Starting phenix.real_space_refine
on Mon May 12 00:47:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b71_15895/05_2025/8b71_15895.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b71_15895/05_2025/8b71_15895.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b71_15895/05_2025/8b71_15895.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b71_15895/05_2025/8b71_15895.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b71_15895/05_2025/8b71_15895.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b71_15895/05_2025/8b71_15895.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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       4      5.49       5
     S      34      5.16       5
     C    5766      2.51       5
     N    1406      2.21       5
     O    1484      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8694
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 552, 4303
          Classifications: {'peptide': 552}
          Link IDs: {'PTRANS': 23, 'TRANS': 528}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Classifications: {'RNA': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 7.86, per 1000 atoms: 0.90
  Number of scatterers: 8694
  At special positions: 0
  Unit cell: (113.847, 88.917, 98.889, 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      34     16.00
     P       4     15.00
     O    1484      8.00
     N    1406      7.00
     C    5766      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: 2.56
  Conformation dependent library (CDL) restraints added in 968.0 milliseconds
  

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2064

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 1 sheets defined
      78.2% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 40
      removed outlier: 6.235A  pdb=" N   ASP A  36 " --> pdb=" O   MET A  32 " (cutoff:3.500A)
      removed outlier: 5.291A  pdb=" N   ALA A  37 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 53
      removed outlier: 4.435A  pdb=" N   THR A  45 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   GLU A  46 " --> pdb=" O   ALA A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 61
      removed outlier: 3.651A  pdb=" N   TRP A  61 " --> pdb=" O   ALA A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 88
    Processing helix  chain 'A' and resid 95 through 101
      removed outlier: 3.631A  pdb=" N   ASN A 101 " --> pdb=" O   VAL A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 137
    Processing helix  chain 'A' and resid 138 through 142
      removed outlier: 4.219A  pdb=" N   ASP A 142 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 161
      removed outlier: 3.814A  pdb=" N   ILE A 147 " --> pdb=" O   TYR A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 170
      removed outlier: 3.670A  pdb=" N   LEU A 170 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 167 through 170'
    Processing helix  chain 'A' and resid 171 through 193
    Processing helix  chain 'A' and resid 216 through 227
    Processing helix  chain 'A' and resid 228 through 229
      No H-bonds generated for 'chain 'A' and resid 228 through 229'
    Processing helix  chain 'A' and resid 230 through 231
      No H-bonds generated for 'chain 'A' and resid 230 through 231'
    Processing helix  chain 'A' and resid 232 through 238
      removed outlier: 4.220A  pdb=" N   SER A 236 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 242
    Processing helix  chain 'A' and resid 245 through 276
    Processing helix  chain 'A' and resid 284 through 295
    Processing helix  chain 'A' and resid 297 through 331
      Proline residue:  A 323  - end of helix
    Processing helix  chain 'A' and resid 336 through 340
    Processing helix  chain 'A' and resid 347 through 365
    Processing helix  chain 'A' and resid 369 through 399
      Proline residue:  A 375  - end of helix
      Proline residue:  A 384  - end of helix
    Processing helix  chain 'A' and resid 403 through 429
    Processing helix  chain 'A' and resid 429 through 463
      Proline residue:  A 435  - end of helix
      Proline residue:  A 441  - end of helix
      removed outlier: 4.398A  pdb=" N   ILE A 463 " --> pdb=" O   GLU A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 498
    Processing helix  chain 'A' and resid 509 through 523
    Processing helix  chain 'A' and resid 540 through 557
    Processing helix  chain 'A' and resid 582 through 591
      removed outlier: 3.887A  pdb=" N   LEU A 586 " --> pdb=" O   SER A 582 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   PHE A 591 " --> pdb=" O   ARG A 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 40
      removed outlier: 6.235A  pdb=" N   ASP B  36 " --> pdb=" O   MET B  32 " (cutoff:3.500A)
      removed outlier: 5.291A  pdb=" N   ALA B  37 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 53
      removed outlier: 4.434A  pdb=" N   THR B  45 " --> pdb=" O   VAL B  41 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   GLU B  46 " --> pdb=" O   ALA B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 61
      removed outlier: 3.651A  pdb=" N   TRP B  61 " --> pdb=" O   ALA B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 88
