Starting phenix.real_space_refine
on Sat Apr 26 17:17:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k24_61989/04_2025/9k24_61989.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k24_61989/04_2025/9k24_61989.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k24_61989/04_2025/9k24_61989.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k24_61989/04_2025/9k24_61989.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k24_61989/04_2025/9k24_61989.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k24_61989/04_2025/9k24_61989.cif"
  }
  resolution = 3.6
  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=   0.002
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: 3
    Type Number    sf(0)   Gaussians
     C    1680      2.51       5
     N     468      2.21       5
     O     534      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 2682
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 447
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 447
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 2.14, per 1000 atoms: 0.80
  Number of scatterers: 2682
  At special positions: 0
  Unit cell: (133.63, 82.17, 31.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     534      8.00
     N     468      7.00
     C    1680      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: 0.65
  Conformation dependent library (CDL) restraints added in 366.4 milliseconds
  

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  648

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 25.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 44
      removed outlier: 6.721A  pdb=" N   GLU B  35 " --> pdb=" O   GLY A  36 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   LEU A  38 " --> pdb=" O   GLU B  35 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   VAL B  37 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 8.477A  pdb=" N   VAL A  40 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   TYR B  39 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
      removed outlier: 8.240A  pdb=" N   SER A  42 " --> pdb=" O   TYR B  39 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   GLY B  41 " --> pdb=" O   SER A  42 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   THR A  44 " --> pdb=" O   GLY B  41 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   LYS B  43 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   GLY B  36 " --> pdb=" O   VAL C  37 " (cutoff:3.500A)
      removed outlier: 7.532A  pdb=" N   TYR C  39 " --> pdb=" O   GLY B  36 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   LEU B  38 " --> pdb=" O   TYR C  39 " (cutoff:3.500A)
      removed outlier: 8.053A  pdb=" N   GLY C  41 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   VAL B  40 " --> pdb=" O   GLY C  41 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49
      removed outlier: 6.426A  pdb=" N   VAL B  48 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 63
      removed outlier: 6.470A  pdb=" N   GLU B  61 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   GLN B  62 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 70 through 72
      removed outlier: 6.336A  pdb=" N   VAL B  71 " --> pdb=" O   THR A  72 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 82
      removed outlier: 6.462A  pdb=" N   THR B  81 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 35 through 44
      removed outlier: 6.726A  pdb=" N   GLU E  35 " --> pdb=" O   GLY D  36 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   LEU D  38 " --> pdb=" O   GLU E  35 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   VAL E  37 " --> pdb=" O   LEU D  38 " (cutoff:3.500A)
      removed outlier: 8.485A  pdb=" N   VAL D  40 " --> pdb=" O   VAL E  37 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   TYR E  39 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 8.245A  pdb=" N   SER D  42 " --> pdb=" O   TYR E  39 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   GLY E  41 " --> pdb=" O   SER D  42 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   THR D  44 " --> pdb=" O   GLY E  41 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   LYS E  43 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   GLY E  36 " --> pdb=" O   VAL F  37 " (cutoff:3.500A)
      removed outlier: 7.538A  pdb=" N   TYR F  39 " --> pdb=" O   GLY E  36 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   LEU E  38 " --> pdb=" O   TYR F  39 " (cutoff:3.500A)
      removed outlier: 8.059A  pdb=" N   GLY F  41 " --> pdb=" O   LEU E  38 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   VAL E  40 " --> pdb=" O   GLY F  41 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'D' and resid 48 through 49
      removed outlier: 6.445A  pdb=" N   VAL E  48 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 53 through 55
    Processing sheet with id=AB1, first strand: chain 'D' and resid 61 through 63
      removed outlier: 6.489A  pdb=" N   GLU E  61 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   GLN E  62 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'D' and resid 70 through 72
      removed outlier: 6.322A  pdb=" N   VAL E  71 " --> pdb=" O   THR D  72 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 81 through 82
      removed outlier: 6.473A  pdb=" N   THR E  81 " --> pdb=" O   VAL F  82 " (cutoff:3.500A)

