Starting phenix.real_space_refine
on Sun Apr 27 08:22:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6mst_9232/04_2025/6mst_9232.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6mst_9232/04_2025/6mst_9232.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6mst_9232/04_2025/6mst_9232.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6mst_9232/04_2025/6mst_9232.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6mst_9232/04_2025/6mst_9232.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6mst_9232/04_2025/6mst_9232.cif"
  }
  resolution = 2.7
  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=   0.010
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: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    3288      2.51       5
     N     924      2.21       5
     O     936      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 5172
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 431
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 1, 'TRANS': 52}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, L
  Time building chain proxies: 2.16, per 1000 atoms: 0.42
  Number of scatterers: 5172
  At special positions: 0
  Unit cell: (75.92, 92.56, 50.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O     936      8.00
     N     924      7.00
     C    3288      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.17
  Conformation dependent library (CDL) restraints added in 612.7 milliseconds
  

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1128

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 14 sheets defined
      0.0% alpha, 27.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 9
      removed outlier: 6.430A  pdb=" N   PHE I   6 " --> pdb=" O   LEU G   7 " (cutoff:3.500A)
      removed outlier: 8.031A  pdb=" N   GLU G   9 " --> pdb=" O   PHE I   6 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   GLY I   8 " --> pdb=" O   GLU G   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 23
      removed outlier: 6.795A  pdb=" N   ARG C  19 " --> pdb=" O   ALA E  20 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   SER E  22 " --> pdb=" O   ARG C  19 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   TYR C  21 " --> pdb=" O   SER E  22 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ARG E  19 " --> pdb=" O   ALA G  20 " (cutoff:3.500A)
      removed outlier: 8.209A  pdb=" N   SER G  22 " --> pdb=" O   ARG E  19 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   TYR E  21 " --> pdb=" O   SER G  22 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   ARG I  19 " --> pdb=" O   ALA K  20 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   SER K  22 " --> pdb=" O   ARG I  19 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   TYR I  21 " --> pdb=" O   SER K  22 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 30
      removed outlier: 6.499A  pdb=" N   TYR A  29 " --> pdb=" O   ILE C  30 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   TYR C  29 " --> pdb=" O   ILE E  30 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   TYR E  29 " --> pdb=" O   ILE G  30 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   TYR I  29 " --> pdb=" O   ILE K  30 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 39
      removed outlier: 6.680A  pdb=" N   ALA A  38 " --> pdb=" O   ARG C  39 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   ALA C  38 " --> pdb=" O   ARG E  39 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   ALA E  38 " --> pdb=" O   ARG G  39 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   ALA I  38 " --> pdb=" O   ARG K  39 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 42 through 43
      removed outlier: 6.669A  pdb=" N   TYR I  42 " --> pdb=" O   ASP G  43 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 46 through 47
      removed outlier: 6.568A  pdb=" N   LYS I  46 " --> pdb=" O   ARG G  47 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 52 through 54
      removed outlier: 6.547A  pdb=" N   VAL A  52 " --> pdb=" O   TRP C  53 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   VAL C  52 " --> pdb=" O   TRP E  53 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   VAL E  52 " --> pdb=" O   TRP G  53 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   VAL I  52 " --> pdb=" O   TRP K  53 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 6 through 9
    Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 23
      removed outlier: 6.809A  pdb=" N   ARG B  19 " --> pdb=" O   ALA D  20 " (cutoff:3.500A)
      removed outlier: 8.213A  pdb=" N   SER D  22 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   TYR B  21 " --> pdb=" O   SER D  22 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   ARG D  19 " --> pdb=" O   ALA F  20 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   SER F  22 " --> pdb=" O   ARG D  19 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   TYR D  21 " --> pdb=" O   SER F  22 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ARG H  19 " --> pdb=" O   ALA J  20 " (cutoff:3.500A)
      removed outlier: 8.213A  pdb=" N   SER J  22 " --> pdb=" O   ARG H  19 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   TYR H  21 " --> pdb=" O   SER J  22 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ARG J  19 " --> pdb=" O   ALA L  20 " (cutoff:3.500A)
      removed outlier: 8.183A  pdb=" N   SER L  22 " --> pdb=" O   ARG J  19 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   TYR J  21 " --> pdb=" O   SER L  22 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 29 through 30
      removed outlier: 6.468A  pdb=" N   TYR B  29 " --> pdb=" O   ILE D  30 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   TYR D  29 " --> pdb=" O   ILE F  30 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   TYR F  29 " --> pdb=" O   ILE H  30 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   TYR H  29 " --> pdb=" O   ILE J  30 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   TYR J  29 " --> pdb=" O   ILE L  30 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 39
      removed outlier: 6.876A  pdb=" N   ALA B  38 " --> pdb=" O   ARG D  39 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ALA D  38 " --> pdb=" O   ARG F  39 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ALA F  38 " --> pdb=" O   ARG H  39 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   ALA H  38 " --> pdb=" O   ARG J  39 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   ALA J  38 " --> pdb=" O   ARG L  39 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 42 through 43
    Processing sheet with id=AB4, first strand: chain 'B' and resid 46 through 47
    Processing sheet with id=AB5, first strand: chain 'B' and resid 52 through 54
      removed outlier: 6.639A  pdb=" N   VAL B  52 " --> pdb=" O   TRP D  53 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   VAL D  52 " --> pdb=" O   TRP F  53 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL F  52 " --> pdb=" O   TRP H  53 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL H  52 " --> pdb=" O   TRP J  53 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   VAL J  52 " --> pdb=" O   TRP L  53 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5

    65 hydrogen bonds defined for protein.