    Processing helix  chain 'B' and resid 95 through 101
      removed outlier: 3.631A  pdb=" N   ASN B 101 " --> pdb=" O   VAL B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 137
    Processing helix  chain 'B' and resid 138 through 142
      removed outlier: 4.220A  pdb=" N   ASP B 142 " --> pdb=" O   ALA B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 161
      removed outlier: 3.814A  pdb=" N   ILE B 147 " --> pdb=" O   TYR B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 170
      removed outlier: 3.670A  pdb=" N   LEU B 170 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 167 through 170'
    Processing helix  chain 'B' and resid 171 through 193
    Processing helix  chain 'B' and resid 216 through 227
    Processing helix  chain 'B' and resid 228 through 229
      No H-bonds generated for 'chain 'B' and resid 228 through 229'
    Processing helix  chain 'B' and resid 230 through 231
      No H-bonds generated for 'chain 'B' and resid 230 through 231'
    Processing helix  chain 'B' and resid 232 through 238
      removed outlier: 4.220A  pdb=" N   SER B 236 " --> pdb=" O   VAL B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 242
    Processing helix  chain 'B' and resid 245 through 276
    Processing helix  chain 'B' and resid 284 through 295
    Processing helix  chain 'B' and resid 297 through 331
      Proline residue:  B 323  - end of helix
    Processing helix  chain 'B' and resid 336 through 340
    Processing helix  chain 'B' and resid 347 through 365
    Processing helix  chain 'B' and resid 369 through 399
      Proline residue:  B 375  - end of helix
      Proline residue:  B 384  - end of helix
    Processing helix  chain 'B' and resid 403 through 429
    Processing helix  chain 'B' and resid 429 through 463
      Proline residue:  B 435  - end of helix
      Proline residue:  B 441  - end of helix
      removed outlier: 4.398A  pdb=" N   ILE B 463 " --> pdb=" O   GLU B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 498
    Processing helix  chain 'B' and resid 509 through 523
    Processing helix  chain 'B' and resid 540 through 557
    Processing helix  chain 'B' and resid 582 through 591
      removed outlier: 3.888A  pdb=" N   LEU B 586 " --> pdb=" O   SER B 582 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   PHE B 591 " --> pdb=" O   ARG B 587 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 529 through 533
      removed outlier: 3.633A  pdb=" N   VAL A 504 " --> pdb=" O   VAL A 478 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   VAL A 561 " --> pdb=" O   MET A 597 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   ALA A 599 " --> pdb=" O   VAL A 561 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   VAL A 563 " --> pdb=" O   ALA A 599 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR B 600 " --> pdb=" O   VAL A 598 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR A 600 " --> pdb=" O   VAL B 598 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   VAL B 561 " --> pdb=" O   MET B 597 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   ALA B 599 " --> pdb=" O   VAL B 561 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   VAL B 563 " --> pdb=" O   ALA B 599 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL B 504 " --> pdb=" O   VAL B 478 " (cutoff:3.500A)

    631 hydrogen bonds defined for protein.
    1857 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: 2.47

  Time building geometry restraints manager: 2.93 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2593
        1.34 -     1.46: 1744
        1.46 -     1.57: 4503
        1.57 -     1.69: 8
        1.69 -     1.81: 62
  Bond restraints: 8910
  Sorted by residual:
  bond pdb="C3'1 2BA A1001 "
       pdb="O3'1 2BA A1001 "
    ideal  model  delta    sigma   weight residual
    1.418  1.344  0.074 2.00e-02 2.50e+03 1.36e+01
  bond pdb="C3'1 2BA B 901 "
       pdb="O3'1 2BA B 901 "
    ideal  model  delta    sigma   weight residual
    1.418  1.345  0.073 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" C5' 2BA A1001 "
       pdb=" O5' 2BA A1001 "
    ideal  model  delta    sigma   weight residual
    1.433  1.365  0.068 2.00e-02 2.50e+03 1.14e+01
  bond pdb=" C5' 2BA B 901 "
       pdb=" O5' 2BA B 901 "
    ideal  model  delta    sigma   weight residual
    1.433  1.365  0.068 2.00e-02 2.50e+03 1.14e+01
  bond pdb=" C3' 2BA B 901 "
       pdb=" O3' 2BA B 901 "
    ideal  model  delta    sigma   weight residual
    1.410  1.352  0.058 2.00e-02 2.50e+03 8.54e+00
  ... (remaining 8905 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 11773
        1.71 -     3.41: 261
        3.41 -     5.12: 67
        5.12 -     6.82: 23
        6.82 -     8.53: 6
  Bond angle restraints: 12130
  Sorted by residual:
  angle pdb=" C2' 2BA A1001 "
        pdb=" C3' 2BA A1001 "
        pdb=" O3' 2BA A1001 "
      ideal   model   delta    sigma   weight residual
     117.41  108.88    8.53 3.00e+00 1.11e-01 8.08e+00
  angle pdb=" C2' 2BA B 901 "
        pdb=" C3' 2BA B 901 "
        pdb=" O3' 2BA B 901 "
      ideal   model   delta    sigma   weight residual