    16 hydrogen bonds defined for protein.
    48 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: 0.57

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 468
        1.29 -     1.35: 420
        1.35 -     1.42: 96
        1.42 -     1.48: 438
        1.48 -     1.54: 1272
  Bond restraints: 2694
  Sorted by residual:
  bond pdb=" N   GLY E  51 "
       pdb=" CA  GLY E  51 "
    ideal  model  delta    sigma   weight residual
    1.445  1.450 -0.006 8.30e-03 1.45e+04 5.03e-01
  bond pdb=" N   GLY B  51 "
       pdb=" CA  GLY B  51 "
    ideal  model  delta    sigma   weight residual
    1.445  1.450 -0.006 8.30e-03 1.45e+04 4.42e-01
  bond pdb=" N   GLY A  51 "
       pdb=" CA  GLY A  51 "
    ideal  model  delta    sigma   weight residual
    1.445  1.450 -0.005 8.30e-03 1.45e+04 3.78e-01
  bond pdb=" N   GLY C  51 "
       pdb=" CA  GLY C  51 "
    ideal  model  delta    sigma   weight residual
    1.445  1.450 -0.005 8.30e-03 1.45e+04 3.71e-01
  bond pdb=" CA  VAL C  95 "
       pdb=" CB  VAL C  95 "
    ideal  model  delta    sigma   weight residual
    1.535  1.542 -0.007 1.24e-02 6.50e+03 3.59e-01
  ... (remaining 2689 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.96: 3362
        0.96 -     1.92: 214
        1.92 -     2.88: 24
        2.88 -     3.84: 30
        3.84 -     4.80: 6
  Bond angle restraints: 3636
  Sorted by residual:
  angle pdb=" N   GLY F  51 "
        pdb=" CA  GLY F  51 "
        pdb=" C   GLY F  51 "
      ideal   model   delta    sigma   weight residual
     111.20  114.28   -3.08 1.39e+00 5.18e-01 4.92e+00
  angle pdb=" N   GLY E  51 "
        pdb=" CA  GLY E  51 "
        pdb=" C   GLY E  51 "
      ideal   model   delta    sigma   weight residual
     111.20  114.28   -3.08 1.39e+00 5.18e-01 4.91e+00
  angle pdb=" N   GLY D  51 "
        pdb=" CA  GLY D  51 "
        pdb=" C   GLY D  51 "
      ideal   model   delta    sigma   weight residual
     111.20  114.26   -3.06 1.39e+00 5.18e-01 4.85e+00
  angle pdb=" N   GLY C  51 "
        pdb=" CA  GLY C  51 "
        pdb=" C   GLY C  51 "
      ideal   model   delta    sigma   weight residual
     111.20  114.26   -3.06 1.39e+00 5.18e-01 4.84e+00
  angle pdb=" N   GLY A  51 "
        pdb=" CA  GLY A  51 "
        pdb=" C   GLY A  51 "
      ideal   model   delta    sigma   weight residual
     111.20  114.26   -3.06 1.39e+00 5.18e-01 4.83e+00
  ... (remaining 3631 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.25: 1349
       15.25 -    30.50: 157
       30.50 -    45.75: 36
       45.75 -    61.00: 24
       61.00 -    76.25: 12
  Dihedral angle restraints: 1578
    sinusoidal: 546
      harmonic: 1032
  Sorted by residual:
  dihedral pdb=" CA  ILE F  88 "
           pdb=" C   ILE F  88 "
           pdb=" N   ALA F  89 "
           pdb=" CA  ALA F  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.55  -17.45     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" CA  ILE E  88 "
           pdb=" C   ILE E  88 "
           pdb=" N   ALA E  89 "
           pdb=" CA  ALA E  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.57  -17.43     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" CA  ILE D  88 "
           pdb=" C   ILE D  88 "
           pdb=" N   ALA D  89 "
           pdb=" CA  ALA D  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.58  -17.42     0      5.00e+00 4.00e-02 1.21e+01
  ... (remaining 1575 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 287
       0.031 -    0.062: 91
       0.062 -    0.092: 20
       0.092 -    0.123: 64
       0.123 -    0.154: 12
  Chirality restraints: 474
  Sorted by residual:
  chirality pdb=" CB  ILE C  88 "
            pdb=" CA  ILE C  88 "
            pdb=" CG1 ILE C  88 "
            pdb=" CG2 ILE C  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.15 2.00e-01 2.50e+01 5.94e-01
  chirality pdb=" CB  ILE E  88 "
            pdb=" CA  ILE E  88 "
            pdb=" CG1 ILE E  88 "
            pdb=" CG2 ILE E  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.15 2.00e-01 2.50e+01 5.80e-01
  chirality pdb=" CB  ILE A  88 "
            pdb=" CA  ILE A  88 "
            pdb=" CG1 ILE A  88 "
            pdb=" CG2 ILE A  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.15 2.00e-01 2.50e+01 5.72e-01
  ... (remaining 471 not shown)