    195 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.33

  Time building geometry restraints manager: 1.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1611
        1.34 -     1.45: 1173
        1.45 -     1.57: 2508
        1.57 -     1.68: 0
        1.68 -     1.80: 48
  Bond restraints: 5340
  Sorted by residual:
  bond pdb=" CA  ALA G  14 "
       pdb=" CB  ALA G  14 "
    ideal  model  delta    sigma   weight residual
    1.534  1.517  0.017 1.45e-02 4.76e+03 1.37e+00
  bond pdb=" CA  ALA F  14 "
       pdb=" CB  ALA F  14 "
    ideal  model  delta    sigma   weight residual
    1.534  1.517  0.017 1.45e-02 4.76e+03 1.36e+00
  bond pdb=" CA  ALA L  14 "
       pdb=" CB  ALA L  14 "
    ideal  model  delta    sigma   weight residual
    1.534  1.518  0.017 1.45e-02 4.76e+03 1.33e+00
  bond pdb=" CA  ALA D  14 "
       pdb=" CB  ALA D  14 "
    ideal  model  delta    sigma   weight residual
    1.534  1.518  0.017 1.45e-02 4.76e+03 1.31e+00
  bond pdb=" CA  ALA C  14 "
       pdb=" CB  ALA C  14 "
    ideal  model  delta    sigma   weight residual
    1.534  1.518  0.017 1.45e-02 4.76e+03 1.31e+00
  ... (remaining 5335 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 6400
        1.25 -     2.51: 590
        2.51 -     3.76: 137
        3.76 -     5.02: 25
        5.02 -     6.27: 12
  Bond angle restraints: 7164
  Sorted by residual:
  angle pdb=" CA  TYR F  21 "
        pdb=" CB  TYR F  21 "
        pdb=" CG  TYR F  21 "
      ideal   model   delta    sigma   weight residual
     113.90  118.11   -4.21 1.80e+00 3.09e-01 5.46e+00
  angle pdb=" CA  TYR J  21 "
        pdb=" CB  TYR J  21 "
        pdb=" CG  TYR J  21 "
      ideal   model   delta    sigma   weight residual
     113.90  118.07   -4.17 1.80e+00 3.09e-01 5.36e+00
  angle pdb=" CA  TYR I  21 "
        pdb=" CB  TYR I  21 "
        pdb=" CG  TYR I  21 "
      ideal   model   delta    sigma   weight residual
     113.90  118.05   -4.15 1.80e+00 3.09e-01 5.31e+00
  angle pdb=" CA  TYR G  21 "
        pdb=" CB  TYR G  21 "
        pdb=" CG  TYR G  21 "
      ideal   model   delta    sigma   weight residual
     113.90  118.05   -4.15 1.80e+00 3.09e-01 5.31e+00
  angle pdb=" CA  TYR H  21 "
        pdb=" CB  TYR H  21 "
        pdb=" CG  TYR H  21 "
      ideal   model   delta    sigma   weight residual
     113.90  118.04   -4.14 1.80e+00 3.09e-01 5.30e+00
  ... (remaining 7159 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     5.92: 2259
        5.92 -    11.84: 465
       11.84 -    17.76: 156
       17.76 -    23.68: 60
       23.68 -    29.60: 12
  Dihedral angle restraints: 2952
    sinusoidal: 1140
      harmonic: 1812
  Sorted by residual:
  dihedral pdb=" CA  ASP H  16 "
           pdb=" C   ASP H  16 "
           pdb=" N   MET H  17 "
           pdb=" CA  MET H  17 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.41  -21.59     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CA  ASP L  16 "
           pdb=" C   ASP L  16 "
           pdb=" N   MET L  17 "
           pdb=" CA  MET L  17 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.46  -21.54     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CA  ASP F  16 "
           pdb=" C   ASP F  16 "
           pdb=" N   MET F  17 "
           pdb=" CA  MET F  17 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.46  -21.54     0      5.00e+00 4.00e-02 1.86e+01
  ... (remaining 2949 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 181
       0.024 -    0.047: 171
       0.047 -    0.071: 142
       0.071 -    0.095: 74
       0.095 -    0.118: 32
  Chirality restraints: 600
  Sorted by residual:
  chirality pdb=" CA  ILE G  30 "
            pdb=" N   ILE G  30 "
            pdb=" C   ILE G  30 "
            pdb=" CB  ILE G  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.50e-01
  chirality pdb=" CA  ILE C  30 "
            pdb=" N   ILE C  30 "
            pdb=" C   ILE C  30 "
            pdb=" CB  ILE C  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.49e-01
  chirality pdb=" CA  ILE L  30 "
            pdb=" N   ILE L  30 "
            pdb=" C   ILE L  30 "
            pdb=" CB  ILE L  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.44e-01
  ... (remaining 597 not shown)

  Planarity restraints: 960
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E  29 "    0.016 2.00e-02 2.50e+03   1.56e-02 4.86e+00