     117.41  108.91    8.50 3.00e+00 1.11e-01 8.03e+00
  angle pdb=" O1P 2BA A1001 "
        pdb=" P   2BA A1001 "
        pdb=" O2P 2BA A1001 "
      ideal   model   delta    sigma   weight residual
     121.18  129.06   -7.88 3.00e+00 1.11e-01 6.89e+00
  angle pdb=" O1P 2BA B 901 "
        pdb=" P   2BA B 901 "
        pdb=" O2P 2BA B 901 "
      ideal   model   delta    sigma   weight residual
     121.18  128.98   -7.80 3.00e+00 1.11e-01 6.77e+00
  angle pdb=" C   LYS A 572 "
        pdb=" N   ARG A 573 "
        pdb=" CA  ARG A 573 "
      ideal   model   delta    sigma   weight residual
     121.54  126.46   -4.92 1.91e+00 2.74e-01 6.63e+00
  ... (remaining 12125 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.65: 5170
       34.65 -    69.31: 110
       69.31 -   103.96: 14
      103.96 -   138.61: 2
      138.61 -   173.26: 8
  Dihedral angle restraints: 5304
    sinusoidal: 2102
      harmonic: 3202
  Sorted by residual:
  dihedral pdb=" C5' 2BA B 901 "
           pdb=" O5' 2BA B 901 "
           pdb=" P   2BA B 901 "
           pdb=" O1P 2BA B 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
     191.97   18.71  173.26     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C5' 2BA A1001 "
           pdb=" O5' 2BA A1001 "
           pdb=" P   2BA A1001 "
           pdb=" O1P 2BA A1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     191.97   18.79  173.18     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb="C5'1 2BA B 901 "
           pdb=" P1  2BA B 901 "
           pdb="O5'1 2BA B 901 "
           pdb="O2P1 2BA B 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
      30.08 -142.04  172.12     1      3.00e+01 1.11e-03 2.12e+01
  ... (remaining 5301 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1251
       0.062 -    0.124: 187
       0.124 -    0.186: 14
       0.186 -    0.248: 0
       0.248 -    0.310: 2
  Chirality restraints: 1454
  Sorted by residual:
  chirality pdb=" C4' 2BA B 901 "
            pdb=" C3' 2BA B 901 "
            pdb=" C5' 2BA B 901 "
            pdb=" O4' 2BA B 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.39   -2.70    0.31 2.00e-01 2.50e+01 2.41e+00
  chirality pdb=" C4' 2BA A1001 "
            pdb=" C3' 2BA A1001 "
            pdb=" C5' 2BA A1001 "
            pdb=" O4' 2BA A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.39   -2.70    0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CA  TYR B  81 "
            pdb=" N   TYR B  81 "
            pdb=" C   TYR B  81 "
            pdb=" CB  TYR B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.71e-01
  ... (remaining 1451 not shown)

  Planarity restraints: 1458
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 280 "    0.040 5.00e-02 4.00e+02   6.15e-02 6.05e+00
        pdb=" N   PRO B 281 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO B 281 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 281 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 280 "   -0.040 5.00e-02 4.00e+02   6.14e-02 6.03e+00
        pdb=" N   PRO A 281 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO A 281 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 281 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B  88 "   -0.038 5.00e-02 4.00e+02   5.84e-02 5.46e+00
        pdb=" N   PRO B  89 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO B  89 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B  89 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1455 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 135
        2.68 -     3.24: 9151
        3.24 -     3.79: 14448
        3.79 -     4.35: 18683
        4.35 -     4.90: 30506
  Nonbonded interactions: 72923
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 277 "
            pdb=" OE1 GLN B 288 "
     model   vdw
     2.129 3.040
  nonbonded pdb=" OG1 THR A 277 "
            pdb=" OE1 GLN A 288 "
     model   vdw
     2.129 3.040
  nonbonded pdb=" OG  SER A 127 "
            pdb=" O   GLY A 368 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" OG  SER B 127 "
            pdb=" O   GLY B 368 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" OG1 THR A 284 "
            pdb=" OG  SER A 287 "
     model   vdw
     2.328 3.040
  ... (remaining 72918 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: 0.04
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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.780
  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:          0.400
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.090
  Find NCS groups from input model:        0.150
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
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      :  0.005   0.074   8910  Z= 0.244
  Angle     :  0.708   8.529  12130  Z= 0.353
  Chirality :  0.045   0.310   1454
  Planarity :  0.005   0.062   1458
  Dihedral  : 17.410 173.263   3240
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  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:  0.64 (0.27), residues: 1092
  helix:  1.16 (0.20), residues: 768
  sheet: -0.30 (0.60), residues: 84
  loop : -1.59 (0.43), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 404 