  Planarity restraints: 450
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  96 "    0.005 2.00e-02 2.50e+03   9.72e-03 9.44e-01
        pdb=" C   LYS A  96 "   -0.017 2.00e-02 2.50e+03
        pdb=" O   LYS A  96 "    0.006 2.00e-02 2.50e+03
        pdb=" N   LYS A  97 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C  96 "    0.005 2.00e-02 2.50e+03   9.56e-03 9.14e-01
        pdb=" C   LYS C  96 "   -0.017 2.00e-02 2.50e+03
        pdb=" O   LYS C  96 "    0.006 2.00e-02 2.50e+03
        pdb=" N   LYS C  97 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B  96 "    0.005 2.00e-02 2.50e+03   9.52e-03 9.06e-01
        pdb=" C   LYS B  96 "   -0.016 2.00e-02 2.50e+03
        pdb=" O   LYS B  96 "    0.006 2.00e-02 2.50e+03
        pdb=" N   LYS B  97 "    0.005 2.00e-02 2.50e+03
  ... (remaining 447 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 1391
        2.98 -     3.46: 2298
        3.46 -     3.94: 4280
        3.94 -     4.42: 4241
        4.42 -     4.90: 8683
  Nonbonded interactions: 20893
  Sorted by model distance:
  nonbonded pdb=" O   ALA E  89 "
            pdb=" N   ALA F  90 "
     model   vdw
     2.503 3.120
  nonbonded pdb=" O   ALA B  89 "
            pdb=" N   ALA C  90 "
     model   vdw
     2.518 3.120
  nonbonded pdb=" O   HIS B  50 "
            pdb=" OG1 THR A  72 "
     model   vdw
     2.564 3.040
  nonbonded pdb=" O   HIS E  50 "
            pdb=" OG1 THR D  72 "
     model   vdw
     2.578 3.040
  nonbonded pdb=" O   LYS E  60 "
            pdb=" N   GLU F  61 "
     model   vdw
     2.589 3.120
  ... (remaining 20888 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