        pdb=" CG  TYR E  29 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TYR E  29 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR E  29 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR E  29 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR E  29 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR E  29 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR E  29 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR G  29 "    0.016 2.00e-02 2.50e+03   1.56e-02 4.85e+00
        pdb=" CG  TYR G  29 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TYR G  29 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR G  29 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR G  29 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR G  29 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR G  29 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR G  29 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H  29 "   -0.015 2.00e-02 2.50e+03   1.56e-02 4.85e+00
        pdb=" CG  TYR H  29 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TYR H  29 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR H  29 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR H  29 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR H  29 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR H  29 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR H  29 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 957 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 1438
        2.82 -     3.34: 3763
        3.34 -     3.86: 9950
        3.86 -     4.38: 11608
        4.38 -     4.90: 20727
  Nonbonded interactions: 47486
  Sorted by model distance:
  nonbonded pdb=" N   SER A   2 "
            pdb=" O   GLY B  31 "
     model   vdw
     2.294 3.120
  nonbonded pdb=" O   GLY C  31 "
            pdb=" N   SER F   2 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" N   SER J   2 "
            pdb=" O   GLY G  31 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" N   SER C   2 "
            pdb=" O   GLY D  31 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" N   SER I   2 "
            pdb=" O   GLY J  31 "
     model   vdw
     2.316 3.120
  ... (remaining 47481 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'L'
}

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 individual isotropic
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:             1.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.820
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8678
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      :  0.006   0.030   5340  Z= 0.289
  Angle     :  0.852   6.273   7164  Z= 0.525
  Chirality :  0.052   0.118    600
  Planarity :  0.004   0.016    960
  Dihedral  :  7.677  29.598   1824
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 1.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -4.58 (0.18), residues: 624
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.48 (0.14), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP E  53 
 HIS   0.001   0.000   HIS B  37 
 PHE   0.019   0.004   PHE C  11 
 TYR   0.037   0.005   TYR E  29 
 ARG   0.003   0.000   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15671 (   65)
  hydrogen bonds       : angle       7.26243 (  195)
  covalent geometry    : bond        0.00600 ( 5340)
  covalent geometry    : angle       0.85178 ( 7164)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.596 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 2.1911
  time to fit residues: 285.8161
Evaluate side-chains
  114 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 47 optimal weight:    0.6980
   chunk 18 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A  41 ASN
B  41 ASN
D  37 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.089259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.074267 restraints weight = 6546.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 1.77
r_work: 0.2851 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2724 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8871
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.031   5340  Z= 0.255
  Angle     :  0.586   5.112   7164  Z= 0.334
  Chirality :  0.042   0.111    600
  Planarity :  0.004   0.032    960
  Dihedral  :  4.853  17.185    744
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  :  6.14 %
    Favored  : 92.32 %
  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: -4.09 (0.19), residues: 624
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.11 (0.15), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G  53 
 HIS   0.002   0.001   HIS J  37 
 PHE   0.014   0.002   PHE D   3 
 TYR   0.021   0.002   TYR C  29 
 ARG   0.007   0.001   ARG L  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03250 (   65)