 HIS   0.002   0.001   HIS A 141 
 PHE   0.015   0.001   PHE B 319 
 TYR   0.013   0.001   TYR A  43 
 ARG   0.002   0.000   ARG B 589 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12554 (  631)
  hydrogen bonds       : angle       5.25652 ( 1857)
  covalent geometry    : bond        0.00545 ( 8910)
  covalent geometry    : angle       0.70791 (12130)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.869 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1762
  time to fit residues: 39.2569
Evaluate side-chains
  128 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 99 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 372 HIS
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 604 HIS
B 372 HIS
** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.160690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.154231 restraints weight = 9507.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.154150 restraints weight = 10140.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.154380 restraints weight = 9476.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.0874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8910  Z= 0.144
  Angle     :  0.595   7.443  12130  Z= 0.302
  Chirality :  0.041   0.161   1454
  Planarity :  0.005   0.054   1458
  Dihedral  : 16.498 179.962   1296
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 10.56 %
    Favored  : 89.01 %
  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:  1.26 (0.27), residues: 1092
  helix:  1.59 (0.19), residues: 766
  sheet: -0.07 (0.60), residues: 84
  loop : -1.19 (0.44), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 404 
 HIS   0.002   0.001   HIS A 141 
 PHE   0.012   0.001   PHE A 242 
 TYR   0.014   0.001   TYR A  43 
 ARG   0.001   0.000   ARG A  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04105 (  631)
  hydrogen bonds       : angle       4.15940 ( 1857)
  covalent geometry    : bond        0.00334 ( 8910)
  covalent geometry    : angle       0.59473 (12130)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 144
  time to evaluate  : 0.907 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 146
  average time/residue: 0.1769
  time to fit residues: 37.7703
Evaluate side-chains
  130 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 128
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain B residue   84 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 78 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 87 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 55 optimal weight:    7.9990
   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 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 604 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.161156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.154208 restraints weight = 9683.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.153871 restraints weight = 11430.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.154166 restraints weight = 10240.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.1157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8910  Z= 0.141
  Angle     :  0.571   7.349  12130  Z= 0.288
  Chirality :  0.040   0.149   1454
  Planarity :  0.005   0.048   1458
  Dihedral  : 16.391 178.237   1296
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 13.04 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.27), residues: 1092
  helix:  1.68 (0.19), residues: 776
  sheet:  0.01 (0.59), residues: 84
  loop : -1.32 (0.44), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 404 
 HIS   0.002   0.001   HIS A 141 
 PHE   0.024   0.001   PHE A 591 
 TYR   0.009   0.001   TYR A 536 
 ARG   0.001   0.000   ARG B  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03866 (  631)
  hydrogen bonds       : angle       3.97085 ( 1857)
  covalent geometry    : bond        0.00327 ( 8910)
  covalent geometry    : angle       0.57100 (12130)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 144
  time to evaluate  : 0.980 
Fit side-chains
  outliers start: 11
  outliers final: 5
  residues processed: 149
  average time/residue: 0.1794
  time to fit residues: 38.8873
Evaluate side-chains
  136 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 131
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  491 ILE
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  588 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 72 optimal weight:    5.9990
   chunk 86 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0670
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.7320

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

Flipped N/Q/H residues before XYZ refinement:
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.161204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.150013 restraints weight = 9675.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.149514 restraints weight = 11890.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.149836 restraints weight = 12565.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8910  Z= 0.139
  Angle     :  0.579   7.047  12130  Z= 0.293
  Chirality :  0.039   0.137   1454
