Starting phenix.real_space_refine
on Mon Apr 28 02:04:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8un2_42391/04_2025/8un2_42391.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8un2_42391/04_2025/8un2_42391.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8un2_42391/04_2025/8un2_42391.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8un2_42391/04_2025/8un2_42391.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8un2_42391/04_2025/8un2_42391.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8un2_42391/04_2025/8un2_42391.cif"
  }
  resolution = 2.3
  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=   0.025
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
     Mn      2      7.51       5
     S      20      5.16       5
     C    4378      2.51       5
     N    1172      2.21       5
     O    1282      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 6854
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 433, 3426
          Classifications: {'peptide': 433}
          Link IDs: {'PCIS': 4, 'PTRANS': 29, 'TRANS': 399}
    Chain: "B"
      Number of atoms: 3426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 433, 3426
          Classifications: {'peptide': 433}
          Link IDs: {'PCIS': 4, 'PTRANS': 29, 'TRANS': 399}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.31, per 1000 atoms: 0.63
  Number of scatterers: 6854
  At special positions: 0
  Unit cell: (92.3832, 108.626, 68.0184, 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)
     Mn      2     24.99
     S      20     16.00
     O    1282      8.00
     N    1172      7.00
     C    4378      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: 1.65
  Conformation dependent library (CDL) restraints added in 915.5 milliseconds
  

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1584

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 8 sheets defined
      34.9% alpha, 20.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 77
    Processing helix  chain 'A' and resid 117 through 121
    Processing helix  chain 'A' and resid 149 through 151
      No H-bonds generated for 'chain 'A' and resid 149 through 151'
    Processing helix  chain 'A' and resid 160 through 171
    Processing helix  chain 'A' and resid 180 through 184
    Processing helix  chain 'A' and resid 191 through 206
      removed outlier: 3.524A  pdb=" N   SER A 203 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 250
      removed outlier: 3.568A  pdb=" N   ALA A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 286
      removed outlier: 3.670A  pdb=" N   GLU A 276 " --> pdb=" O   THR A 272 " (cutoff:3.500A)
      Proline residue:  A 280  - end of helix
    Processing helix  chain 'A' and resid 301 through 315
    Processing helix  chain 'A' and resid 326 through 329
    Processing helix  chain 'A' and resid 345 through 350
      removed outlier: 3.596A  pdb=" N   ASP A 349 " --> pdb=" O   ALA A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 360
      removed outlier: 3.555A  pdb=" N   VAL A 358 " --> pdb=" O   PRO A 355 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ASP A 360 " --> pdb=" O   ASP A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 396
    Processing helix  chain 'A' and resid 413 through 433
      removed outlier: 4.141A  pdb=" N   GLU A 417 " --> pdb=" O   TRP A 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 77
    Processing helix  chain 'B' and resid 117 through 121
    Processing helix  chain 'B' and resid 149 through 151
      No H-bonds generated for 'chain 'B' and resid 149 through 151'
    Processing helix  chain 'B' and resid 160 through 171
    Processing helix  chain 'B' and resid 180 through 184
    Processing helix  chain 'B' and resid 191 through 206
      removed outlier: 3.524A  pdb=" N   SER B 203 " --> pdb=" O   PHE B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 250
      removed outlier: 3.569A  pdb=" N   ALA B 238 " --> pdb=" O   GLU B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 286
      removed outlier: 3.670A  pdb=" N   GLU B 276 " --> pdb=" O   THR B 272 " (cutoff:3.500A)
      Proline residue:  B 280  - end of helix
    Processing helix  chain 'B' and resid 301 through 315
    Processing helix  chain 'B' and resid 326 through 329
    Processing helix  chain 'B' and resid 345 through 350
      removed outlier: 3.596A  pdb=" N   ASP B 349 " --> pdb=" O   ALA B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 360