  hydrogen bonds       : angle       4.78756 (  195)
  covalent geometry    : bond        0.00576 ( 5340)
  covalent geometry    : angle       0.58630 ( 7164)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 136
  time to evaluate  : 0.573 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.8724 (mtt180) cc_final: 0.8258 (mtm180)
REVERT: A   34 LYS cc_start: 0.8963 (mttt) cc_final: 0.8666 (mtmt)
REVERT: B   39 ARG cc_start: 0.8820 (ttt90) cc_final: 0.8466 (tmm-80)
REVERT: B   46 LYS cc_start: 0.8790 (mttt) cc_final: 0.8497 (mttp)
REVERT: C   12 ASP cc_start: 0.8866 (t70) cc_final: 0.8577 (t70)
REVERT: C   15 ARG cc_start: 0.8552 (mtt180) cc_final: 0.7176 (mpp-170)
REVERT: C   34 LYS cc_start: 0.8926 (mttt) cc_final: 0.8638 (mttp)
REVERT: C   39 ARG cc_start: 0.8712 (ttt180) cc_final: 0.8115 (ttp-170)
REVERT: E   12 ASP cc_start: 0.8816 (t70) cc_final: 0.8606 (t70)
REVERT: D   39 ARG cc_start: 0.8792 (ttm-80) cc_final: 0.8356 (ttp-170)
REVERT: F   39 ARG cc_start: 0.8709 (ttt90) cc_final: 0.7989 (ttp-170)
REVERT: F   46 LYS cc_start: 0.8264 (mttt) cc_final: 0.7916 (mttp)
REVERT: H   12 ASP cc_start: 0.8927 (t70) cc_final: 0.8641 (t70)
REVERT: H   15 ARG cc_start: 0.8491 (mtt180) cc_final: 0.7331 (mpp-170)
REVERT: I   34 LYS cc_start: 0.8814 (mttt) cc_final: 0.8558 (mtmt)
REVERT: J   34 LYS cc_start: 0.8822 (mttt) cc_final: 0.8584 (mttp)
REVERT: L   15 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.6436 (mpt180)
REVERT: G   26 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8915 (mt-10)
  outliers start: 7
  outliers final: 4
  residues processed: 141
  average time/residue: 1.8869
  time to fit residues: 273.2110
Evaluate side-chains
  133 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 128
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 SER
Chi-restraints excluded: chain F residue    2 SER
Chi-restraints excluded: chain K residue    2 SER
Chi-restraints excluded: chain L residue    2 SER
Chi-restraints excluded: chain L residue   15 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 7 optimal weight:    0.2980
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3305 r_free = 0.3305 target = 0.091239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.076046 restraints weight = 6494.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 1.78
r_work: 0.2898 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2774 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   5340  Z= 0.131
  Angle     :  0.472   3.759   7164  Z= 0.274
  Chirality :  0.040   0.112    600
  Planarity :  0.003   0.036    960
  Dihedral  :  4.321  16.125    744
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  :  8.99 %
    Favored  : 89.47 %
  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: -3.91 (0.20), residues: 624
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.98 (0.15), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP G  53 
 HIS   0.001   0.000   HIS I  37 
 PHE   0.009   0.001   PHE D   3 
 TYR   0.010   0.001   TYR F  29 
 ARG   0.008   0.001   ARG E  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02381 (   65)
  hydrogen bonds       : angle       4.53759 (  195)
  covalent geometry    : bond        0.00289 ( 5340)
  covalent geometry    : angle       0.47212 ( 7164)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 125
  time to evaluate  : 0.530 
Fit side-chains
REVERT: A    2 SER cc_start: 0.9061 (t) cc_final: 0.8760 (t)
REVERT: A   15 ARG cc_start: 0.8660 (mtt180) cc_final: 0.8245 (mtm180)
REVERT: A   34 LYS cc_start: 0.8964 (mttt) cc_final: 0.8668 (mtmt)
REVERT: B   39 ARG cc_start: 0.8800 (ttt90) cc_final: 0.8453 (tmm-80)
REVERT: C   12 ASP cc_start: 0.8894 (t70) cc_final: 0.8590 (t70)
REVERT: C   15 ARG cc_start: 0.8533 (mtt180) cc_final: 0.7148 (mpp-170)
REVERT: C   17 MET cc_start: 0.9322 (ttp) cc_final: 0.9087 (ttp)
REVERT: C   34 LYS cc_start: 0.8908 (mttt) cc_final: 0.8645 (mtmt)
REVERT: C   39 ARG cc_start: 0.8689 (ttt180) cc_final: 0.8104 (ttp-170)
REVERT: D   39 ARG cc_start: 0.8833 (ttm-80) cc_final: 0.8420 (ttp-170)
REVERT: F   39 ARG cc_start: 0.8708 (ttt90) cc_final: 0.7991 (ttp-170)
REVERT: H   12 ASP cc_start: 0.8825 (t70) cc_final: 0.8616 (t0)
REVERT: H   42 TYR cc_start: 0.8916 (t80) cc_final: 0.8609 (t80)
REVERT: G   26 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8859 (mt-10)
  outliers start: 7
  outliers final: 6
  residues processed: 130
  average time/residue: 1.8721
  time to fit residues: 250.3167
Evaluate side-chains
  128 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 122
