Starting phenix.real_space_refine
on Thu Mar 13 03:37:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b71_15895/03_2025/8b71_15895.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b71_15895/03_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_15895/03_2025/8b71_15895.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b71_15895/03_2025/8b71_15895.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b71_15895/03_2025/8b71_15895.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b71_15895/03_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-5624/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: 8.11, per 1000 atoms: 0.93
  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: 2.40
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.80
  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: 2.66

  Time building geometry restraints manager: 2.75 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:             0.790
  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:          0.410
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     25.940
  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:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.300
-------------------------------------------------------------------------------
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= 0.351
  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 

*********************** 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  : 0.971 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1885
  time to fit residues: 41.7991
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  : 0.980 
-------------------------------------------------------------------------------
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 = 10140.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.154380 restraints weight = 9476.168|
|-----------------------------------------------------------------------------|
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= 0.222
  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 

*********************** 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  : 0.912 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 146
  average time/residue: 0.1795
  time to fit residues: 38.1159
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  : 0.971 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 78 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 55 optimal weight:    7.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.3746 r_free = 0.3746 target = 0.160711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.145503 restraints weight = 9689.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.145645 restraints weight = 9216.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.145645 restraints weight = 9015.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8910  Z= 0.246
  Angle     :  0.584   7.367  12130  Z= 0.295
  Chirality :  0.041   0.148   1454
  Planarity :  0.005   0.048   1458
  Dihedral  : 16.461 179.863   1296
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.36 %
    Favored  : 85.34 %
  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 (0.27), residues: 1092
  helix:  1.70 (0.19), residues: 764
  sheet: -0.07 (0.59), residues: 84
  loop : -1.25 (0.43), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 404 
 HIS   0.002   0.001   HIS A 141 
 PHE   0.024   0.001   PHE B 591 
 TYR   0.009   0.001   TYR B  95 
 ARG   0.001   0.000   ARG B  82 

*********************** 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: 12
    poor density    : 143
  time to evaluate  : 0.902 
Fit side-chains
REVERT: A  430 PHE cc_start: 0.7618 (t80) cc_final: 0.7407 (t80)
REVERT: A  547 LEU cc_start: 0.7995 (tp) cc_final: 0.7747 (tp)
REVERT: B  430 PHE cc_start: 0.7576 (t80) cc_final: 0.7361 (t80)
  outliers start: 12
  outliers final: 8
  residues processed: 149
  average time/residue: 0.1766
  time to fit residues: 38.5255
Evaluate side-chains
  137 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
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  499 ASP
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  499 ASP
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:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 82 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 72 optimal weight:    5.9990
   chunk 86 optimal weight:    0.0970
   chunk 75 optimal weight:    0.7980
   chunk 68 optimal weight:    0.0030
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4219 r_free = 0.4219 target = 0.205267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.187713 restraints weight = 9738.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.188477 restraints weight = 8420.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.189700 restraints weight = 7551.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8910  Z= 0.201
  Angle     :  0.573   7.219  12130  Z= 0.291
  Chirality :  0.039   0.138   1454
  Planarity :  0.004   0.045   1458
  Dihedral  : 16.216 177.522   1296
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.81 %
    Favored  : 81.14 %
  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:  0.13 (0.59), residues: 84
  loop : -1.42 (0.44), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 404 
 HIS   0.013   0.001   HIS A 575 
 PHE   0.024   0.001   PHE A 591 
 TYR   0.008   0.001   TYR A 536 
 ARG   0.001   0.000   ARG A 462 

*********************** 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
  164 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 145
  time to evaluate  : 0.887 
Fit side-chains
REVERT: A  477 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8220 (mt)
REVERT: B  477 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8246 (mt)
  outliers start: 19
  outliers final: 6
  residues processed: 157
  average time/residue: 0.1634
  time to fit residues: 38.0194
Evaluate side-chains
  138 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 130
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
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  588 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 57 optimal weight:    0.3980
   chunk 103 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0470
   chunk 51 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   overall best weight:    0.5878

