Starting phenix.real_space_refine
on Fri Aug 22 23:35:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b71_15895/08_2025/8b71_15895.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b71_15895/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b71_15895/08_2025/8b71_15895.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b71_15895/08_2025/8b71_15895.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b71_15895/08_2025/8b71_15895.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b71_15895/08_2025/8b71_15895.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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
          Unusual residues: {'2BA': 1}
          Classifications: {'RNA_mixed': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.38, per 1000 atoms: 0.50
  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: 1.37
  Conformation dependent library (CDL) restraints added in 516.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.25
  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: 1.52

  Time building geometry restraints manager: 1.66 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: 0.02
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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.310
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   16.280
-------------------------------------------------------------------------------
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 : 12.10
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG B 589 
 TYR   0.013   0.001   TYR A  43 
 PHE   0.015   0.001   PHE B 319 
 TRP   0.012   0.001   TRP B 404 
 HIS   0.002   0.001   HIS A 141 

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

*********************** 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  : 0.345 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0854
  time to fit residues: 19.1727
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  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    0.3980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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**
B 604 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.162211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.149453 restraints weight = 9553.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.148996 restraints weight = 11053.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.149113 restraints weight = 10785.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.149215 restraints weight = 10273.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.149235 restraints weight = 9871.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.0940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8910  Z= 0.135
  Angle     :  0.586   7.394  12130  Z= 0.298
  Chirality :  0.041   0.163   1454
  Planarity :  0.005   0.053   1458
  Dihedral  : 16.434 178.131   1296
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 10.13 %
    Favored  : 89.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.27), residues: 1092
  helix:  1.63 (0.19), residues: 766
  sheet:  0.00 (0.60), residues: 84
  loop : -1.23 (0.44), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 462 
 TYR   0.015   0.001   TYR A  43 
 PHE   0.012   0.001   PHE A 242 
 TRP   0.007   0.001   TRP A 520 
 HIS   0.002   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8910)
  covalent geometry    : angle       0.58616 (12130)
  hydrogen bonds       : bond        0.03992 (  631)
  hydrogen bonds       : angle       4.11870 ( 1857)

*********************** 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
  147 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 141
  time to evaluate  : 0.396 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 143
  average time/residue: 0.0850
  time to fit residues: 17.9994
Evaluate side-chains
  129 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 125
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  471 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 71 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 103 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 73 optimal weight:    0.4980
   chunk 56 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.161361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.154430 restraints weight = 9600.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.154066 restraints weight = 11426.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.154419 restraints weight = 10007.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.154399 restraints weight = 8003.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.154495 restraints weight = 8107.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.1180

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= 0.142
  Angle     :  0.572   7.335  12130  Z= 0.289
  Chirality :  0.040   0.149   1454
  Planarity :  0.005   0.048   1458
  Dihedral  : 16.377 177.758   1296
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 13.04 %
    Favored  : 86.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.27), residues: 1092
  helix:  1.68 (0.19), residues: 774
  sheet:  0.00 (0.59), residues: 84
  loop : -1.41 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  82 
 TYR   0.009   0.001   TYR B  43 
 PHE   0.021   0.001   PHE B 591 
 TRP   0.010   0.001   TRP B 404 
 HIS   0.002   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8910)
  covalent geometry    : angle       0.57235 (12130)
  hydrogen bonds       : bond        0.03884 (  631)
  hydrogen bonds       : angle       3.97322 ( 1857)

*********************** 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
  147 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 141
  time to evaluate  : 0.268 
Fit side-chains
  outliers start: 6
  outliers final: 2
  residues processed: 147
  average time/residue: 0.0846
  time to fit residues: 18.2864
Evaluate side-chains
  132 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 130
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  588 VAL
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 8 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 74 optimal weight:    0.0770
   chunk 86 optimal weight:    0.6980
   chunk 90 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 103 optimal weight:    0.4980
   chunk 23 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   overall best weight:    0.6340