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:             1.870
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     11.760
  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:             0.000
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6316
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      :  0.002   0.017   2694  Z= 0.106
  Angle     :  0.589   4.802   3636  Z= 0.337
  Chirality :  0.053   0.154    474
  Planarity :  0.002   0.010    450
  Dihedral  : 17.480  76.250    930
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.90 %
    Favored  : 87.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 26.09 %
    Favored  : 73.91 %
  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: -2.81 (0.38), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.29), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B  50 
 PHE   0.010   0.003   PHE C  94 
 TYR   0.004   0.001   TYR F  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10113 (   16)
  hydrogen bonds       : angle       6.43806 (   48)
  covalent geometry    : bond        0.00195 ( 2694)
  covalent geometry    : angle       0.58897 ( 3636)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.290 
Fit side-chains
REVERT: B   58 LYS cc_start: 0.7748 (mttt) cc_final: 0.7492 (tptp)
REVERT: A   45 LYS cc_start: 0.8531 (tmtt) cc_final: 0.8259 (tttm)
REVERT: A   58 LYS cc_start: 0.8179 (mttt) cc_final: 0.7589 (tptp)
REVERT: C   58 LYS cc_start: 0.8036 (mttt) cc_final: 0.7620 (tptp)
REVERT: E   58 LYS cc_start: 0.7931 (mttt) cc_final: 0.7646 (tptp)
REVERT: D   58 LYS cc_start: 0.8000 (mttt) cc_final: 0.7492 (tptp)
REVERT: F   58 LYS cc_start: 0.8138 (mttt) cc_final: 0.7473 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.2563
  time to fit residues: 9.0535
Evaluate side-chains
  31 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 9 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 17 optimal weight:    8.9990
   chunk 21 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    4.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4797 r_free = 0.4797 target = 0.202442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.187755 restraints weight = 3647.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4686 r_free = 0.4686 target = 0.191198 restraints weight = 1888.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.193575 restraints weight = 1135.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.4717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6992
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.028   2694  Z= 0.273
  Angle     :  0.698   5.250   3636  Z= 0.398
  Chirality :  0.055   0.139    474
  Planarity :  0.004   0.012    450
  Dihedral  :  7.554  25.124    384
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.20 %
    Favored  : 82.80 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 25.00 %
    Favored  : 73.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.77 (0.31), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.86 (0.24), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS F  50 
 PHE   0.003   0.002   PHE B  94 
 TYR   0.013   0.003   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02104 (   16)
  hydrogen bonds       : angle       4.12273 (   48)
  covalent geometry    : bond        0.00551 ( 2694)
  covalent geometry    : angle       0.69802 ( 3636)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.261 
Fit side-chains
REVERT: B   45 LYS cc_start: 0.9000 (tmtt) cc_final: 0.8760 (tttp)
REVERT: B   58 LYS cc_start: 0.8250 (mttt) cc_final: 0.7922 (tptp)
REVERT: A   34 LYS cc_start: 0.5378 (pttm) cc_final: 0.5112 (tptp)
REVERT: A   58 LYS cc_start: 0.8253 (mttt) cc_final: 0.7955 (tptp)
REVERT: C   58 LYS cc_start: 0.8474 (mttt) cc_final: 0.8108 (tptp)
REVERT: E   58 LYS cc_start: 0.8247 (mttt) cc_final: 0.8026 (tptp)
REVERT: D   34 LYS cc_start: 0.5246 (pttm) cc_final: 0.4921 (tptp)
REVERT: D   58 LYS cc_start: 0.8298 (mttt) cc_final: 0.8026 (tptp)
REVERT: F   58 LYS cc_start: 0.8218 (mttt) cc_final: 0.7939 (tptp)
  outliers start: 4
  outliers final: 3
  residues processed: 44
  average time/residue: 0.2690
  time to fit residues: 13.1880
Evaluate side-chains
  41 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain E residue   72 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0050
   chunk 22 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   overall best weight:    3.2002

