Starting phenix.real_space_refine
on Wed Sep 17 03:15:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k24_61989/09_2025/9k24_61989.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k24_61989/09_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_61989/09_2025/9k24_61989.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k24_61989/09_2025/9k24_61989.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k24_61989/09_2025/9k24_61989.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k24_61989/09_2025/9k24_61989.cif"
  }
  resolution = 3.6
  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=   0.002
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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2682
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      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:
    A, C, E, D, F
  Time building chain proxies: 0.54, per 1000 atoms: 0.20
  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: 0.19
  Conformation dependent library (CDL) restraints added in 84.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.06
  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: 0.27

  Time building geometry restraints manager: 0.26 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  selection = chain 'C'
  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:             3.090
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     3.550
  Find NCS groups from input model:        0.030
  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:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.820
-------------------------------------------------------------------------------
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 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: -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
 TYR   0.004   0.001   TYR F  39 
 PHE   0.010   0.003   PHE C  94 
 HIS   0.001   0.000   HIS B  50 

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

*********************** 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  : 0.063 
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: 0.0954
  time to fit residues: 3.3288
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  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
C  79 GLN
F  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4814 r_free = 0.4814 target = 0.205610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.188885 restraints weight = 3655.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.192138 restraints weight = 2074.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4722 r_free = 0.4722 target = 0.194731 restraints weight = 1336.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4738 r_free = 0.4738 target = 0.196482 restraints weight = 922.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4749 r_free = 0.4749 target = 0.197743 restraints weight = 677.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.4766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6786
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2694  Z= 0.165
  Angle     :  0.577   4.919   3636  Z= 0.326
  Chirality :  0.052   0.148    474
  Planarity :  0.003   0.009    450
  Dihedral  :  6.144  22.153    384
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.59 %
    Favored  : 84.41 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 26.09 %
    Favored  : 71.74 %
  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: -3.19 (0.35), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.43 (0.27), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR B  39 
 PHE   0.003   0.001   PHE C  94 
 HIS   0.001   0.000   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 2694)
  covalent geometry    : angle       0.57653 ( 3636)
  hydrogen bonds       : bond        0.01964 (   16)
  hydrogen bonds       : angle       3.76818 (   48)

*********************** 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
  39 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.074 
Fit side-chains
REVERT: B   58 LYS cc_start: 0.8022 (mttt) cc_final: 0.7705 (tptp)
REVERT: A   45 LYS cc_start: 0.8759 (tmtt) cc_final: 0.8348 (tttm)
REVERT: A   58 LYS cc_start: 0.8205 (mttt) cc_final: 0.7748 (tptp)
REVERT: C   58 LYS cc_start: 0.8407 (mttt) cc_final: 0.7908 (tptp)
REVERT: E   58 LYS cc_start: 0.8252 (mttt) cc_final: 0.7808 (tptp)
REVERT: D   58 LYS cc_start: 0.8295 (mttt) cc_final: 0.7819 (tptp)
REVERT: F   58 LYS cc_start: 0.8257 (mttt) cc_final: 0.7756 (tptp)
  outliers start: 6
  outliers final: 2
  residues processed: 38
  average time/residue: 0.0976
  time to fit residues: 4.1825
Evaluate side-chains
  35 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B 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 2 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 7 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0270
   chunk 35 optimal weight:    9.9990
   chunk 22 optimal weight:    8.9990
   overall best weight:    2.7444

-------------------------------------------------------------------------------
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**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4779 r_free = 0.4779 target = 0.202324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.187283 restraints weight = 3745.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.190695 restraints weight = 1973.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.192966 restraints weight = 1201.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4707 r_free = 0.4707 target = 0.194585 restraints weight = 815.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4717 r_free = 0.4717 target = 0.195672 restraints weight = 598.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.4938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6959
moved from start:          0.3795

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= 0.180
  Angle     :  0.584   4.813   3636  Z= 0.327
  Chirality :  0.052   0.140    474
  Planarity :  0.003   0.007    450
  Dihedral  :  6.369  23.368    384
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.13 %
    Favored  : 83.87 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 25.00 %
    Favored  : 73.19 %
  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: -3.47 (0.33), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.25), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.002   TYR D  39 
 PHE   0.001   0.000   PHE D  94 
 HIS   0.001   0.000   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 2694)
  covalent geometry    : angle       0.58367 ( 3636)
  hydrogen bonds       : bond        0.01681 (   16)
  hydrogen bonds       : angle       3.78649 (   48)