      removed outlier: 3.556A  pdb=" N   VAL B 358 " --> pdb=" O   PRO B 355 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ASP B 360 " --> pdb=" O   ASP B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 396
    Processing helix  chain 'B' and resid 413 through 433
      removed outlier: 4.142A  pdb=" N   GLU B 417 " --> pdb=" O   TRP B 413 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 18
      removed outlier: 3.671A  pdb=" N   GLY A  24 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   GLU A  18 " --> pdb=" O   ILE A  22 " (cutoff:3.500A)
      removed outlier: 5.697A  pdb=" N   ILE A  22 " --> pdb=" O   GLU A  18 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE A  89 " --> pdb=" O   THR A  63 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38
    Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54
      removed outlier: 3.640A  pdb=" N   GLY A  44 " --> pdb=" O   ARG A 110 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL A 127 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 288 through 289
      removed outlier: 7.582A  pdb=" N   ILE A 176 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   MET A 212 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ILE A 178 " --> pdb=" O   MET A 212 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   SER A 214 " --> pdb=" O   ILE A 178 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   TYR A 144 " --> pdb=" O   GLY A 175 " (cutoff:3.500A)
      removed outlier: 8.417A  pdb=" N   GLU A 177 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL A 146 " --> pdb=" O   GLU A 177 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   LEU A 179 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   TYR A 406 " --> pdb=" O   SER A 147 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   TYR A 401 " --> pdb=" O   VAL A 366 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE A 368 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 7.368A  pdb=" N   LEU A 321 " --> pdb=" O   VAL A 366 " (cutoff:3.500A)
      removed outlier: 6.016A  pdb=" N   ILE A 368 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   LEU A 323 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   ALA A 370 " --> pdb=" O   LEU A 323 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ILE A 293 " --> pdb=" O   ASP A 324 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 18
      removed outlier: 3.672A  pdb=" N   GLY B  24 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   GLU B  18 " --> pdb=" O   ILE B  22 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   ILE B  22 " --> pdb=" O   GLU B  18 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE B  89 " --> pdb=" O   THR B  63 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 38
    Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54
      removed outlier: 3.641A  pdb=" N   GLY B  44 " --> pdb=" O   ARG B 110 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL B 127 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 288 through 289
      removed outlier: 7.582A  pdb=" N   ILE B 176 " --> pdb=" O   THR B 210 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   MET B 212 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ILE B 178 " --> pdb=" O   MET B 212 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   SER B 214 " --> pdb=" O   ILE B 178 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   TYR B 144 " --> pdb=" O   GLY B 175 " (cutoff:3.500A)
      removed outlier: 8.417A  pdb=" N   GLU B 177 " --> pdb=" O   TYR B 144 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL B 146 " --> pdb=" O   GLU B 177 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   LEU B 179 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   TYR B 406 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 5.103A  pdb=" N   TYR B 401 " --> pdb=" O   VAL B 366 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE B 368 " --> pdb=" O   TYR B 401 " (cutoff:3.500A)
      removed outlier: 7.368A  pdb=" N   LEU B 321 " --> pdb=" O   VAL B 366 " (cutoff:3.500A)
      removed outlier: 6.016A  pdb=" N   ILE B 368 " --> pdb=" O   LEU B 321 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   LEU B 323 " --> pdb=" O   ILE B 368 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   ALA B 370 " --> pdb=" O   LEU B 323 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ILE B 293 " --> pdb=" O   ASP B 324 " (cutoff:3.500A)

    278 hydrogen bonds defined for protein.