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 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 = 0.4794 r_free = 0.4794 target = 0.202143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.187982 restraints weight = 3743.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.191324 restraints weight = 1951.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.193626 restraints weight = 1179.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.4925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.4117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   2694  Z= 0.208
  Angle     :  0.641   6.224   3636  Z= 0.351
  Chirality :  0.053   0.163    474
  Planarity :  0.003   0.008    450
  Dihedral  :  6.682  23.737    384
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.01 %
    Favored  : 81.99 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 23.19 %
    Favored  : 73.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.00 (0.30), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.04 (0.23), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS A  50 
 PHE   0.002   0.000   PHE A  94 
 TYR   0.006   0.002   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01573 (   16)
  hydrogen bonds       : angle       3.85639 (   48)
  covalent geometry    : bond        0.00420 ( 2694)
  covalent geometry    : angle       0.64071 ( 3636)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7614 (tttt) cc_final: 0.7173 (ttpt)
REVERT: A   45 LYS cc_start: 0.8719 (tmtt) cc_final: 0.8454 (tttm)
REVERT: A   58 LYS cc_start: 0.8333 (mttt) cc_final: 0.8071 (tptp)
REVERT: C   75 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7566 (t)
  outliers start: 9
  outliers final: 4
  residues processed: 46
  average time/residue: 0.2295
  time to fit residues: 11.9526
Evaluate side-chains
  42 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain E residue   72 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 2 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 29 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  62 GLN
F  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4970 r_free = 0.4970 target = 0.222832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4868 r_free = 0.4868 target = 0.213158 restraints weight = 3566.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4891 r_free = 0.4891 target = 0.215569 restraints weight = 1914.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4905 r_free = 0.4905 target = 0.217076 restraints weight = 1166.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.4925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.5234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.022   2694  Z= 0.248
  Angle     :  0.753   9.337   3636  Z= 0.402
  Chirality :  0.054   0.131    474
  Planarity :  0.003   0.011    450
  Dihedral  :  6.852  24.227    384
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.24 %
    Favored  : 78.76 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 26.09 %
    Favored  : 70.65 %
  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: -4.27 (0.29), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.22), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B  50 
 PHE   0.003   0.001   PHE A  94 
 TYR   0.006   0.002   TYR D  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01668 (   16)
  hydrogen bonds       : angle       3.80587 (   48)
  covalent geometry    : bond        0.00496 ( 2694)
  covalent geometry    : angle       0.75346 ( 3636)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 LYS cc_start: 0.8869 (tttt) cc_final: 0.8612 (tttm)
REVERT: A   45 LYS cc_start: 0.8715 (tmtt) cc_final: 0.8357 (tttm)
REVERT: A   58 LYS cc_start: 0.8393 (mttt) cc_final: 0.8095 (tptp)
REVERT: C   58 LYS cc_start: 0.8421 (tptp) cc_final: 0.8129 (tptp)
REVERT: C   75 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7648 (t)
REVERT: D   43 LYS cc_start: 0.7803 (tttt) cc_final: 0.7365 (ttpt)
REVERT: F   43 LYS cc_start: 0.7830 (tttt) cc_final: 0.7371 (ttmt)
REVERT: F   58 LYS cc_start: 0.8345 (tptp) cc_final: 0.8074 (tptp)
REVERT: F   75 THR cc_start: 0.8152 (OUTLIER) cc_final: 0.7741 (t)
  outliers start: 9
  outliers final: 7
  residues processed: 53
  average time/residue: 0.2749
  time to fit residues: 16.3085
Evaluate side-chains
  51 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain F residue   75 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0980
   chunk 11 optimal weight:   10.0000
   chunk 12 optimal weight:    0.0000
   chunk 3 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:   10.0000
   overall best weight:    0.7786