*********************** 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
  40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.118 
Fit side-chains
REVERT: B   45 LYS cc_start: 0.8893 (tttt) cc_final: 0.8667 (tttm)
REVERT: C   58 LYS cc_start: 0.8389 (mttt) cc_final: 0.8148 (tptp)
REVERT: F   75 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7661 (t)
  outliers start: 5
  outliers final: 3
  residues processed: 39
  average time/residue: 0.0998
  time to fit residues: 4.3881
Evaluate side-chains
  37 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain F residue   75 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 14 optimal weight:    3.9990
   chunk 18 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   chunk 27 optimal weight:    0.2980
   chunk 34 optimal weight:    0.4980
   chunk 1 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 23 optimal weight:   10.0000
   overall best weight:    1.7384

-------------------------------------------------------------------------------
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 = 0.5024 r_free = 0.5024 target = 0.230068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4905 r_free = 0.4905 target = 0.217173 restraints weight = 3519.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4931 r_free = 0.4931 target = 0.220236 restraints weight = 1867.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4950 r_free = 0.4950 target = 0.222321 restraints weight = 1128.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4960 r_free = 0.4960 target = 0.223629 restraints weight = 751.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4969 r_free = 0.4969 target = 0.224697 restraints weight = 553.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.4985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6870
moved from start:          0.4260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.014   2694  Z= 0.128
  Angle     :  0.566   6.550   3636  Z= 0.311
  Chirality :  0.052   0.132    474
  Planarity :  0.002   0.012    450
  Dihedral  :  5.348  22.281    384
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.71 %
    Favored  : 86.29 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 27.90 %
    Favored  : 70.29 %
  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: -3.25 (0.34), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.47 (0.26), residues: 372

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 2694)
  covalent geometry    : angle       0.56579 ( 3636)
  hydrogen bonds       : bond        0.01252 (   16)
  hydrogen bonds       : angle       3.46665 (   48)

*********************** 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
  40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.102 
Fit side-chains
REVERT: B   45 LYS cc_start: 0.8937 (tttt) cc_final: 0.8697 (tttp)
REVERT: B   58 LYS cc_start: 0.8230 (tptp) cc_final: 0.7996 (tptp)
REVERT: A   45 LYS cc_start: 0.8726 (tmtt) cc_final: 0.8511 (tttm)
REVERT: C   58 LYS cc_start: 0.8339 (mttt) cc_final: 0.7994 (tptp)
REVERT: F   58 LYS cc_start: 0.8310 (tptp) cc_final: 0.7988 (tptp)
REVERT: F   75 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7607 (t)
  outliers start: 5
  outliers final: 4
  residues processed: 38
  average time/residue: 0.0865
  time to fit residues: 3.8413
Evaluate side-chains
  40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   72 THR
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 14 optimal weight:    5.9990
   chunk 35 optimal weight:    8.9990
   chunk 27 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 30 optimal weight:    0.1980
   chunk 18 optimal weight:    7.9990
   chunk 31 optimal weight:    7.9990
   chunk 29 optimal weight:    9.9990
   overall best weight:    1.7384

-------------------------------------------------------------------------------
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**
** E  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5013 r_free = 0.5013 target = 0.228505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4896 r_free = 0.4896 target = 0.216000 restraints weight = 3493.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4922 r_free = 0.4922 target = 0.218923 restraints weight = 1845.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4939 r_free = 0.4939 target = 0.220941 restraints weight = 1124.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4949 r_free = 0.4949 target = 0.222317 restraints weight = 752.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4957 r_free = 0.4957 target = 0.223259 restraints weight = 548.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.4975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
moved from start:          0.4540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   2694  Z= 0.126
  Angle     :  0.550   7.284   3636  Z= 0.297
  Chirality :  0.051   0.130    474
  Planarity :  0.002   0.008    450
  Dihedral  :  5.203  21.667    384
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.44 %
    Favored  : 86.56 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 25.00 %
    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 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: -3.13 (0.34), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.38 (0.26), residues: 372

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 2694)
  covalent geometry    : angle       0.55030 ( 3636)
  hydrogen bonds       : bond        0.01085 (   16)
  hydrogen bonds       : angle       3.31863 (   48)