    744 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.87

  Time building geometry restraints manager: 1.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2204
        1.33 -     1.45: 989
        1.45 -     1.57: 3801
        1.57 -     1.69: 0
        1.69 -     1.80: 38
  Bond restraints: 7032
  Sorted by residual:
  bond pdb=" CB  ARG B   5 "
       pdb=" CG  ARG B   5 "
    ideal  model  delta    sigma   weight residual
    1.520  1.459  0.061 3.00e-02 1.11e+03 4.18e+00
  bond pdb=" CB  ARG A   5 "
       pdb=" CG  ARG A   5 "
    ideal  model  delta    sigma   weight residual
    1.520  1.459  0.061 3.00e-02 1.11e+03 4.18e+00
  bond pdb=" CB  VAL B 254 "
       pdb=" CG2 VAL B 254 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.71e+00
  bond pdb=" CB  VAL A 254 "
       pdb=" CG2 VAL A 254 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.63e+00
  bond pdb=" CB  PRO B 122 "
       pdb=" CG  PRO B 122 "
    ideal  model  delta    sigma   weight residual
    1.506  1.449  0.057 3.90e-02 6.57e+02 2.11e+00
  ... (remaining 7027 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 9021
        1.49 -     2.98: 467
        2.98 -     4.46: 76
        4.46 -     5.95: 12
        5.95 -     7.44: 8
  Bond angle restraints: 9584
  Sorted by residual:
  angle pdb=" C   PRO B 412 "
        pdb=" N   TRP B 413 "
        pdb=" CA  TRP B 413 "
      ideal   model   delta    sigma   weight residual
     123.91  130.05   -6.14 1.66e+00 3.63e-01 1.37e+01
  angle pdb=" C   PRO A 412 "
        pdb=" N   TRP A 413 "
        pdb=" CA  TRP A 413 "
      ideal   model   delta    sigma   weight residual
     123.91  130.03   -6.12 1.66e+00 3.63e-01 1.36e+01
  angle pdb=" CA  PRO B  60 "
        pdb=" N   PRO B  60 "
        pdb=" CD  PRO B  60 "
      ideal   model   delta    sigma   weight residual
     112.00  108.19    3.81 1.40e+00 5.10e-01 7.39e+00
  angle pdb=" CA  PRO A  60 "
        pdb=" N   PRO A  60 "
        pdb=" CD  PRO A  60 "
      ideal   model   delta    sigma   weight residual
     112.00  108.23    3.77 1.40e+00 5.10e-01 7.26e+00
  angle pdb=" CA  VAL A  59 "
        pdb=" C   VAL A  59 "
        pdb=" N   PRO A  60 "
      ideal   model   delta    sigma   weight residual
     118.88  122.91   -4.03 1.54e+00 4.22e-01 6.86e+00
  ... (remaining 9579 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.57: 3756
       16.57 -    33.13: 338
       33.13 -    49.70: 78
       49.70 -    66.26: 18
       66.26 -    82.83: 10
  Dihedral angle restraints: 4200
    sinusoidal: 1724
      harmonic: 2476
  Sorted by residual:
  dihedral pdb=" CA  ILE B 178 "
           pdb=" C   ILE B 178 "
           pdb=" N   LEU B 179 "
           pdb=" CA  LEU B 179 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.57   18.43     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  ALA A 134 "
           pdb=" C   ALA A 134 "
           pdb=" N   PRO A 135 "
           pdb=" CA  PRO A 135 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.60  -18.40     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  ILE A 178 "
           pdb=" C   ILE A 178 "
           pdb=" N   LEU A 179 "
           pdb=" CA  LEU A 179 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.60   18.40     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 4197 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 531
       0.035 -    0.070: 333
       0.070 -    0.105: 120
       0.105 -    0.140: 49
       0.140 -    0.174: 15
  Chirality restraints: 1048
  Sorted by residual:
  chirality pdb=" CA  GLU A 387 "
            pdb=" N   GLU A 387 "
            pdb=" C   GLU A 387 "
            pdb=" CB  GLU A 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.61e-01
  chirality pdb=" CA  GLU B 387 "
            pdb=" N   GLU B 387 "
            pdb=" C   GLU B 387 "
            pdb=" CB  GLU B 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.10e-01
  chirality pdb=" CB  ILE A 176 "
            pdb=" CA  ILE A 176 "
            pdb=" CG1 ILE A 176 "
            pdb=" CG2 ILE A 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.54e-01
  ... (remaining 1045 not shown)

  Planarity restraints: 1260
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 279 "    0.051 5.00e-02 4.00e+02   7.60e-02 9.25e+00
        pdb=" N   PRO B 280 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO B 280 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B 280 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 279 "   -0.050 5.00e-02 4.00e+02   7.56e-02 9.15e+00
        pdb=" N   PRO A 280 "    0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A 280 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 280 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 340 "    0.036 5.00e-02 4.00e+02   5.38e-02 4.63e+00
        pdb=" N   PRO A 341 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 341 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 341 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1257 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 40
        2.59 -     3.17: 5243
