B  350 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.6344 (mt0)
  outliers start: 30
  outliers final: 18
  residues processed: 71
  average time/residue: 0.1872
  time to fit residues: 18.7670
Evaluate side-chains
  68 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 43
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 GLN
Chi-restraints excluded: chain A residue   84 ASN
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue   92 LYS
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  350 GLN
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  362 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 29 optimal weight:    6.9990
   chunk 31 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4386 r_free = 0.4386 target = 0.194809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.158852 restraints weight = 8897.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.4009 rms_B_bonded: 1.50
r_work: 0.3800 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3649 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.3289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8206  Z= 0.153
  Angle     :  0.527  11.213  11766  Z= 0.272
  Chirality :  0.035   0.200   1406
  Planarity :  0.004   0.034    996
  Dihedral  : 20.829 154.719   2818
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 26.76 %
    Favored  : 68.55 %
  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: -0.97 (0.35), residues: 570
  helix:  0.90 (0.42), residues: 160
  sheet: -0.48 (0.49), residues: 90
  loop : -1.55 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 352 
 HIS   0.002   0.001   HIS A 162 
 PHE   0.023   0.001   PHE A 320 
 TYR   0.008   0.001   TYR A 314 
 ARG   0.008   0.000   ARG B 193 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 48
  time to evaluate  : 0.589 
Fit side-chains
REVERT: A  131 ASP cc_start: 0.6957 (OUTLIER) cc_final: 0.6690 (t0)
REVERT: A  316 MET cc_start: 0.6624 (ptp) cc_final: 0.6351 (ptt)
REVERT: B   53 ARG cc_start: 0.6218 (OUTLIER) cc_final: 0.5597 (ppt170)
REVERT: B   82 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.7438 (mp10)
REVERT: B   92 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8008 (mmtt)
REVERT: B  156 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6530 (pt0)
REVERT: B  282 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6581 (tpp)
REVERT: B  304 ASN cc_start: 0.6943 (m-40) cc_final: 0.6666 (m-40)
REVERT: B  350 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6395 (mt0)
  outliers start: 24
  outliers final: 13
  residues processed: 67
  average time/residue: 0.1827
  time to fit residues: 17.1794
Evaluate side-chains
  66 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 46
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASN
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain B residue   53 ARG
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue   92 LYS
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  350 GLN
Chi-restraints excluded: chain B residue  361 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 69 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
B 347 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.188589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.153204 restraints weight = 8935.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 1.38
r_work: 0.3735 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3586 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8206  Z= 0.344
  Angle     :  0.671  12.501  11766  Z= 0.342
  Chirality :  0.042   0.270   1406
  Planarity :  0.005   0.040    996
  Dihedral  : 21.111 157.900   2818
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 26.76 %
    Favored  : 68.16 %
  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: -1.20 (0.34), residues: 570
  helix:  0.83 (0.42), residues: 148
  sheet: -0.64 (0.49), residues: 90
  loop : -1.68 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 177 
 HIS   0.007   0.001   HIS A 162 
 PHE   0.031   0.002   PHE A 320 
 TYR   0.016   0.002   TYR A 195 
 ARG   0.006   0.000   ARG B 193 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 45
  time to evaluate  : 0.597 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.6547 (mp10)
REVERT: A  131 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6902 (t0)
REVERT: A  316 MET cc_start: 0.6793 (ptp) cc_final: 0.6521 (ptt)
REVERT: B   53 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5719 (ppt170)
REVERT: B   82 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.7554 (mp10)
REVERT: B   92 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7639 (mttm)
REVERT: B  156 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6555 (pt0)
REVERT: B  282 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6716 (tpp)
REVERT: B  304 ASN cc_start: 0.7041 (m-40) cc_final: 0.6704 (m-40)
REVERT: B  350 GLN cc_start: 0.6768 (OUTLIER) cc_final: 0.6347 (mt0)
  outliers start: 26
  outliers final: 16
  residues processed: 64
  average time/residue: 0.1763
  time to fit residues: 16.0039
Evaluate side-chains
  68 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 44
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 GLN
Chi-restraints excluded: chain A residue   84 ASN
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain B residue   53 ARG
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue   92 LYS
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  350 GLN
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  362 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 60 optimal weight:    6.9990
   chunk 69 optimal weight:    8.9990
   chunk 5 optimal weight:    0.3980
   chunk 57 optimal weight:    0.8980
   chunk 18 optimal weight:    0.2980
   chunk 22 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.194486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.159216 restraints weight = 8812.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.4014 rms_B_bonded: 1.42
r_work: 0.3809 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3659 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.3402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8206  Z= 0.161
  Angle     :  0.517   7.912  11766  Z= 0.270
  Chirality :  0.035   0.202   1406
  Planarity :  0.004   0.033    996
  Dihedral  : 20.835 156.116   2818
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 27.15 %
    Favored  : 68.75 %
  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: -0.91 (0.35), residues: 570
  helix:  0.98 (0.42), residues: 158
  sheet: -0.46 (0.50), residues: 90
  loop : -1.52 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 352 
 HIS   0.004   0.001   HIS A 162 
 PHE   0.023   0.001   PHE A 320 
 TYR   0.008   0.001   TYR A 160 
 ARG   0.008   0.000   ARG B 193 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 46
  time to evaluate  : 0.624 
Fit side-chains
REVERT: A  131 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6712 (t0)
REVERT: A  283 MET cc_start: 0.7044 (mmp) cc_final: 0.6650 (tpp)
REVERT: A  316 MET cc_start: 0.6607 (ptp) cc_final: 0.6357 (ptt)
REVERT: B   53 ARG cc_start: 0.6138 (OUTLIER) cc_final: 0.5518 (ppt170)
REVERT: B   82 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.7469 (mp10)
REVERT: B   92 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7993 (mmtt)
REVERT: B  156 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6575 (pt0)
REVERT: B  282 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6689 (tpp)
REVERT: B  304 ASN cc_start: 0.7031 (m-40) cc_final: 0.6726 (m-40)
REVERT: B  350 GLN cc_start: 0.6726 (OUTLIER) cc_final: 0.6330 (mt0)
  outliers start: 21
  outliers final: 14
  residues processed: 63
  average time/residue: 0.1746
  time to fit residues: 15.6837
Evaluate side-chains
  65 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 44
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASN
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain B residue   53 ARG
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue   84 ASN
Chi-restraints excluded: chain B residue   92 LYS
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  350 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 64 optimal weight:   20.0000
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 66 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 9 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 48 optimal weight:    6.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
B 347 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.193092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.157666 restraints weight = 8850.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.4001 rms_B_bonded: 1.40
r_work: 0.3792 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3643 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8206  Z= 0.190
  Angle     :  0.532   7.741  11766  Z= 0.277
  Chirality :  0.036   0.210   1406
  Planarity :  0.004   0.037    996
  Dihedral  : 20.857 155.645   2818
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 26.56 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.35), residues: 570
  helix:  1.03 (0.42), residues: 158
  sheet: -0.52 (0.49), residues: 90
  loop : -1.44 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 177 
 HIS   0.005   0.001   HIS A 162 
 PHE   0.025   0.002   PHE A 320 
 TYR   0.010   0.001   TYR A 195 
 ARG   0.007   0.000   ARG B 193 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4229.18 seconds
wall clock time: 75 minutes 29.27 seconds (4529.27 seconds total)