*********************** 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
  48 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 36
  time to evaluate  : 0.106 
Fit side-chains
REVERT: B   45 LYS cc_start: 0.8938 (tttt) cc_final: 0.8544 (tttp)
REVERT: B   46 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7840 (tp30)
REVERT: B   58 LYS cc_start: 0.8286 (tptp) cc_final: 0.8030 (tptp)
REVERT: A   45 LYS cc_start: 0.8752 (tmtt) cc_final: 0.8477 (tttm)
REVERT: C   58 LYS cc_start: 0.8243 (mttt) cc_final: 0.7993 (tptp)
REVERT: D   58 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8062 (tptp)
REVERT: F   46 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7522 (mp0)
REVERT: F   58 LYS cc_start: 0.8246 (tptp) cc_final: 0.7943 (tptp)
REVERT: F   75 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7557 (t)
  outliers start: 12
  outliers final: 6
  residues processed: 41
  average time/residue: 0.0976
  time to fit residues: 4.5739
Evaluate side-chains
  46 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 36
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
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   72 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   88 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 15 optimal weight:    0.0270
   chunk 30 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 4 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   chunk 24 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    2.4046

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN
** B  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4972 r_free = 0.4972 target = 0.223902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4855 r_free = 0.4855 target = 0.211671 restraints weight = 3593.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4878 r_free = 0.4878 target = 0.214491 restraints weight = 1896.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4897 r_free = 0.4897 target = 0.216438 restraints weight = 1159.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4907 r_free = 0.4907 target = 0.217737 restraints weight = 779.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4917 r_free = 0.4917 target = 0.218771 restraints weight = 575.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.4728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.5044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.013   2694  Z= 0.166
  Angle     :  0.594   9.082   3636  Z= 0.319
  Chirality :  0.052   0.133    474
  Planarity :  0.002   0.007    450
  Dihedral  :  5.669  22.849    384
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.59 %
    Favored  : 84.41 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 27.17 %
    Favored  : 69.20 %
  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: -3.26 (0.33), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.47 (0.25), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.002   TYR A  39 
 PHE   0.001   0.000   PHE E  94 
 HIS   0.000   0.000   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 2694)
  covalent geometry    : angle       0.59370 ( 3636)
  hydrogen bonds       : bond        0.01119 (   16)
  hydrogen bonds       : angle       3.41214 (   48)

*********************** 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
  55 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.120 
Fit side-chains
REVERT: B   45 LYS cc_start: 0.8976 (tttt) cc_final: 0.8681 (tttp)
REVERT: B   58 LYS cc_start: 0.8369 (tptp) cc_final: 0.8138 (tptp)
REVERT: A   43 LYS cc_start: 0.7627 (tttt) cc_final: 0.7375 (tttp)
REVERT: A   45 LYS cc_start: 0.8817 (tmtt) cc_final: 0.8597 (tttm)
REVERT: C   43 LYS cc_start: 0.7439 (tttt) cc_final: 0.7009 (ttpt)
REVERT: C   58 LYS cc_start: 0.8231 (mttt) cc_final: 0.7923 (tptp)
REVERT: D   43 LYS cc_start: 0.7710 (tttt) cc_final: 0.7134 (ttpt)
REVERT: F   46 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7620 (mp0)
REVERT: F   58 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7972 (tptp)
REVERT: F   75 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7594 (t)
  outliers start: 10
  outliers final: 5
  residues processed: 49
  average time/residue: 0.1157
  time to fit residues: 6.3978
Evaluate side-chains
  51 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain F residue   46 GLU
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 13 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9980
   chunk 5 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.4837 r_free = 0.4837 target = 0.206229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4686 r_free = 0.4686 target = 0.189199 restraints weight = 3520.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4720 r_free = 0.4720 target = 0.192679 restraints weight = 1951.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.195161 restraints weight = 1234.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4762 r_free = 0.4762 target = 0.196970 restraints weight = 854.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4773 r_free = 0.4773 target = 0.198259 restraints weight = 629.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.4786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6788
moved from start:          0.4921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   2694  Z= 0.099
  Angle     :  0.622  10.831   3636  Z= 0.303
  Chirality :  0.051   0.129    474
  Planarity :  0.002   0.009    450
  Dihedral  :  4.694  21.118    384
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 26.81 %
    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 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: -2.91 (0.36), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.21 (0.27), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR B  39 
 PHE   0.002   0.000   PHE B  94 
 HIS   0.001   0.000   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 ( 2694)
  covalent geometry    : angle       0.62215 ( 3636)
  hydrogen bonds       : bond        0.01029 (   16)
  hydrogen bonds       : angle       3.34937 (   48)