  Planarity :  0.004   0.045   1458
  Dihedral  : 16.263 177.854   1296
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 17.78 %
    Favored  : 80.50 %
  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:  1.32 (0.26), residues: 1092
  helix:  1.64 (0.19), residues: 776
  sheet:  0.12 (0.58), residues: 84
  loop : -1.43 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 404 
 HIS   0.002   0.001   HIS A 141 
 PHE   0.021   0.001   PHE A 591 
 TYR   0.009   0.001   TYR B  43 
 ARG   0.001   0.000   ARG B 519 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03779 (  631)
  hydrogen bonds       : angle       3.97962 ( 1857)
  covalent geometry    : bond        0.00330 ( 8910)
  covalent geometry    : angle       0.57857 (12130)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 1.014 
Fit side-chains
REVERT: A  477 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8174 (mt)
REVERT: B  257 MET cc_start: 0.7787 (tmm) cc_final: 0.7569 (ttp)
REVERT: B  477 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8186 (mt)
  outliers start: 16
  outliers final: 7
  residues processed: 152
  average time/residue: 0.1688
  time to fit residues: 37.8444
Evaluate side-chains
  134 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  477 ILE
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  588 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 103 optimal weight:    0.1980
   chunk 36 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 41 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.159698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.152713 restraints weight = 9631.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.152370 restraints weight = 11416.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.152666 restraints weight = 10389.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8910  Z= 0.151
  Angle     :  0.591   7.454  12130  Z= 0.293
  Chirality :  0.041   0.171   1454
  Planarity :  0.004   0.043   1458
  Dihedral  : 16.161 179.413   1296
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 19.29 %
    Favored  : 78.23 %
  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:  1.34 (0.27), residues: 1092
  helix:  1.65 (0.19), residues: 776
  sheet:  0.19 (0.58), residues: 84
  loop : -1.40 (0.44), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 404 
 HIS   0.002   0.001   HIS B 141 
 PHE   0.024   0.001   PHE A 591 
 TYR   0.009   0.001   TYR B  95 
 ARG   0.001   0.000   ARG B 589 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03874 (  631)
  hydrogen bonds       : angle       3.97448 ( 1857)
  covalent geometry    : bond        0.00359 ( 8910)
  covalent geometry    : angle       0.59083 (12130)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 137
  time to evaluate  : 0.966 
Fit side-chains
REVERT: A  440 MET cc_start: 0.8554 (mmp) cc_final: 0.8332 (mmp)
REVERT: B  440 MET cc_start: 0.8540 (mmp) cc_final: 0.8322 (mmp)
  outliers start: 23
  outliers final: 8
  residues processed: 156
  average time/residue: 0.1718
  time to fit residues: 39.7880
Evaluate side-chains
  139 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  491 ILE
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  588 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 103 optimal weight:    0.6980
   chunk 107 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 66 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 13 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 ASN
** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.160890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.154672 restraints weight = 9573.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.154622 restraints weight = 9511.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.154829 restraints weight = 8985.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8910  Z= 0.140
  Angle     :  0.585   7.841  12130  Z= 0.293
  Chirality :  0.040   0.164   1454
  Planarity :  0.004   0.045   1458
  Dihedral  : 15.999 179.983   1296
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 20.26 %
    Favored  : 78.12 %
  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:  1.38 (0.27), residues: 1092
  helix:  1.71 (0.19), residues: 774
  sheet:  0.29 (0.58), residues: 84
  loop : -1.54 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 404 
 HIS   0.007   0.001   HIS B 453 
 PHE   0.022   0.001   PHE A 591 
 TYR   0.007   0.001   TYR A 536 
 ARG   0.001   0.000   ARG A  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03804 (  631)
  hydrogen bonds       : angle       3.97967 ( 1857)
  covalent geometry    : bond        0.00333 ( 8910)
  covalent geometry    : angle       0.58531 (12130)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 0.940 
Fit side-chains
  outliers start: 15
  outliers final: 12
  residues processed: 157
  average time/residue: 0.1924
  time to fit residues: 42.7732
Evaluate side-chains
  144 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  491 ILE
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  588 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 5 optimal weight:    0.6980
   chunk 95 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 525 ASN