-------------------------------------------------------------------------------
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 = 0.3755 r_free = 0.3755 target = 0.162110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.150106 restraints weight = 9765.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.150209 restraints weight = 8227.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.150033 restraints weight = 8170.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.150044 restraints weight = 8007.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.150051 restraints weight = 7726.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.1374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8910  Z= 0.133
  Angle     :  0.582   7.223  12130  Z= 0.291
  Chirality :  0.040   0.135   1454
  Planarity :  0.004   0.045   1458
  Dihedral  : 16.284 176.813   1296
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.38 %
    Favored  : 81.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.26), residues: 1092
  helix:  1.67 (0.19), residues: 776
  sheet:  0.10 (0.58), residues: 84
  loop : -1.47 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 519 
 TYR   0.009   0.001   TYR A  43 
 PHE   0.020   0.001   PHE B 591 
 TRP   0.024   0.001   TRP B 404 
 HIS   0.002   0.000   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8910)
  covalent geometry    : angle       0.58221 (12130)
  hydrogen bonds       : bond        0.03755 (  631)
  hydrogen bonds       : angle       3.95438 ( 1857)

*********************** 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
  159 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A  397 ILE cc_start: 0.7694 (pt) cc_final: 0.7426 (mt)
REVERT: A  477 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8196 (mt)
REVERT: B  397 ILE cc_start: 0.7693 (pt) cc_final: 0.7426 (mt)
  outliers start: 17
  outliers final: 8
  residues processed: 155
  average time/residue: 0.0767
  time to fit residues: 17.8816
Evaluate side-chains
  135 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 126
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
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  491 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  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 52 optimal weight:    0.6980
   chunk 95 optimal weight:    0.3980
   chunk 56 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 96 optimal weight:    9.9990
   chunk 84 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 100 optimal weight:    0.1980
   chunk 79 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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
B 411 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.175414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.155305 restraints weight = 10602.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.155069 restraints weight = 10680.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.155158 restraints weight = 10010.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.155340 restraints weight = 9555.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.155542 restraints weight = 9394.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.1557

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= 0.131
  Angle     :  0.563   6.924  12130  Z= 0.282
  Chirality :  0.040   0.138   1454
  Planarity :  0.004   0.042   1458
  Dihedral  : 16.089 176.297   1296
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 19.29 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.27), residues: 1092
  helix:  1.74 (0.19), residues: 774
  sheet:  0.18 (0.57), residues: 84
  loop : -1.50 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  82 
 TYR   0.008   0.001   TYR A  43 
 PHE   0.029   0.001   PHE B 591 
 TRP   0.016   0.001   TRP B 404 
 HIS   0.002   0.000   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8910)
  covalent geometry    : angle       0.56330 (12130)
  hydrogen bonds       : bond        0.03754 (  631)
  hydrogen bonds       : angle       3.89684 ( 1857)

*********************** 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
  152 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  440 MET cc_start: 0.8585 (mmp) cc_final: 0.8381 (mmp)
REVERT: A  477 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8231 (mt)
  outliers start: 17
  outliers final: 6
  residues processed: 147
  average time/residue: 0.0773
  time to fit residues: 16.9326
Evaluate side-chains
  136 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 129
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
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  491 ILE
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  491 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0670
   chunk 78 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0170
   chunk 75 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 109 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.4756

-------------------------------------------------------------------------------
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
B 249 ASN
B 525 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.163545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.149707 restraints weight = 9657.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.149995 restraints weight = 8784.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.150050 restraints weight = 8314.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.150064 restraints weight = 8128.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.150064 restraints weight = 8123.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8910  Z= 0.130
  Angle     :  0.565   6.824  12130  Z= 0.285
  Chirality :  0.039   0.165   1454
  Planarity :  0.004   0.044   1458
  Dihedral  : 15.836 175.261   1296
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 18.53 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.26), residues: 1092
  helix:  1.77 (0.19), residues: 772
  sheet:  0.23 (0.57), residues: 84
  loop : -1.56 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 519 
 TYR   0.007   0.001   TYR A 536 
 PHE   0.016   0.001   PHE A 591 
 TRP   0.017   0.001   TRP B 404 
 HIS   0.002   0.000   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8910)
  covalent geometry    : angle       0.56511 (12130)
  hydrogen bonds       : bond        0.03694 (  631)
  hydrogen bonds       : angle       3.90885 ( 1857)