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5146 r_free = 0.5146 target = 0.240652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5044 r_free = 0.5044 target = 0.230390 restraints weight = 3282.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.5065 r_free = 0.5065 target = 0.233169 restraints weight = 1662.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.5083 r_free = 0.5083 target = 0.235043 restraints weight = 973.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.5105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6840
moved from start:          0.4854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2694  Z= 0.093
  Angle     :  0.594   7.318   3636  Z= 0.305
  Chirality :  0.052   0.146    474
  Planarity :  0.002   0.009    450
  Dihedral  :  4.763  20.529    384
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.95 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 26.45 %
    Favored  : 72.10 %
  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: -3.59 (0.31), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.73 (0.24), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS C  50 
 PHE   0.003   0.000   PHE B  94 
 TYR   0.004   0.001   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01330 (   16)
  hydrogen bonds       : angle       3.56076 (   48)
  covalent geometry    : bond        0.00186 ( 2694)
  covalent geometry    : angle       0.59413 ( 3636)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A   45 LYS cc_start: 0.8668 (tmtt) cc_final: 0.8392 (tttm)
REVERT: A   58 LYS cc_start: 0.8120 (mttt) cc_final: 0.7914 (tptp)
REVERT: C   75 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7471 (t)
REVERT: D   58 LYS cc_start: 0.8322 (tptp) cc_final: 0.8014 (tptp)
REVERT: F   43 LYS cc_start: 0.7662 (tttt) cc_final: 0.7254 (ttpt)
REVERT: F   58 LYS cc_start: 0.8193 (tptp) cc_final: 0.7988 (tptp)
REVERT: F   75 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7596 (t)
  outliers start: 4
  outliers final: 2
  residues processed: 39
  average time/residue: 0.2180
  time to fit residues: 9.8284
Evaluate side-chains
  39 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain F residue   75 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 15 optimal weight:    0.7980
   chunk 5 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  62 GLN
** E  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4967 r_free = 0.4967 target = 0.221718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4867 r_free = 0.4867 target = 0.212070 restraints weight = 3572.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4890 r_free = 0.4890 target = 0.214538 restraints weight = 1894.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4907 r_free = 0.4907 target = 0.216156 restraints weight = 1136.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.4923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.5593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.020   2694  Z= 0.249
  Angle     :  0.704   7.879   3636  Z= 0.377
  Chirality :  0.053   0.128    474
  Planarity :  0.003   0.009    450
  Dihedral  :  6.349  21.970    384
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  : 19.62 %
    Favored  : 79.84 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 24.28 %
    Favored  : 71.01 %
  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: -4.02 (0.30), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.06 (0.23), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B  50 
 PHE   0.002   0.000   PHE A  94 
 TYR   0.007   0.002   TYR D  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01391 (   16)
  hydrogen bonds       : angle       3.72116 (   48)
  covalent geometry    : bond        0.00501 ( 2694)
  covalent geometry    : angle       0.70438 ( 3636)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 LYS cc_start: 0.8789 (tttp) cc_final: 0.8565 (tttm)
REVERT: B   46 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7856 (tp30)
REVERT: A   34 LYS cc_start: 0.5583 (pttt) cc_final: 0.5192 (tptp)
REVERT: A   45 LYS cc_start: 0.8742 (tmtt) cc_final: 0.8479 (tttm)
REVERT: A   58 LYS cc_start: 0.8335 (mttt) cc_final: 0.8059 (tptp)
REVERT: C   58 LYS cc_start: 0.8434 (tptp) cc_final: 0.8114 (tptp)
REVERT: C   75 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7641 (t)
REVERT: D   58 LYS cc_start: 0.8540 (tptp) cc_final: 0.8307 (tptp)
REVERT: F   58 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7975 (tptp)
REVERT: F   75 THR cc_start: 0.8091 (OUTLIER) cc_final: 0.7692 (t)
  outliers start: 13
  outliers final: 8
  residues processed: 52
  average time/residue: 0.2653
  time to fit residues: 15.3772
Evaluate side-chains
  53 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain D residue   34 LYS
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain F residue   58 LYS
Chi-restraints excluded: chain F residue   75 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 27 optimal weight:    0.0170
   chunk 9 optimal weight:    0.0370
   chunk 5 optimal weight:    9.9990
   chunk 20 optimal weight:    0.2980
   chunk 12 optimal weight:    0.4980
   chunk 16 optimal weight:    0.0010
   chunk 30 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.1702