        3.17 -     3.74: 10501
        3.74 -     4.32: 16114
        4.32 -     4.90: 26060
  Nonbonded interactions: 57958
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 292 "
            pdb="MN    MN A 501 "
     model   vdw
     2.009 2.320
  nonbonded pdb=" OE2 GLU B 292 "
            pdb="MN    MN B 501 "
     model   vdw
     2.014 2.320
  nonbonded pdb=" OE1 GLN A 369 "
            pdb="MN    MN A 501 "
     model   vdw
     2.155 2.320
  nonbonded pdb=" OE1 GLN B 369 "
            pdb="MN    MN B 501 "
     model   vdw
     2.164 2.320
  nonbonded pdb=" OD2 ASP B 324 "
            pdb="MN    MN B 501 "
     model   vdw
     2.196 2.320
  ... (remaining 57953 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.770
  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:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     19.090
  Find NCS groups from input model:        0.110
  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:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
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      :  0.009   0.061   7032  Z= 0.378
  Angle     :  0.795   7.438   9584  Z= 0.461
  Chirality :  0.054   0.174   1048
  Planarity :  0.008   0.076   1260
  Dihedral  : 14.149  82.828   2616
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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: -2.74 (0.25), residues: 862
  helix: -4.08 (0.13), residues: 230
  sheet: -0.94 (0.41), residues: 154
  loop : -0.81 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP B 198 
 HIS   0.010   0.002   HIS A 352 
 PHE   0.013   0.002   PHE A 347 
 TYR   0.019   0.002   TYR A 144 
 ARG   0.007   0.001   ARG A   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27668 (  278)
  hydrogen bonds       : angle       9.07532 (  744)
  covalent geometry    : bond        0.00910 ( 7032)
  covalent geometry    : angle       0.79500 ( 9584)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.765 
Fit side-chains
REVERT: A   43 ASP cc_start: 0.7893 (t70) cc_final: 0.7591 (m-30)
REVERT: A  119 GLU cc_start: 0.7450 (pm20) cc_final: 0.7136 (pm20)
REVERT: A  126 ARG cc_start: 0.7975 (mtt-85) cc_final: 0.7690 (mtt-85)
REVERT: A  273 GLU cc_start: 0.7066 (pm20) cc_final: 0.6475 (pm20)
REVERT: A  276 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7126 (mt-10)
REVERT: A  286 ASP cc_start: 0.7718 (t70) cc_final: 0.7445 (t0)
REVERT: A  349 ASP cc_start: 0.7296 (m-30) cc_final: 0.7054 (m-30)
REVERT: A  391 LYS cc_start: 0.7802 (tttm) cc_final: 0.7537 (tttm)
REVERT: A  428 GLN cc_start: 0.7918 (mt0) cc_final: 0.7485 (mt0)
REVERT: B   21 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7141 (mm-30)
REVERT: B  110 ARG cc_start: 0.7849 (mtt180) cc_final: 0.7634 (mtt180)
REVERT: B  118 GLN cc_start: 0.7459 (tp40) cc_final: 0.7125 (mm-40)
REVERT: B  119 GLU cc_start: 0.7410 (pm20) cc_final: 0.6998 (pm20)
REVERT: B  159 MET cc_start: 0.8620 (ttm) cc_final: 0.8350 (ttp)
REVERT: B  192 ASP cc_start: 0.8022 (m-30) cc_final: 0.7747 (m-30)
REVERT: B  241 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7544 (ttp-170)
REVERT: B  257 LYS cc_start: 0.8274 (tppp) cc_final: 0.8036 (tptm)
REVERT: B  273 GLU cc_start: 0.6856 (pm20) cc_final: 0.6465 (pm20)
REVERT: B  276 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7264 (mt-10)
REVERT: B  369 GLN cc_start: 0.6582 (mt0) cc_final: 0.6361 (mt0)
REVERT: B  377 GLU cc_start: 0.7130 (mp0) cc_final: 0.6816 (mp0)
REVERT: B  431 ASP cc_start: 0.7113 (m-30) cc_final: 0.6815 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 1.6362
  time to fit residues: 271.4183
Evaluate side-chains
  139 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 50 optimal weight:    0.4980
   chunk 78 optimal weight:    0.6980
   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  67 GLN
A 121 GLN
A 186 ASN
A 221 HIS
A 343 GLN
A 356 ASN
A 369 GLN
B 121 GLN
B 221 HIS
B 343 GLN
B 423 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.112866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.102679 restraints weight = 8479.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 1.35
r_work: 0.3302 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7032  Z= 0.165
  Angle     :  0.557   5.181   9584  Z= 0.293
  Chirality :  0.046   0.143   1048
  Planarity :  0.006   0.044   1260
  Dihedral  :  4.925  18.027    950
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 11.08 %
    Favored  : 87.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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: -0.95 (0.26), residues: 862
  helix: -0.90 (0.26), residues: 256
  sheet: -0.63 (0.42), residues: 154
  loop : -0.32 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 198 
 HIS   0.004   0.001   HIS A 352 
 PHE   0.010   0.001   PHE B 347 
 TYR   0.017   0.001   TYR B 144 
 ARG   0.007   0.001   ARG A  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04159 (  278)
  hydrogen bonds       : angle       5.75091 (  744)
  covalent geometry    : bond        0.00392 ( 7032)