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 SER
Chi-restraints excluded: chain E residue    2 SER
Chi-restraints excluded: chain F residue    2 SER
Chi-restraints excluded: chain J residue    2 SER
Chi-restraints excluded: chain K residue    2 SER
Chi-restraints excluded: chain L residue    2 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.0970
   chunk 6 optimal weight:    2.9990
   chunk 44 optimal weight:    0.2980
   chunk 58 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    1.4182

-------------------------------------------------------------------------------
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 = 0.3267 r_free = 0.3267 target = 0.088687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.073479 restraints weight = 6631.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 1.78
r_work: 0.2846 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8876
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025   5340  Z= 0.243
  Angle     :  0.522   4.629   7164  Z= 0.305
  Chirality :  0.041   0.111    600
  Planarity :  0.004   0.037    960
  Dihedral  :  4.590  17.227    744
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  :  9.87 %
    Favored  : 87.72 %
  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: -3.79 (0.20), residues: 624
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.16), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G  53 
 HIS   0.001   0.000   HIS J  37 
 PHE   0.012   0.002   PHE D   3 
 TYR   0.013   0.002   TYR C  42 
 ARG   0.008   0.001   ARG E  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02645 (   65)
  hydrogen bonds       : angle       4.51156 (  195)
  covalent geometry    : bond        0.00550 ( 5340)
  covalent geometry    : angle       0.52150 ( 7164)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 0.760 
Fit side-chains
REVERT: A    2 SER cc_start: 0.9015 (t) cc_final: 0.8735 (t)
REVERT: A   15 ARG cc_start: 0.8705 (mtt180) cc_final: 0.8283 (mtm180)
REVERT: A   34 LYS cc_start: 0.8981 (mttt) cc_final: 0.8677 (mtmt)
REVERT: B   39 ARG cc_start: 0.8824 (ttt90) cc_final: 0.8489 (tmm-80)
REVERT: C   12 ASP cc_start: 0.8896 (t70) cc_final: 0.8626 (t70)
REVERT: C   15 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8171 (mtm180)
REVERT: C   34 LYS cc_start: 0.8961 (mttt) cc_final: 0.8703 (mttt)
REVERT: C   39 ARG cc_start: 0.8722 (ttt180) cc_final: 0.8104 (ttp-170)
REVERT: D   39 ARG cc_start: 0.8832 (ttm-80) cc_final: 0.8419 (ttp-170)
REVERT: F   39 ARG cc_start: 0.8679 (ttt90) cc_final: 0.7964 (ttp-170)
REVERT: F   46 LYS cc_start: 0.8219 (mttt) cc_final: 0.7837 (mttp)
REVERT: H   12 ASP cc_start: 0.8913 (t70) cc_final: 0.8609 (t70)
REVERT: H   15 ARG cc_start: 0.8439 (mtt180) cc_final: 0.7283 (mpp-170)
REVERT: H   42 TYR cc_start: 0.8910 (t80) cc_final: 0.8632 (t80)
REVERT: L   15 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6653 (mpt180)
REVERT: G   26 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8865 (mt-10)
  outliers start: 11
  outliers final: 6
  residues processed: 138
  average time/residue: 2.1748
  time to fit residues: 308.9982
Evaluate side-chains
  135 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 128
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 SER
Chi-restraints excluded: chain E residue    2 SER
Chi-restraints excluded: chain F residue    2 SER
Chi-restraints excluded: chain J residue    2 SER
Chi-restraints excluded: chain K residue    2 SER
Chi-restraints excluded: chain L residue    2 SER
Chi-restraints excluded: chain L residue   15 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 9 optimal weight:    0.3980
   chunk 26 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 27 optimal weight:    0.4980
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   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 = 0.3274 r_free = 0.3274 target = 0.089054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.073759 restraints weight = 6534.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 1.78
r_work: 0.2854 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2730 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8868
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   5340  Z= 0.203
  Angle     :  0.490   4.673   7164  Z= 0.287
  Chirality :  0.040   0.112    600
  Planarity :  0.003   0.026    960
  Dihedral  :  4.503  16.770    744
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 11.40 %
    Favored  : 86.62 %
  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: -3.75 (0.21), residues: 624