B 249 ASN
** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 525 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.160566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.146129 restraints weight = 9804.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.146344 restraints weight = 9168.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.146344 restraints weight = 8646.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8910  Z= 0.142
  Angle     :  0.591   8.844  12130  Z= 0.294
  Chirality :  0.040   0.153   1454
  Planarity :  0.004   0.044   1458
  Dihedral  : 15.842 178.472   1296
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 20.80 %
    Favored  : 77.48 %
  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:  1.37 (0.26), residues: 1092
  helix:  1.71 (0.19), residues: 774
  sheet:  0.31 (0.58), residues: 84
  loop : -1.57 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 404 
 HIS   0.012   0.002   HIS A 453 
 PHE   0.027   0.001   PHE B 591 
 TYR   0.007   0.001   TYR B 536 
 ARG   0.002   0.000   ARG A 161 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03778 (  631)
  hydrogen bonds       : angle       3.92066 ( 1857)
  covalent geometry    : bond        0.00332 ( 8910)
  covalent geometry    : angle       0.59064 (12130)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A  547 LEU cc_start: 0.7923 (tp) cc_final: 0.7464 (mp)
REVERT: B  397 ILE cc_start: 0.7531 (pt) cc_final: 0.7319 (mt)
REVERT: B  591 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8233 (m-10)
  outliers start: 16
  outliers final: 12
  residues processed: 151
  average time/residue: 0.1766
  time to fit residues: 38.6423
Evaluate side-chains
  143 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  491 ILE
Chi-restraints excluded: chain A residue  525 ASN
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  525 ASN
Chi-restraints excluded: chain B residue  588 VAL
Chi-restraints excluded: chain B residue  591 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 31 optimal weight:    0.0970
   chunk 29 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 18 optimal weight:    0.3980
   chunk 13 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 105 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 525 ASN
** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 ASN
** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 525 ASN
** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.161697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.147537 restraints weight = 9786.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.147744 restraints weight = 8941.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.147744 restraints weight = 8564.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8910  Z= 0.139
  Angle     :  0.602   9.145  12130  Z= 0.302
  Chirality :  0.040   0.153   1454
  Planarity :  0.004   0.045   1458
  Dihedral  : 15.782 177.527   1296
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 21.12 %
    Favored  : 76.94 %
  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:  1.38 (0.26), residues: 1092
  helix:  1.70 (0.19), residues: 776
  sheet:  0.27 (0.57), residues: 84
  loop : -1.50 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A 404 
 HIS   0.012   0.002   HIS A 453 
 PHE   0.025   0.001   PHE B 591 
 TYR   0.007   0.001   TYR B 536 
 ARG   0.001   0.000   ARG B 528 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03781 (  631)
  hydrogen bonds       : angle       3.96526 ( 1857)
  covalent geometry    : bond        0.00327 ( 8910)
  covalent geometry    : angle       0.60167 (12130)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.952 
Fit side-chains
REVERT: A  257 MET cc_start: 0.7750 (tmm) cc_final: 0.7549 (ttt)
REVERT: A  547 LEU cc_start: 0.7847 (tp) cc_final: 0.7299 (mp)
  outliers start: 18
  outliers final: 12
  residues processed: 152
  average time/residue: 0.1748
  time to fit residues: 38.7929
Evaluate side-chains
  139 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  491 ILE
Chi-restraints excluded: chain A residue  525 ASN
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  525 ASN
Chi-restraints excluded: chain B residue  588 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0980
   chunk 97 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0770
   chunk 49 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 525 ASN
** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 ASN
** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 525 ASN
** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.162642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.148445 restraints weight = 9743.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.148204 restraints weight = 11442.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.148319 restraints weight = 12300.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8910  Z= 0.133
  Angle     :  0.591   9.597  12130  Z= 0.294
  Chirality :  0.040   0.140   1454
  Planarity :  0.004   0.044   1458
  Dihedral  : 15.769 175.616   1296
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 20.91 %