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

Flipped N/Q/H residues before XYZ refinement:
** E  87 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 = 0.5134 r_free = 0.5134 target = 0.240105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.5029 r_free = 0.5029 target = 0.229501 restraints weight = 3446.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.5054 r_free = 0.5054 target = 0.232298 restraints weight = 1830.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.5074 r_free = 0.5074 target = 0.234185 restraints weight = 1088.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.5094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6790
moved from start:          0.5112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2694  Z= 0.082
  Angle     :  0.587   9.924   3636  Z= 0.295
  Chirality :  0.052   0.137    474
  Planarity :  0.002   0.009    450
  Dihedral  :  4.177  18.820    384
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 25.36 %
    Favored  : 71.01 %
  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: -3.17 (0.34), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.41 (0.26), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C  50 
 PHE   0.004   0.001   PHE B  94 
 TYR   0.005   0.001   TYR E  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01255 (   16)
  hydrogen bonds       : angle       3.56233 (   48)
  covalent geometry    : bond        0.00161 ( 2694)
  covalent geometry    : angle       0.58704 ( 3636)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 34
  time to evaluate  : 0.275 
Fit side-chains
REVERT: B   46 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7737 (tp30)
REVERT: A   45 LYS cc_start: 0.8623 (tmtt) cc_final: 0.8374 (tttm)
REVERT: A   58 LYS cc_start: 0.8047 (mttt) cc_final: 0.7710 (tptp)
REVERT: C   46 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7957 (mm-30)
REVERT: C   58 LYS cc_start: 0.8431 (tptp) cc_final: 0.8074 (tptp)
REVERT: C   75 THR cc_start: 0.7869 (OUTLIER) cc_final: 0.7527 (t)
REVERT: E   46 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7857 (tp30)
REVERT: D   58 LYS cc_start: 0.8361 (tptp) cc_final: 0.8008 (tptp)
REVERT: F   58 LYS cc_start: 0.8298 (tptp) cc_final: 0.7919 (tptp)
REVERT: F   75 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7529 (t)
  outliers start: 10
  outliers final: 3
  residues processed: 39
  average time/residue: 0.2159
  time to fit residues: 9.8010
Evaluate side-chains
  41 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   88 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 20 optimal weight:    8.9990
   chunk 19 optimal weight:    8.9990
   chunk 27 optimal weight:    2.9990
   chunk 12 optimal weight:    7.9990
   chunk 5 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   chunk 32 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    4.9588

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

Flipped N/Q/H residues before XYZ refinement:
E  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4659 r_free = 0.4659 target = 0.190740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.176825 restraints weight = 3813.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.179954 restraints weight = 1998.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.182051 restraints weight = 1218.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.4570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.6033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.026   2694  Z= 0.317
  Angle     :  0.775   9.820   3636  Z= 0.413
  Chirality :  0.055   0.127    474
  Planarity :  0.004   0.012    450
  Dihedral  :  6.673  23.467    384
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  : 19.89 %
    Favored  : 79.03 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 24.64 %
    Favored  : 70.65 %
  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: -4.16 (0.30), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.16 (0.23), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B  50 
 PHE   0.002   0.001   PHE A  94 
 TYR   0.008   0.003   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01478 (   16)
  hydrogen bonds       : angle       3.72912 (   48)
  covalent geometry    : bond        0.00639 ( 2694)
  covalent geometry    : angle       0.77509 ( 3636)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 LYS cc_start: 0.8915 (tttp) cc_final: 0.8702 (tttm)
REVERT: B   46 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8099 (tp30)
REVERT: A   34 LYS cc_start: 0.5400 (pttt) cc_final: 0.5074 (tptp)
REVERT: A   58 LYS cc_start: 0.8355 (mttt) cc_final: 0.7724 (tptp)
REVERT: C   58 LYS cc_start: 0.8453 (tptp) cc_final: 0.8029 (tptp)
REVERT: E   46 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8189 (tp30)
REVERT: D   58 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8251 (tptp)
REVERT: F   58 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8005 (tptp)
  outliers start: 13
  outliers final: 8
  residues processed: 50
  average time/residue: 0.2213
  time to fit residues: 12.5809
Evaluate side-chains
  55 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain F residue   58 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0770
   chunk 24 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.7940