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.85 (0.16), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  18 
 HIS   0.001   0.000   HIS J  37 
 PHE   0.011   0.002   PHE D   3 
 TYR   0.011   0.001   TYR E  42 
 ARG   0.006   0.000   ARG E  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02409 (   65)
  hydrogen bonds       : angle       4.45401 (  195)
  covalent geometry    : bond        0.00458 ( 5340)
  covalent geometry    : angle       0.48987 ( 7164)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 126
  time to evaluate  : 0.642 
Fit side-chains
REVERT: A    2 SER cc_start: 0.9074 (t) cc_final: 0.8756 (t)
REVERT: A   15 ARG cc_start: 0.8718 (mtt180) cc_final: 0.8290 (mtm180)
REVERT: A   34 LYS cc_start: 0.8967 (mttt) cc_final: 0.8702 (mttp)
REVERT: B   39 ARG cc_start: 0.8834 (ttt90) cc_final: 0.8512 (tmm-80)
REVERT: C   12 ASP cc_start: 0.8899 (t70) cc_final: 0.8624 (t70)
REVERT: C   15 ARG cc_start: 0.8540 (mtt180) cc_final: 0.7464 (mtm-85)
REVERT: C   34 LYS cc_start: 0.8953 (mttt) cc_final: 0.8708 (mttt)
REVERT: C   39 ARG cc_start: 0.8711 (ttt180) cc_final: 0.8115 (ttp-170)
REVERT: D   39 ARG cc_start: 0.8844 (ttm-80) cc_final: 0.8441 (ttp-170)
REVERT: F   39 ARG cc_start: 0.8677 (ttt90) cc_final: 0.7972 (ttp-170)
REVERT: F   46 LYS cc_start: 0.8249 (mttt) cc_final: 0.8013 (mttm)
REVERT: H   12 ASP cc_start: 0.8904 (t70) cc_final: 0.8595 (t70)
REVERT: H   15 ARG cc_start: 0.8436 (mtt180) cc_final: 0.7244 (mpp-170)
REVERT: H   42 TYR cc_start: 0.8932 (t80) cc_final: 0.8638 (t80)
REVERT: L   15 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6434 (mpt180)
REVERT: G   26 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8852 (mt-10)
  outliers start: 9
  outliers final: 6
  residues processed: 133
  average time/residue: 1.7156
  time to fit residues: 235.0562
Evaluate side-chains
  131 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 124
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 SER
Chi-restraints excluded: chain E residue    2 SER
Chi-restraints excluded: chain F residue    2 SER
Chi-restraints excluded: chain J residue    2 SER
Chi-restraints excluded: chain K residue    2 SER
Chi-restraints excluded: chain L residue    2 SER
Chi-restraints excluded: chain L residue   15 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 47 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 54 optimal weight:    0.4980
   chunk 23 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3311 r_free = 0.3311 target = 0.090762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.075527 restraints weight = 6444.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 1.76
r_work: 0.2901 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2775 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8842
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   5340  Z= 0.128
  Angle     :  0.441   3.881   7164  Z= 0.260
  Chirality :  0.040   0.113    600
  Planarity :  0.003   0.023    960
  Dihedral  :  4.243  15.643    744
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 11.40 %
    Favored  : 86.62 %
  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: -3.72 (0.21), residues: 624
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.83 (0.16), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  18 
 HIS   0.001   0.000   HIS I  37 
 PHE   0.008   0.001   PHE J  11 
 TYR   0.010   0.001   TYR I  42 
 ARG   0.005   0.000   ARG E  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02089 (   65)
  hydrogen bonds       : angle       4.35854 (  195)
  covalent geometry    : bond        0.00284 ( 5340)
  covalent geometry    : angle       0.44053 ( 7164)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 0.716 
Fit side-chains
REVERT: A    2 SER cc_start: 0.9016 (t) cc_final: 0.8719 (t)
REVERT: A   15 ARG cc_start: 0.8706 (mtt180) cc_final: 0.8311 (mtm180)
REVERT: A   34 LYS cc_start: 0.8965 (mttt) cc_final: 0.8711 (mttp)
REVERT: B   12 ASP cc_start: 0.8685 (t70) cc_final: 0.8470 (t70)
REVERT: B   39 ARG cc_start: 0.8765 (ttt90) cc_final: 0.8455 (tmm-80)
REVERT: C   12 ASP cc_start: 0.8853 (t70) cc_final: 0.8586 (t70)
REVERT: C   15 ARG cc_start: 0.8501 (mtt180) cc_final: 0.7420 (mtm-85)
REVERT: C   34 LYS cc_start: 0.8952 (mttt) cc_final: 0.8718 (mttt)
REVERT: C   39 ARG cc_start: 0.8729 (ttt180) cc_final: 0.8149 (ttp-170)
REVERT: D   39 ARG cc_start: 0.8841 (ttm-80) cc_final: 0.8443 (ttp-170)
REVERT: D   46 LYS cc_start: 0.8501 (mttm) cc_final: 0.7763 (tttt)
REVERT: F   39 ARG cc_start: 0.8677 (ttt90) cc_final: 0.7972 (ttp-170)
REVERT: H   12 ASP cc_start: 0.8924 (t70) cc_final: 0.8651 (t0)