-------------------------------------------------------------------------------
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**
** B 249 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 = 0.3761 r_free = 0.3761 target = 0.162889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.156820 restraints weight = 9626.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.156860 restraints weight = 9411.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.157055 restraints weight = 8685.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8910  Z= 0.213
  Angle     :  0.562   7.012  12130  Z= 0.282
  Chirality :  0.039   0.167   1454
  Planarity :  0.004   0.042   1458
  Dihedral  : 15.964 176.803   1296
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 19.29 %
    Favored  : 78.56 %
  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:  1.41 (0.27), residues: 1092
  helix:  1.74 (0.19), residues: 774
  sheet:  0.15 (0.58), residues: 84
  loop : -1.46 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 404 
 HIS   0.008   0.001   HIS B 453 
 PHE   0.014   0.001   PHE B 565 
 TYR   0.009   0.001   TYR A  43 
 ARG   0.001   0.000   ARG B 519 

*********************** 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
  159 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.960 
Fit side-chains
REVERT: A  440 MET cc_start: 0.8559 (mmp) cc_final: 0.8317 (mmp)
REVERT: B  440 MET cc_start: 0.8486 (mmp) cc_final: 0.8272 (mmp)
REVERT: B  477 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8139 (mt)
  outliers start: 20
  outliers final: 11
  residues processed: 155
  average time/residue: 0.1756
  time to fit residues: 39.8320
Evaluate side-chains
  149 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 137
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 103 optimal weight:    0.5980
   chunk 107 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 249 ASN
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 525 ASN
** B 249 ASN ** 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 = 0.3755 r_free = 0.3755 target = 0.162384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.148511 restraints weight = 9628.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.148722 restraints weight = 8889.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.148722 restraints weight = 8392.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8910  Z= 0.210
  Angle     :  0.576   9.087  12130  Z= 0.288
  Chirality :  0.040   0.155   1454
  Planarity :  0.004   0.044   1458
  Dihedral  : 15.790 177.382   1296
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 20.15 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.27), residues: 1092
  helix:  1.77 (0.19), residues: 774
  sheet:  0.27 (0.58), residues: 84
  loop : -1.52 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 404 
 HIS   0.005   0.001   HIS B 453 
 PHE   0.012   0.001   PHE A 591 
 TYR   0.007   0.001   TYR A 536 
 ARG   0.001   0.000   ARG A 519 

*********************** 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
  158 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.869 
Fit side-chains
REVERT: B  477 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8299 (mt)
  outliers start: 19
  outliers final: 12
  residues processed: 156
  average time/residue: 0.1899
  time to fit residues: 42.3783
Evaluate side-chains
  141 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
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  477 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 5 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 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 = 0.3741 r_free = 0.3741 target = 0.161081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.147149 restraints weight = 9798.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.147503 restraints weight = 8942.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.147543 restraints weight = 8405.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.1799

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= 0.234
  Angle     :  0.599   9.285  12130  Z= 0.294
  Chirality :  0.040   0.149   1454
  Planarity :  0.004   0.044   1458
  Dihedral  : 15.787 179.286   1296
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 20.91 %
    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:  1.48 (0.26), residues: 1092
  helix:  1.78 (0.19), residues: 774
  sheet:  0.27 (0.58), residues: 84
  loop : -1.45 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 404 
 HIS   0.007   0.001   HIS B 453 
 PHE   0.009   0.001   PHE A 242 
 TYR   0.008   0.001   TYR B  95 
 ARG   0.002   0.000   ARG B 528 

*********************** 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
  149 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 0.979 
Fit side-chains
REVERT: A  547 LEU cc_start: 0.7900 (tp) cc_final: 0.7467 (mp)
REVERT: B  477 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8282 (mt)
REVERT: B  547 LEU cc_start: 0.7817 (tp) cc_final: 0.7398 (mp)
  outliers start: 15
  outliers final: 12
  residues processed: 147
  average time/residue: 0.1851
  time to fit residues: 39.7199
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  : 0.992 
-------------------------------------------------------------------------------
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  477 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0970
   chunk 13 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 105 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.162205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.148118 restraints weight = 9774.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.148532 restraints weight = 9109.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.148532 restraints weight = 8470.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8910  Z= 0.218
  Angle     :  0.605   9.638  12130  Z= 0.300
  Chirality :  0.040   0.141   1454
  Planarity :  0.004   0.045   1458
  Dihedral  : 15.788 179.292   1296
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 21.44 %
    Favored  : 76.51 %
  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:  1.50 (0.26), residues: 1092
  helix:  1.80 (0.19), residues: 774
  sheet:  0.24 (0.58), residues: 84
  loop : -1.44 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 404 
 HIS   0.007   0.001   HIS B 453 
 PHE   0.009   0.001   PHE B 242 
 TYR   0.007   0.001   TYR A 536 
 ARG   0.001   0.000   ARG A 528 