    Favored  : 77.16 %
  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:  1.43 (0.26), residues: 1092
  helix:  1.76 (0.19), residues: 774
  sheet:  0.21 (0.57), residues: 84
  loop : -1.53 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 404 
 HIS   0.010   0.001   HIS A 453 
 PHE   0.025   0.001   PHE A 591 
 TYR   0.007   0.001   TYR B 536 
 ARG   0.001   0.000   ARG B 519 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03734 (  631)
  hydrogen bonds       : angle       3.90637 ( 1857)
  covalent geometry    : bond        0.00308 ( 8910)
  covalent geometry    : angle       0.59071 (12130)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.931 
Fit side-chains
REVERT: B  547 LEU cc_start: 0.7675 (tp) cc_final: 0.7147 (mp)
  outliers start: 18
  outliers final: 14
  residues processed: 150
  average time/residue: 0.1737
  time to fit residues: 37.9235
Evaluate side-chains
  145 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  491 ILE
Chi-restraints excluded: chain A residue  525 ASN
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  525 ASN
Chi-restraints excluded: chain B residue  588 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 76 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 57 optimal weight:    9.9990
   chunk 22 optimal weight:    0.0270
   chunk 65 optimal weight:    0.9980
   chunk 92 optimal weight:    5.9990
   chunk 106 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.7238

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 525 ASN
** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 ASN
** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 525 ASN
** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.162406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.150562 restraints weight = 9764.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.150683 restraints weight = 9253.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.150683 restraints weight = 8926.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   8910  Z= 0.144
  Angle     :  0.620  10.498  12130  Z= 0.308
  Chirality :  0.041   0.206   1454
  Planarity :  0.004   0.045   1458
  Dihedral  : 15.851 175.228   1296
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 21.44 %
    Favored  : 76.83 %
  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:  1.42 (0.26), residues: 1092
  helix:  1.73 (0.19), residues: 776
  sheet:  0.23 (0.57), residues: 84
  loop : -1.49 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 404 
 HIS   0.008   0.001   HIS A 453 
 PHE   0.019   0.001   PHE B 591 
 TYR   0.007   0.001   TYR B  95 
 ARG   0.001   0.000   ARG B 528 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03779 (  631)
  hydrogen bonds       : angle       3.98778 ( 1857)
  covalent geometry    : bond        0.00345 ( 8910)
  covalent geometry    : angle       0.62032 (12130)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.915 
Fit side-chains
REVERT: B  514 LYS cc_start: 0.8419 (tptm) cc_final: 0.8146 (tptp)
REVERT: B  547 LEU cc_start: 0.7729 (tp) cc_final: 0.7389 (mp)
  outliers start: 16
  outliers final: 14
  residues processed: 147
  average time/residue: 0.1781
  time to fit residues: 38.1549
Evaluate side-chains
  143 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  491 ILE
Chi-restraints excluded: chain A residue  525 ASN
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  525 ASN
Chi-restraints excluded: chain B residue  588 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 91 optimal weight:    5.9990
   chunk 104 optimal weight:    0.6980
   chunk 44 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 69 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 525 ASN
** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 ASN
** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 525 ASN
** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.162226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.148368 restraints weight = 9784.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.148127 restraints weight = 9637.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.148223 restraints weight = 9610.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8910  Z= 0.139
  Angle     :  0.606  10.259  12130  Z= 0.297
  Chirality :  0.040   0.208   1454
  Planarity :  0.004   0.044   1458
  Dihedral  : 15.958 175.119   1296
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 21.23 %
    Favored  : 77.16 %
  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:  1.43 (0.26), residues: 1092
  helix:  1.73 (0.19), residues: 776
  sheet:  0.27 (0.58), residues: 84
  loop : -1.47 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 404 
 HIS   0.007   0.001   HIS A 453 
 PHE   0.017   0.001   PHE B 591 
 TYR   0.007   0.001   TYR B  95 
 ARG   0.001   0.000   ARG B 528 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03722 (  631)
  hydrogen bonds       : angle       3.94107 ( 1857)
  covalent geometry    : bond        0.00326 ( 8910)
  covalent geometry    : angle       0.60578 (12130)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2526.93 seconds
wall clock time: 45 minutes 27.12 seconds (2727.12 seconds total)