  covalent geometry    : angle       0.55701 ( 9584)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 165
  time to evaluate  : 0.785 
Fit side-chains
REVERT: A  300 LYS cc_start: 0.8228 (mmtp) cc_final: 0.8010 (mmtp)
REVERT: B   31 MET cc_start: 0.8704 (tpt) cc_final: 0.8501 (tpt)
REVERT: B  242 ASP cc_start: 0.7503 (m-30) cc_final: 0.7288 (m-30)
  outliers start: 8
  outliers final: 3
  residues processed: 169
  average time/residue: 1.6165
  time to fit residues: 283.6249
Evaluate side-chains
  158 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 155
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 GLN
Chi-restraints excluded: chain B residue  343 GLN
Chi-restraints excluded: chain B residue  394 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 54 optimal weight:    0.4980
   chunk 23 optimal weight:    0.5980
   chunk 77 optimal weight:    0.0010
   chunk 50 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 423 HIS
A 428 GLN
B 118 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.112879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.102448 restraints weight = 8475.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.38
r_work: 0.3297 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7032  Z= 0.136
  Angle     :  0.517   5.297   9584  Z= 0.269
  Chirality :  0.046   0.137   1048
  Planarity :  0.005   0.036   1260
  Dihedral  :  4.629  16.806    950
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.24 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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:  0.13 (0.28), residues: 862
  helix:  0.79 (0.30), residues: 256
  sheet: -0.45 (0.43), residues: 154
  loop : -0.01 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 198 
 HIS   0.003   0.001   HIS B 318 
 PHE   0.012   0.001   PHE B 347 
 TYR   0.013   0.001   TYR B 144 
 ARG   0.008   0.001   ARG A  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04151 (  278)
  hydrogen bonds       : angle       5.29079 (  744)
  covalent geometry    : bond        0.00324 ( 7032)
  covalent geometry    : angle       0.51651 ( 9584)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 161
  time to evaluate  : 0.844 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6937 (mp0)
REVERT: B   67 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7642 (tm-30)
REVERT: B  242 ASP cc_start: 0.7545 (m-30) cc_final: 0.7316 (m-30)
  outliers start: 13
  outliers final: 5
  residues processed: 166
  average time/residue: 1.6832
  time to fit residues: 289.7391
Evaluate side-chains
  158 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 151
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  394 LYS
Chi-restraints excluded: chain B residue   67 GLN
Chi-restraints excluded: chain B residue  264 ASP
Chi-restraints excluded: chain B residue  300 LYS
Chi-restraints excluded: chain B residue  363 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0980
   chunk 71 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 343 GLN
A 422 GLN
A 428 GLN
B 343 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.113247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.103069 restraints weight = 8537.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.36
r_work: 0.3306 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7032  Z= 0.136
  Angle     :  0.516   7.374   9584  Z= 0.265
  Chirality :  0.046   0.135   1048
  Planarity :  0.005   0.038   1260
  Dihedral  :  4.530  17.812    950
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.38 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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:  0.58 (0.28), residues: 862
  helix:  1.44 (0.31), residues: 256
  sheet: -0.30 (0.43), residues: 154
  loop :  0.14 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 198 
 HIS   0.003   0.001   HIS B 318 
 PHE   0.011   0.001   PHE B 347 
 TYR   0.013   0.001   TYR A 144 
 ARG   0.008   0.001   ARG B  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03928 (  278)
  hydrogen bonds       : angle       5.09729 (  744)
  covalent geometry    : bond        0.00326 ( 7032)
  covalent geometry    : angle       0.51601 ( 9584)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 0.762 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6888 (mp0)
REVERT: B  242 ASP cc_start: 0.7528 (m-30) cc_final: 0.7292 (m-30)
REVERT: B  405 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7360 (mt-10)
  outliers start: 15
  outliers final: 8
  residues processed: 162
  average time/residue: 1.6687
  time to fit residues: 280.0272
Evaluate side-chains
  160 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 151
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  343 GLN
Chi-restraints excluded: chain A residue  394 LYS
Chi-restraints excluded: chain B residue  264 ASP
Chi-restraints excluded: chain B residue  300 LYS
Chi-restraints excluded: chain B residue  343 GLN
Chi-restraints excluded: chain B residue  363 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 428 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.112766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.102589 restraints weight = 8398.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.34