*********************** 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
  154 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A  547 LEU cc_start: 0.7910 (tp) cc_final: 0.7501 (mp)
REVERT: B  547 LEU cc_start: 0.7860 (tp) cc_final: 0.7492 (mp)
  outliers start: 19
  outliers final: 13
  residues processed: 152
  average time/residue: 0.1858
  time to fit residues: 41.4104
Evaluate side-chains
  141 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
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  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:    2.9990
   chunk 13 optimal weight:    0.0670
   chunk 97 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 49 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.9122

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.195079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.175840 restraints weight = 9918.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.175936 restraints weight = 8461.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.176400 restraints weight = 7717.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1908

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= 0.232
  Angle     :  0.605   9.724  12130  Z= 0.297
  Chirality :  0.040   0.138   1454
  Planarity :  0.004   0.044   1458
  Dihedral  : 15.901 179.393   1296
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 21.34 %
    Favored  : 77.05 %
  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:  1.47 (0.26), residues: 1092
  helix:  1.77 (0.19), residues: 774
  sheet:  0.23 (0.58), residues: 84
  loop : -1.45 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 404 
 HIS   0.005   0.001   HIS B 453 
 PHE   0.008   0.001   PHE B 242 
 TYR   0.008   0.001   TYR B  95 
 ARG   0.001   0.000   ARG B 519 

*********************** 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
  151 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 136
  time to evaluate  : 0.954 
Fit side-chains
REVERT: A  547 LEU cc_start: 0.7822 (tp) cc_final: 0.7472 (mp)
REVERT: B  547 LEU cc_start: 0.7813 (tp) cc_final: 0.7468 (mp)
  outliers start: 15
  outliers final: 13
  residues processed: 147
  average time/residue: 0.1706
  time to fit residues: 37.1014
Evaluate side-chains
  144 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
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  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:    5.9990
   chunk 76 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   chunk 22 optimal weight:    0.7980
   chunk 65 optimal weight:    0.3980
   chunk 92 optimal weight:    6.9990
   chunk 106 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.161912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.149878 restraints weight = 9742.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.149893 restraints weight = 9355.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.149893 restraints weight = 9262.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.1995

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= 0.224
  Angle     :  0.619   9.871  12130  Z= 0.308
  Chirality :  0.041   0.167   1454
  Planarity :  0.004   0.045   1458
  Dihedral  : 15.996 179.887   1296
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 21.55 %
    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:  1.45 (0.26), residues: 1092
  helix:  1.75 (0.19), residues: 774
  sheet:  0.28 (0.58), residues: 84
  loop : -1.47 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 404 
 HIS   0.008   0.001   HIS A 453 
 PHE   0.009   0.001   PHE A 242 
 TYR   0.007   0.001   TYR B  95 
 ARG   0.001   0.000   ARG A 528 

********************** 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
  147 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 1.027 
Fit side-chains
REVERT: A  547 LEU cc_start: 0.7882 (tp) cc_final: 0.7538 (mp)
REVERT: B  547 LEU cc_start: 0.7845 (tp) cc_final: 0.7499 (mp)
  outliers start: 14
  outliers final: 13
  residues processed: 145
  average time/residue: 0.1777
  time to fit residues: 37.9904
Evaluate side-chains
  137 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
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  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:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0470
   chunk 15 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 104 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 69 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
A 249 ASN
** A 288 GLN ** 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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.162330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.148476 restraints weight = 9759.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.148594 restraints weight = 8873.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.148596 restraints weight = 8503.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.2039

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= 0.213
  Angle     :  0.607   9.793  12130  Z= 0.298
  Chirality :  0.040   0.137   1454
  Planarity :  0.004   0.044   1458
  Dihedral  : 16.074 178.592   1296
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 21.34 %
    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:  1.47 (0.26), residues: 1092
  helix:  1.76 (0.19), residues: 774
  sheet:  0.33 (0.58), residues: 84
  loop : -1.42 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 404 
 HIS   0.014   0.001   HIS A 453 
 PHE   0.009   0.001   PHE A 242 
 TYR   0.007   0.001   TYR B  43 
 ARG   0.001   0.000   ARG A 528 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2474.96 seconds
wall clock time: 44 minutes 19.07 seconds (2659.07 seconds total)