*********************** 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: 7
    poor density    : 37
  time to evaluate  : 0.099 
Fit side-chains
REVERT: B   45 LYS cc_start: 0.8945 (tttt) cc_final: 0.8501 (tttp)
REVERT: B   46 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7904 (tp30)
REVERT: B   58 LYS cc_start: 0.8178 (tptp) cc_final: 0.7976 (tptp)
REVERT: A   43 LYS cc_start: 0.7551 (tttt) cc_final: 0.7328 (tttp)
REVERT: A   45 LYS cc_start: 0.8815 (tmtt) cc_final: 0.8576 (tttm)
REVERT: C   43 LYS cc_start: 0.7351 (tttt) cc_final: 0.6904 (ttmt)
REVERT: C   58 LYS cc_start: 0.8227 (mttt) cc_final: 0.7726 (tptp)
REVERT: E   46 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8072 (tp30)
REVERT: D   43 LYS cc_start: 0.7531 (tttt) cc_final: 0.6920 (ttpt)
REVERT: F   58 LYS cc_start: 0.8284 (tptp) cc_final: 0.7890 (tptp)
REVERT: F   75 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7523 (t)
  outliers start: 7
  outliers final: 4
  residues processed: 40
  average time/residue: 0.1098
  time to fit residues: 4.9610
Evaluate side-chains
  44 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
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   72 THR
Chi-restraints excluded: chain E residue   46 GLU
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 31 optimal weight:    6.9990
   chunk 7 optimal weight:    0.7980
   chunk 35 optimal weight:    8.9990
   chunk 29 optimal weight:    9.9990
   chunk 17 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 15 optimal weight:    8.9990
   chunk 2 optimal weight:    8.9990
   chunk 21 optimal weight:    0.0570
   overall best weight:    3.3704

-------------------------------------------------------------------------------
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**
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  79 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 = 0.4697 r_free = 0.4697 target = 0.194241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.178496 restraints weight = 3793.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.181545 restraints weight = 2134.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.183715 restraints weight = 1368.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4618 r_free = 0.4618 target = 0.185285 restraints weight = 962.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.186405 restraints weight = 722.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.4639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.5512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.018   2694  Z= 0.224
  Angle     :  0.708  10.276   3636  Z= 0.360
  Chirality :  0.052   0.129    474
  Planarity :  0.003   0.010    450
  Dihedral  :  5.911  22.819    384
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.55 %
    Favored  : 81.45 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 24.64 %
    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 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: -3.30 (0.34), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.51 (0.26), residues: 372

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 2694)
  covalent geometry    : angle       0.70836 ( 3636)
  hydrogen bonds       : bond        0.01172 (   16)
  hydrogen bonds       : angle       3.43572 (   48)

*********************** 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: 12
    poor density    : 44
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 LYS cc_start: 0.9003 (tttt) cc_final: 0.8618 (tttp)
REVERT: B   46 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7993 (tp30)
REVERT: B   58 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8154 (tptp)
REVERT: A   45 LYS cc_start: 0.8848 (tmtt) cc_final: 0.8630 (tttm)
REVERT: A   58 LYS cc_start: 0.8319 (tptp) cc_final: 0.7875 (tptp)
REVERT: C   58 LYS cc_start: 0.8310 (mttt) cc_final: 0.7891 (tptp)
REVERT: E   46 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8020 (tp30)
REVERT: D   43 LYS cc_start: 0.7767 (tttt) cc_final: 0.7542 (tttp)
REVERT: F   43 LYS cc_start: 0.7611 (tttt) cc_final: 0.7037 (ttmt)
REVERT: F   46 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7432 (mp0)
REVERT: F   58 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8075 (tptp)
  outliers start: 12
  outliers final: 5
  residues processed: 49
  average time/residue: 0.1202
  time to fit residues: 6.6243
Evaluate side-chains
  52 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue   71 VAL
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 F residue   46 GLU
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 28 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0980
   chunk 35 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    2.8188

-------------------------------------------------------------------------------
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  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4979 r_free = 0.4979 target = 0.223203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4860 r_free = 0.4860 target = 0.212441 restraints weight = 3578.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4885 r_free = 0.4885 target = 0.215007 restraints weight = 1921.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4904 r_free = 0.4904 target = 0.216826 restraints weight = 1177.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4916 r_free = 0.4916 target = 0.218075 restraints weight = 779.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4926 r_free = 0.4926 target = 0.218977 restraints weight = 554.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.4946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.5732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.015   2694  Z= 0.186
  Angle     :  0.707  11.134   3636  Z= 0.349
  Chirality :  0.052   0.134    474
  Planarity :  0.003   0.011    450
  Dihedral  :  5.665  23.402    384
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.90 %
    Favored  : 87.10 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 26.09 %
    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 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: -3.41 (0.34), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.26), residues: 372