r_work: 0.3297 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7032  Z= 0.158
  Angle     :  0.530   8.613   9584  Z= 0.270
  Chirality :  0.047   0.137   1048
  Planarity :  0.005   0.040   1260
  Dihedral  :  4.604  18.370    950
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 14.32 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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:  0.83 (0.28), residues: 862
  helix:  1.76 (0.31), residues: 256
  sheet: -0.22 (0.43), residues: 154
  loop :  0.24 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 198 
 HIS   0.003   0.001   HIS B 318 
 PHE   0.013   0.001   PHE A 347 
 TYR   0.014   0.001   TYR A 144 
 ARG   0.009   0.001   ARG B  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04060 (  278)
  hydrogen bonds       : angle       5.05772 (  744)
  covalent geometry    : bond        0.00384 ( 7032)
  covalent geometry    : angle       0.52983 ( 9584)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.864 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6919 (mp0)
REVERT: A  405 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7557 (mt-10)
REVERT: B  242 ASP cc_start: 0.7507 (m-30) cc_final: 0.7267 (m-30)
REVERT: B  364 ASN cc_start: 0.8788 (m-40) cc_final: 0.8457 (m-40)
REVERT: B  405 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7385 (tt0)
  outliers start: 14
  outliers final: 8
  residues processed: 158
  average time/residue: 2.1314
  time to fit residues: 349.1226
Evaluate side-chains
  159 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 150
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  394 LYS
Chi-restraints excluded: chain B residue  264 ASP
Chi-restraints excluded: chain B residue  300 LYS
Chi-restraints excluded: chain B residue  363 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 65 optimal weight:    0.0270
   chunk 62 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 50 optimal weight:    0.4980
   chunk 83 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.8240

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

Flipped N/Q/H residues before XYZ refinement:
A 343 GLN
A 428 GLN
B 343 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.110858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.100768 restraints weight = 8457.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.36
r_work: 0.3300 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7032  Z= 0.161
  Angle     :  0.531   6.899   9584  Z= 0.274
  Chirality :  0.047   0.137   1048
  Planarity :  0.005   0.042   1260
  Dihedral  :  4.631  18.678    950
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.73 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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:  0.92 (0.29), residues: 862
  helix:  1.85 (0.31), residues: 256
  sheet: -0.21 (0.43), residues: 154
  loop :  0.30 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 194 
 HIS   0.003   0.001   HIS B 318 
 PHE   0.011   0.001   PHE B 347 
 TYR   0.015   0.001   TYR A 144 
 ARG   0.009   0.001   ARG B  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04096 (  278)
  hydrogen bonds       : angle       5.04161 (  744)
  covalent geometry    : bond        0.00392 ( 7032)
  covalent geometry    : angle       0.53064 ( 9584)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 151
  time to evaluate  : 0.849 
Fit side-chains
REVERT: A  113 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7312 (mmt)
REVERT: A  273 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6941 (mp0)
REVERT: B  242 ASP cc_start: 0.7522 (m-30) cc_final: 0.7282 (m-30)
REVERT: B  364 ASN cc_start: 0.8783 (m-40) cc_final: 0.8423 (m-40)
REVERT: B  405 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7290 (tt0)
  outliers start: 17
  outliers final: 10
  residues processed: 159
  average time/residue: 1.9811
  time to fit residues: 325.6726
Evaluate side-chains
  161 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 149
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  343 GLN
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  394 LYS
Chi-restraints excluded: chain B residue  264 ASP
Chi-restraints excluded: chain B residue  300 LYS
Chi-restraints excluded: chain B residue  343 GLN
Chi-restraints excluded: chain B residue  363 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 428 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.110903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.100893 restraints weight = 8383.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.34
r_work: 0.3303 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.3332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7032  Z= 0.164
  Angle     :  0.546   6.956   9584  Z= 0.281
  Chirality :  0.047   0.137   1048
  Planarity :  0.005   0.044   1260
  Dihedral  :  4.657  18.830    950