*********************** 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: 22
    poor density    : 137
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A  440 MET cc_start: 0.8552 (mmp) cc_final: 0.8347 (mmp)
  outliers start: 22
  outliers final: 13
  residues processed: 157
  average time/residue: 0.0928
  time to fit residues: 21.0730
Evaluate side-chains
  142 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 18 optimal weight:    0.2980
   chunk 23 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 525 ASN
B 249 ASN
** B 288 GLN ** 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 = 0.3762 r_free = 0.3762 target = 0.163041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.148362 restraints weight = 9820.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.147758 restraints weight = 10227.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.147989 restraints weight = 9996.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.148246 restraints weight = 9584.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.148287 restraints weight = 8931.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
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      :  0.004   0.040   8910  Z= 0.148
  Angle     :  0.590   9.602  12130  Z= 0.293
  Chirality :  0.040   0.154   1454
  Planarity :  0.004   0.044   1458
  Dihedral  : 15.819 177.937   1296
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 19.83 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.26), residues: 1092
  helix:  1.78 (0.19), residues: 772
  sheet:  0.29 (0.58), residues: 84
  loop : -1.52 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 528 
 TYR   0.009   0.001   TYR B  95 
 PHE   0.011   0.001   PHE A 591 
 TRP   0.018   0.001   TRP B 404 
 HIS   0.002   0.000   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8910)
  covalent geometry    : angle       0.58953 (12130)
  hydrogen bonds       : bond        0.03753 (  631)
  hydrogen bonds       : angle       3.87060 ( 1857)

*********************** 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
  151 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 0.345 
Fit side-chains
REVERT: B  547 LEU cc_start: 0.7888 (tp) cc_final: 0.7504 (mp)
  outliers start: 14
  outliers final: 13
  residues processed: 150
  average time/residue: 0.0857
  time to fit residues: 18.7607
Evaluate side-chains
  142 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 103 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 525 ASN
B 249 ASN
** B 288 GLN ** 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 = 0.3889 r_free = 0.3889 target = 0.174084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.153935 restraints weight = 10615.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.153551 restraints weight = 10942.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.153997 restraints weight = 10460.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.154279 restraints weight = 9788.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.154402 restraints weight = 9107.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8910  Z= 0.152
  Angle     :  0.628  10.028  12130  Z= 0.309
  Chirality :  0.041   0.147   1454
  Planarity :  0.004   0.045   1458
  Dihedral  : 15.827 179.006   1296
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 20.69 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.26), residues: 1092
  helix:  1.75 (0.19), residues: 774
  sheet:  0.26 (0.58), residues: 84
  loop : -1.51 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 528 
 TYR   0.009   0.001   TYR B  95 
 PHE   0.008   0.001   PHE B 242 
 TRP   0.023   0.001   TRP A 404 
 HIS   0.008   0.001   HIS B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 8910)
  covalent geometry    : angle       0.62789 (12130)
  hydrogen bonds       : bond        0.03781 (  631)
  hydrogen bonds       : angle       3.94281 ( 1857)

*********************** 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
  145 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A  408 MET cc_start: 0.7098 (tpt) cc_final: 0.6894 (tpt)
REVERT: A  547 LEU cc_start: 0.7931 (tp) cc_final: 0.7499 (mp)
REVERT: B  547 LEU cc_start: 0.7911 (tp) cc_final: 0.7534 (mp)
  outliers start: 15
  outliers final: 14
  residues processed: 143
  average time/residue: 0.0795
  time to fit residues: 17.0011
Evaluate side-chains
  138 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 26 optimal weight:    0.3980
   chunk 66 optimal weight:    0.1980
   chunk 92 optimal weight:    0.0570
   chunk 41 optimal weight:    2.9990
   chunk 90 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   overall best weight:    0.4698

-------------------------------------------------------------------------------
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
B 249 ASN
** B 288 GLN ** 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 = 0.3761 r_free = 0.3761 target = 0.163363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.152429 restraints weight = 9642.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.151949 restraints weight = 11884.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.152050 restraints weight = 13195.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.152111 restraints weight = 12268.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.152124 restraints weight = 11308.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.1992