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 2694)
  covalent geometry    : angle       0.70650 ( 3636)
  hydrogen bonds       : bond        0.01196 (   16)
  hydrogen bonds       : angle       3.48550 (   48)

*********************** 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
  50 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 LYS cc_start: 0.8900 (tttt) cc_final: 0.8522 (tttp)
REVERT: B   46 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7837 (tp30)
REVERT: A   45 LYS cc_start: 0.8721 (tmtt) cc_final: 0.8474 (tttm)
REVERT: E   46 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7915 (tp30)
REVERT: F   75 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7688 (t)
  outliers start: 8
  outliers final: 4
  residues processed: 47
  average time/residue: 0.1100
  time to fit residues: 5.8238
Evaluate side-chains
  46 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
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   71 VAL
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 F residue   75 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    0.0370
   chunk 32 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 27 optimal weight:    8.9990
   chunk 9 optimal weight:    0.0040
   chunk 11 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    1.2076

-------------------------------------------------------------------------------
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 = 0.5055 r_free = 0.5055 target = 0.230688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4943 r_free = 0.4943 target = 0.220010 restraints weight = 3486.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4969 r_free = 0.4969 target = 0.222743 restraints weight = 1857.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4988 r_free = 0.4988 target = 0.224617 restraints weight = 1111.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4998 r_free = 0.4998 target = 0.225772 restraints weight = 729.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.5007 r_free = 0.5007 target = 0.226716 restraints weight = 523.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.5027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.5662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   2694  Z= 0.110
  Angle     :  0.670  10.635   3636  Z= 0.326
  Chirality :  0.051   0.130    474
  Planarity :  0.002   0.015    450
  Dihedral  :  4.701  20.941    384
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.10 %
    Favored  : 87.90 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 24.64 %
    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 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: -3.01 (0.36), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.29 (0.28), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR B  39 
 PHE   0.002   0.000   PHE E  94 
 HIS   0.001   0.000   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 2694)
  covalent geometry    : angle       0.66952 ( 3636)
  hydrogen bonds       : bond        0.01136 (   16)
  hydrogen bonds       : angle       3.44157 (   48)

********************** 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
  45 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.102 
Fit side-chains
REVERT: B   45 LYS cc_start: 0.8865 (tttt) cc_final: 0.8501 (tttp)
REVERT: B   46 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7795 (tp30)
REVERT: A   45 LYS cc_start: 0.8682 (tmtt) cc_final: 0.8431 (tttm)
REVERT: E   46 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7888 (tp30)
REVERT: F   75 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7633 (t)
  outliers start: 9
  outliers final: 6
  residues processed: 41
  average time/residue: 0.0988
  time to fit residues: 4.6536
Evaluate side-chains
  43 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
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   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 F residue   75 THR
Chi-restraints excluded: chain F residue   88 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9980
   chunk 14 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 35 optimal weight:    7.9990
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    8.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4979 r_free = 0.4979 target = 0.223090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4870 r_free = 0.4870 target = 0.212640 restraints weight = 3501.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4894 r_free = 0.4894 target = 0.215220 restraints weight = 1870.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4912 r_free = 0.4912 target = 0.216947 restraints weight = 1132.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4922 r_free = 0.4922 target = 0.218115 restraints weight = 747.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4931 r_free = 0.4931 target = 0.219023 restraints weight = 539.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.4950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6988
moved from start:          0.5947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2694  Z= 0.176
  Angle     :  0.690  10.502   3636  Z= 0.345
  Chirality :  0.051   0.132    474
  Planarity :  0.003   0.013    450
  Dihedral  :  5.440  22.647    384
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.20 %
    Favored  : 82.80 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 25.00 %
    Favored  : 71.74 %
  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: -3.26 (0.35), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.48 (0.26), residues: 372

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 2694)
  covalent geometry    : angle       0.68953 ( 3636)
  hydrogen bonds       : bond        0.01130 (   16)
  hydrogen bonds       : angle       3.46485 (   48)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 735.18 seconds
wall clock time: 13 minutes 26.16 seconds (806.16 seconds total)