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 16.08 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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:  1.04 (0.29), residues: 862
  helix:  1.96 (0.32), residues: 256
  sheet: -0.17 (0.43), residues: 154
  loop :  0.38 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 198 
 HIS   0.003   0.001   HIS B 318 
 PHE   0.013   0.001   PHE A 347 
 TYR   0.015   0.001   TYR A 144 
 ARG   0.010   0.001   ARG A 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04116 (  278)
  hydrogen bonds       : angle       5.02355 (  744)
  covalent geometry    : bond        0.00400 ( 7032)
  covalent geometry    : angle       0.54632 ( 9584)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.774 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7005 (mp0)
REVERT: B   67 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7701 (tm-30)
REVERT: B  242 ASP cc_start: 0.7527 (m-30) cc_final: 0.7288 (m-30)
REVERT: B  364 ASN cc_start: 0.8791 (m-40) cc_final: 0.8432 (m-40)
REVERT: B  405 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7315 (tt0)
  outliers start: 17
  outliers final: 9
  residues processed: 155
  average time/residue: 1.7205
  time to fit residues: 276.4706
Evaluate side-chains
  159 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 148
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  394 LYS
Chi-restraints excluded: chain B residue   67 GLN
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue  264 ASP
Chi-restraints excluded: chain B residue  300 LYS
Chi-restraints excluded: chain B residue  363 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 54 optimal weight:    0.6980
   chunk 44 optimal weight:    0.2980
   chunk 33 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 76 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0000
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 343 GLN
A 428 GLN
B 343 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.112060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.102075 restraints weight = 8473.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 1.35
r_work: 0.3322 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7032  Z= 0.121
  Angle     :  0.527   7.211   9584  Z= 0.269
  Chirality :  0.046   0.138   1048
  Planarity :  0.005   0.042   1260
  Dihedral  :  4.472  17.673    950
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 16.49 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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:  1.17 (0.29), residues: 862
  helix:  2.09 (0.32), residues: 256
  sheet: -0.12 (0.43), residues: 154
  loop :  0.45 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 198 
 HIS   0.002   0.001   HIS B 318 
 PHE   0.014   0.001   PHE A 347 
 TYR   0.014   0.001   TYR A 144 
 ARG   0.011   0.001   ARG A  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03673 (  278)
  hydrogen bonds       : angle       4.92109 (  744)
  covalent geometry    : bond        0.00288 ( 7032)
  covalent geometry    : angle       0.52724 ( 9584)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 0.900 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6939 (mp0)
REVERT: B  242 ASP cc_start: 0.7501 (m-30) cc_final: 0.7261 (m-30)
REVERT: B  364 ASN cc_start: 0.8782 (m-40) cc_final: 0.8425 (m-40)
REVERT: B  405 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7238 (tt0)
  outliers start: 17
  outliers final: 11
  residues processed: 163
  average time/residue: 1.8207
  time to fit residues: 307.2200
Evaluate side-chains
  161 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 149
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  343 GLN
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  394 LYS
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue  264 ASP
Chi-restraints excluded: chain B residue  300 LYS
Chi-restraints excluded: chain B residue  343 GLN
Chi-restraints excluded: chain B residue  363 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0970
   chunk 45 optimal weight:    0.8980
   chunk 56 optimal weight:    0.1980
   chunk 67 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 343 GLN
A 428 GLN
B 343 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.112161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.101982 restraints weight = 8533.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 1.37
r_work: 0.3318 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.3458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7032  Z= 0.127
  Angle     :  0.542   8.114   9584  Z= 0.276
  Chirality :  0.046   0.139   1048
  Planarity :  0.005   0.039   1260
  Dihedral  :  4.456  17.785    950
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.03 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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 (0.29), residues: 862
  helix:  2.09 (0.32), residues: 256
  sheet: -0.13 (0.43), residues: 154
  loop :  0.51 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 198 
 HIS   0.002   0.001   HIS B 318 
 PHE   0.012   0.001   PHE A 347 
 TYR   0.014   0.001   TYR A 187 