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= 0.130
  Angle     :  0.608   9.959  12130  Z= 0.297
  Chirality :  0.040   0.137   1454
  Planarity :  0.004   0.044   1458
  Dihedral  : 15.776 175.941   1296
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 20.69 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.26), residues: 1092
  helix:  1.79 (0.19), residues: 774
  sheet:  0.29 (0.58), residues: 84
  loop : -1.51 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 528 
 TYR   0.007   0.001   TYR A 536 
 PHE   0.009   0.001   PHE B 242 
 TRP   0.035   0.001   TRP B 404 
 HIS   0.013   0.002   HIS A 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8910)
  covalent geometry    : angle       0.60843 (12130)
  hydrogen bonds       : bond        0.03666 (  631)
  hydrogen bonds       : angle       3.87597 ( 1857)

*********************** 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
  148 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  547 LEU cc_start: 0.7900 (tp) cc_final: 0.7602 (mp)
REVERT: B  396 TRP cc_start: 0.7939 (m100) cc_final: 0.7664 (m100)
REVERT: B  547 LEU cc_start: 0.7802 (tp) cc_final: 0.7511 (mp)
  outliers start: 17
  outliers final: 12
  residues processed: 146
  average time/residue: 0.0783
  time to fit residues: 17.0906
Evaluate side-chains
  138 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 18 optimal weight:    0.0470
   chunk 50 optimal weight:    0.2980
   chunk 15 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   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 525 ASN
** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 ASN
** B 288 GLN ** 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 = 0.3759 r_free = 0.3759 target = 0.163275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.149658 restraints weight = 9694.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.149949 restraints weight = 8823.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.149949 restraints weight = 8358.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.149949 restraints weight = 8358.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.149949 restraints weight = 8358.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   8910  Z= 0.138
  Angle     :  0.619  10.018  12130  Z= 0.307
  Chirality :  0.040   0.181   1454
  Planarity :  0.004   0.045   1458
  Dihedral  : 15.814 174.865   1296
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 21.12 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.26), residues: 1092
  helix:  1.79 (0.19), residues: 774
  sheet:  0.33 (0.58), residues: 84
  loop : -1.47 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 528 
 TYR   0.007   0.001   TYR A 536 
 PHE   0.009   0.001   PHE B 242 
 TRP   0.025   0.001   TRP B 404 
 HIS   0.013   0.002   HIS B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8910)
  covalent geometry    : angle       0.61922 (12130)
  hydrogen bonds       : bond        0.03693 (  631)
  hydrogen bonds       : angle       3.92056 ( 1857)

********************** 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
  143 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  396 TRP cc_start: 0.8009 (m100) cc_final: 0.7737 (m100)
REVERT: A  547 LEU cc_start: 0.7945 (tp) cc_final: 0.7611 (mp)
REVERT: B  396 TRP cc_start: 0.8009 (m100) cc_final: 0.7755 (m100)
REVERT: B  547 LEU cc_start: 0.7861 (tp) cc_final: 0.7536 (mp)
  outliers start: 15
  outliers final: 12
  residues processed: 141
  average time/residue: 0.0810
  time to fit residues: 17.2048
Evaluate side-chains
  134 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0050
   chunk 12 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   chunk 102 optimal weight:    0.3980
   chunk 89 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 96 optimal weight:    7.9990
   chunk 74 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    0.8398

-------------------------------------------------------------------------------
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 525 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.162364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.148594 restraints weight = 9727.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.148311 restraints weight = 11845.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.148397 restraints weight = 12546.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.148718 restraints weight = 11014.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.148722 restraints weight = 10392.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8910  Z= 0.143
  Angle     :  0.610   9.865  12130  Z= 0.299
  Chirality :  0.040   0.138   1454
  Planarity :  0.004   0.044   1458
  Dihedral  : 15.948 175.460   1296
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 21.01 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.26), residues: 1092
  helix:  1.75 (0.19), residues: 776
  sheet:  0.23 (0.58), residues: 84
  loop : -1.40 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 528 
 TYR   0.008   0.001   TYR B  95 
 PHE   0.008   0.001   PHE A 242 
 TRP   0.035   0.001   TRP A 404 
 HIS   0.010   0.001   HIS A 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8910)
  covalent geometry    : angle       0.61049 (12130)
  hydrogen bonds       : bond        0.03706 (  631)
  hydrogen bonds       : angle       3.88075 ( 1857)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1426.30 seconds
wall clock time: 25 minutes 37.47 seconds (1537.47 seconds total)