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

Flipped N/Q/H residues before XYZ refinement:
** E  87 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 = 0.5053 r_free = 0.5053 target = 0.230845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4942 r_free = 0.4942 target = 0.220512 restraints weight = 3460.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4967 r_free = 0.4967 target = 0.223108 restraints weight = 1864.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4987 r_free = 0.4987 target = 0.224919 restraints weight = 1128.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.5009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6913
moved from start:          0.5601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2694  Z= 0.094
  Angle     :  0.639  10.849   3636  Z= 0.313
  Chirality :  0.052   0.127    474
  Planarity :  0.002   0.010    450
  Dihedral  :  4.708  20.211    384
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 26.81 %
    Favored  : 71.01 %
  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: -3.46 (0.34), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.26), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS D  50 
 PHE   0.003   0.000   PHE E  94 
 TYR   0.005   0.001   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01267 (   16)
  hydrogen bonds       : angle       3.71507 (   48)
  covalent geometry    : bond        0.00183 ( 2694)
  covalent geometry    : angle       0.63928 ( 3636)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.292 
Fit side-chains
REVERT: B   46 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7773 (tp30)
REVERT: A   58 LYS cc_start: 0.8252 (mttt) cc_final: 0.7834 (tptp)
REVERT: C   58 LYS cc_start: 0.8352 (tptp) cc_final: 0.7894 (tptp)
REVERT: E   46 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7845 (tp30)
REVERT: D   58 LYS cc_start: 0.8422 (tptp) cc_final: 0.8140 (tptp)
REVERT: F   58 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7956 (tptp)
  outliers start: 6
  outliers final: 2
  residues processed: 37
  average time/residue: 0.2375
  time to fit residues: 10.0882
Evaluate side-chains
  38 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain F residue   58 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 7 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0050
   chunk 26 optimal weight:    0.0980
   chunk 4 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 27 optimal weight:    0.3980
   chunk 30 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.6996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5102 r_free = 0.5102 target = 0.235960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4991 r_free = 0.4991 target = 0.225065 restraints weight = 3441.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.5014 r_free = 0.5014 target = 0.227751 restraints weight = 1866.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.5032 r_free = 0.5032 target = 0.229631 restraints weight = 1136.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.5052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6846
moved from start:          0.5535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   2694  Z= 0.086
  Angle     :  0.631  11.780   3636  Z= 0.299
  Chirality :  0.051   0.128    474
  Planarity :  0.002   0.010    450
  Dihedral  :  4.045  18.366    384
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.37 %
    Favored  : 87.63 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 26.45 %
    Favored  : 71.01 %
  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: -3.08 (0.36), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.34 (0.28), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  50 
 PHE   0.002   0.000   PHE B  94 
 TYR   0.004   0.001   TYR E  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01003 (   16)
  hydrogen bonds       : angle       3.37808 (   48)
  covalent geometry    : bond        0.00170 ( 2694)
  covalent geometry    : angle       0.63122 ( 3636)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.288 
Fit side-chains
REVERT: B   46 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7751 (tp30)
REVERT: A   46 GLU cc_start: 0.8002 (tp30) cc_final: 0.7737 (tp30)
REVERT: A   58 LYS cc_start: 0.8101 (mttt) cc_final: 0.7722 (tptp)
REVERT: C   58 LYS cc_start: 0.8326 (tptp) cc_final: 0.7902 (tptp)
REVERT: E   46 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7905 (tp30)
REVERT: D   58 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7968 (tptp)
REVERT: F   58 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7933 (tptp)
  outliers start: 7
  outliers final: 3
  residues processed: 33
  average time/residue: 0.2244
  time to fit residues: 8.6030
Evaluate side-chains
  36 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain F residue   58 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 11 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 35 optimal weight:    0.0870
   chunk 33 optimal weight:    8.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    3.3964

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

Flipped N/Q/H residues before XYZ refinement:
** B  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  87 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 = 0.4945 r_free = 0.4945 target = 0.219873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4825 r_free = 0.4825 target = 0.208909 restraints weight = 3541.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4851 r_free = 0.4851 target = 0.211565 restraints weight = 1902.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4870 r_free = 0.4870 target = 0.213395 restraints weight = 1160.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.4660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.6016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   2694  Z= 0.221
  Angle     :  0.726  11.293   3636  Z= 0.364
  Chirality :  0.053   0.130    474
  Planarity :  0.003   0.010    450
  Dihedral  :  5.781  23.071    384
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.47 %
    Favored  : 82.53 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 25.72 %
    Favored  : 71.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.69 (0.33), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.80 (0.25), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B  50 
 PHE   0.001   0.000   PHE A  94 
 TYR   0.009   0.002   TYR E  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01158 (   16)
  hydrogen bonds       : angle       3.53664 (   48)
  covalent geometry    : bond        0.00444 ( 2694)
  covalent geometry    : angle       0.72587 ( 3636)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1379.90 seconds
wall clock time: 24 minutes 55.44 seconds (1495.44 seconds total)