 ARG   0.011   0.001   ARG A  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03704 (  278)
  hydrogen bonds       : angle       4.89709 (  744)
  covalent geometry    : bond        0.00306 ( 7032)
  covalent geometry    : angle       0.54207 ( 9584)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 0.788 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6916 (mp0)
REVERT: B  242 ASP cc_start: 0.7519 (m-30) cc_final: 0.7278 (m-30)
REVERT: B  364 ASN cc_start: 0.8776 (m-40) cc_final: 0.8427 (m-40)
REVERT: B  405 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7254 (tt0)
  outliers start: 16
  outliers final: 14
  residues processed: 156
  average time/residue: 1.7640
  time to fit residues: 285.0147
Evaluate side-chains
  164 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 149
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  343 GLN
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  394 LYS
Chi-restraints excluded: chain A residue  407 GLU
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  264 ASP
Chi-restraints excluded: chain B residue  300 LYS
Chi-restraints excluded: chain B residue  343 GLN
Chi-restraints excluded: chain B residue  363 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0770
   chunk 44 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 69 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0570
   chunk 25 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.4656

-------------------------------------------------------------------------------
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 = 0.3576 r_free = 0.3576 target = 0.112499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.102331 restraints weight = 8547.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 1.37
r_work: 0.3325 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7032  Z= 0.117
  Angle     :  0.536   9.227   9584  Z= 0.271
  Chirality :  0.046   0.139   1048
  Planarity :  0.005   0.039   1260
  Dihedral  :  4.423  17.428    950
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.43 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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:  1.25 (0.29), residues: 862
  helix:  2.14 (0.32), residues: 256
  sheet: -0.13 (0.43), residues: 154
  loop :  0.54 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 198 
 HIS   0.002   0.001   HIS B 318 
 PHE   0.011   0.001   PHE A 347 
 TYR   0.014   0.001   TYR A 187 
 ARG   0.009   0.001   ARG A 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03597 (  278)
  hydrogen bonds       : angle       4.85843 (  744)
  covalent geometry    : bond        0.00280 ( 7032)
  covalent geometry    : angle       0.53647 ( 9584)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 164
  time to evaluate  : 1.237 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6931 (mp0)
REVERT: B  233 GLU cc_start: 0.7656 (mp0) cc_final: 0.7373 (mp0)
REVERT: B  242 ASP cc_start: 0.7503 (m-30) cc_final: 0.7270 (m-30)
REVERT: B  364 ASN cc_start: 0.8778 (m-40) cc_final: 0.8429 (m-40)
  outliers start: 14
  outliers final: 11
  residues processed: 169
  average time/residue: 2.3502
  time to fit residues: 411.7064
Evaluate side-chains
  174 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 162
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  394 LYS
Chi-restraints excluded: chain A residue  407 GLU
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue  264 ASP
Chi-restraints excluded: chain B residue  300 LYS
Chi-restraints excluded: chain B residue  363 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 28 optimal weight:    0.2980
   chunk 65 optimal weight:    0.0470
   chunk 7 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
A 343 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.112563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.102454 restraints weight = 8515.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 1.37
r_work: 0.3326 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.3536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7032  Z= 0.118
  Angle     :  0.530   7.736   9584  Z= 0.270
  Chirality :  0.046   0.138   1048
  Planarity :  0.005   0.038   1260
  Dihedral  :  4.400  17.457    950
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.97 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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:  1.53 (0.29), residues: 862
  helix:  2.57 (0.32), residues: 242
  sheet: -0.11 (0.43), residues: 154
  loop :  0.72 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 198 
 HIS   0.002   0.001   HIS B 318 
 PHE   0.012   0.001   PHE A 347 
 TYR   0.014   0.001   TYR A 187 
 ARG   0.009   0.001   ARG A 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03625 (  278)
  hydrogen bonds       : angle       4.83803 (  744)
  covalent geometry    : bond        0.00281 ( 7032)
  covalent geometry    : angle       0.53031 ( 9584)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7698.89 seconds
wall clock time: 134 minutes 57.49 seconds (8097.49 seconds total)