REVERT: H   42 TYR cc_start: 0.8920 (t80) cc_final: 0.8711 (t80)
REVERT: I   26 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8795 (mt-10)
REVERT: K   39 ARG cc_start: 0.8324 (ttp-170) cc_final: 0.7887 (ttp-110)
REVERT: L   15 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6264 (mpt180)
REVERT: G   26 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8833 (mt-10)
  outliers start: 9
  outliers final: 5
  residues processed: 129
  average time/residue: 1.9648
  time to fit residues: 260.8404
Evaluate side-chains
  127 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 121
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 SER
Chi-restraints excluded: chain F residue    2 SER
Chi-restraints excluded: chain K residue    2 SER
Chi-restraints excluded: chain L residue    2 SER
Chi-restraints excluded: chain L residue   15 ARG
Chi-restraints excluded: chain L residue   17 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 = 0.3269 r_free = 0.3269 target = 0.088614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.073398 restraints weight = 6519.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 1.77
r_work: 0.2845 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8876
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.027   5340  Z= 0.255
  Angle     :  0.520   5.361   7164  Z= 0.304
  Chirality :  0.041   0.111    600
  Planarity :  0.004   0.032    960
  Dihedral  :  4.572  16.322    744
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 12.50 %
    Favored  : 86.18 %
  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 (0.21), residues: 624
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.80 (0.16), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  18 
 HIS   0.001   0.001   HIS J  37 
 PHE   0.013   0.002   PHE D   3 
 TYR   0.011   0.001   TYR G  42 
 ARG   0.008   0.000   ARG B  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02524 (   65)
  hydrogen bonds       : angle       4.40692 (  195)
  covalent geometry    : bond        0.00576 ( 5340)
  covalent geometry    : angle       0.51960 ( 7164)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 127
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A    2 SER cc_start: 0.9090 (t) cc_final: 0.8778 (t)
REVERT: A   15 ARG cc_start: 0.8740 (mtt180) cc_final: 0.8230 (mtm-85)
REVERT: A   34 LYS cc_start: 0.8957 (mttt) cc_final: 0.8744 (mttp)
REVERT: B   39 ARG cc_start: 0.8832 (ttt90) cc_final: 0.8521 (tmm-80)
REVERT: C   12 ASP cc_start: 0.8886 (t70) cc_final: 0.8587 (t70)
REVERT: C   15 ARG cc_start: 0.8530 (mtt180) cc_final: 0.7446 (mtm-85)
REVERT: C   34 LYS cc_start: 0.8982 (mttt) cc_final: 0.8733 (mttp)
REVERT: C   39 ARG cc_start: 0.8703 (ttt180) cc_final: 0.8110 (ttp-170)
REVERT: D   39 ARG cc_start: 0.8868 (ttm-80) cc_final: 0.8471 (ttp-170)
REVERT: D   46 LYS cc_start: 0.8476 (mttm) cc_final: 0.7758 (tttt)
REVERT: F   39 ARG cc_start: 0.8698 (ttt90) cc_final: 0.7976 (ttp-170)
REVERT: F   46 LYS cc_start: 0.8320 (mttt) cc_final: 0.8080 (mttm)
REVERT: H   12 ASP cc_start: 0.8836 (t70) cc_final: 0.8525 (t70)
REVERT: H   15 ARG cc_start: 0.8428 (mtt180) cc_final: 0.7247 (mpp-170)
REVERT: H   42 TYR cc_start: 0.8891 (t80) cc_final: 0.8643 (t80)
REVERT: I   26 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8802 (mt-10)
REVERT: L   15 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.6523 (mpt180)
REVERT: G   26 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8857 (mt-10)
  outliers start: 6
  outliers final: 4
  residues processed: 132
  average time/residue: 1.6553
  time to fit residues: 224.9536
Evaluate side-chains
  131 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 126
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 SER
Chi-restraints excluded: chain F residue    2 SER
Chi-restraints excluded: chain K residue    2 SER
Chi-restraints excluded: chain L residue    2 SER
Chi-restraints excluded: chain L residue   15 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3306 r_free = 0.3306 target = 0.090314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.075290 restraints weight = 6418.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 1.74
r_work: 0.2895 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2771 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8846
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   5340  Z= 0.150
  Angle     :  0.459   4.352   7164  Z= 0.270
  Chirality :  0.040   0.112    600
  Planarity :  0.003   0.024    960
  Dihedral  :  4.338  15.862    744
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 12.28 %
    Favored  : 86.18 %
  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: -3.68 (0.21), residues: 624
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.80 (0.16), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  18 
 HIS   0.001   0.000   HIS D  37 
 PHE   0.010   0.001   PHE D   3 
 TYR   0.020   0.001   TYR C  42 
 ARG   0.006   0.000   ARG B  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02252 (   65)
  hydrogen bonds       : angle       4.32415 (  195)
  covalent geometry    : bond        0.00333 ( 5340)
  covalent geometry    : angle       0.45879 ( 7164)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 128
  time to evaluate  : 0.564 
Fit side-chains
REVERT: A    2 SER cc_start: 0.9043 (t) cc_final: 0.8729 (t)
REVERT: A   15 ARG cc_start: 0.8692 (mtt180) cc_final: 0.7684 (mtm-85)
REVERT: A   34 LYS cc_start: 0.8966 (mttt) cc_final: 0.8710 (mttp)
REVERT: B   12 ASP cc_start: 0.8675 (t70) cc_final: 0.8431 (t70)
REVERT: B   39 ARG cc_start: 0.8816 (ttt90) cc_final: 0.8519 (tmm-80)
REVERT: C   12 ASP cc_start: 0.8849 (t70) cc_final: 0.8588 (t70)
REVERT: C   17 MET cc_start: 0.9276 (ttp) cc_final: 0.9056 (ttp)
REVERT: C   34 LYS cc_start: 0.8957 (mttt) cc_final: 0.8717 (mttp)
REVERT: C   39 ARG cc_start: 0.8703 (ttt180) cc_final: 0.8140 (ttp-170)
REVERT: E   15 ARG cc_start: 0.8526 (mtt180) cc_final: 0.7229 (mpp-170)
REVERT: D   39 ARG cc_start: 0.8853 (ttm-80) cc_final: 0.8461 (ttp-170)
REVERT: D   46 LYS cc_start: 0.8474 (mttm) cc_final: 0.7760 (tttt)
REVERT: F   39 ARG cc_start: 0.8671 (ttt90) cc_final: 0.7976 (ttp-170)
REVERT: F   46 LYS cc_start: 0.8317 (mttt) cc_final: 0.8079 (ttmm)
REVERT: H   12 ASP cc_start: 0.8908 (t70) cc_final: 0.8626 (t0)
REVERT: I   26 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8814 (mt-10)
REVERT: G   26 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8836 (mt-10)
  outliers start: 7
  outliers final: 4
  residues processed: 133
  average time/residue: 1.5347
  time to fit residues: 210.4577
Evaluate side-chains
  130 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 SER
Chi-restraints excluded: chain F residue    2 SER
Chi-restraints excluded: chain K residue    2 SER
Chi-restraints excluded: chain L residue    2 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.3254 r_free = 0.3254 target = 0.087676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.072496 restraints weight = 6493.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 1.76
r_work: 0.2831 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2704 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8888
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.030   5340  Z= 0.319
  Angle     :  0.563   5.901   7164  Z= 0.328
  Chirality :  0.042   0.111    600
  Planarity :  0.004   0.033    960
  Dihedral  :  4.736  17.496    744
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 12.50 %
    Favored  : 86.40 %
  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: -3.67 (0.21), residues: 624
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.79 (0.16), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  18 
 HIS   0.002   0.001   HIS J  37 
 PHE   0.014   0.002   PHE D   3 
 TYR   0.032   0.002   TYR H  42 
 ARG   0.007   0.001   ARG I  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02922 (   65)
  hydrogen bonds       : angle       4.42902 (  195)
  covalent geometry    : bond        0.00722 ( 5340)
  covalent geometry    : angle       0.56276 ( 7164)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 128
  time to evaluate  : 0.522 
Fit side-chains
REVERT: A    2 SER cc_start: 0.9034 (t) cc_final: 0.8781 (t)
REVERT: A   15 ARG cc_start: 0.8752 (mtt180) cc_final: 0.8245 (mtm-85)
REVERT: A   34 LYS cc_start: 0.8951 (mttt) cc_final: 0.8738 (mttp)
REVERT: B   39 ARG cc_start: 0.8830 (ttt90) cc_final: 0.8506 (tmm-80)
REVERT: C   12 ASP cc_start: 0.8905 (t70) cc_final: 0.8610 (t70)
REVERT: C   15 ARG cc_start: 0.8523 (mtt180) cc_final: 0.7448 (mtm-85)
REVERT: C   17 MET cc_start: 0.9264 (ttp) cc_final: 0.9056 (ttp)
REVERT: C   34 LYS cc_start: 0.8969 (mttt) cc_final: 0.8724 (mttp)
REVERT: C   39 ARG cc_start: 0.8681 (ttt180) cc_final: 0.8113 (ttp-170)
REVERT: C   46 LYS cc_start: 0.8308 (ttmm) cc_final: 0.7387 (tmtm)
REVERT: D   39 ARG cc_start: 0.8844 (ttm-80) cc_final: 0.8503 (ttp-170)
REVERT: D   46 LYS cc_start: 0.8482 (mttm) cc_final: 0.7754 (tttt)
REVERT: F   39 ARG cc_start: 0.8697 (ttt90) cc_final: 0.7978 (ttp-170)
REVERT: F   46 LYS cc_start: 0.8379 (mttt) cc_final: 0.8135 (mttm)
REVERT: H   12 ASP cc_start: 0.8832 (t70) cc_final: 0.8523 (t70)
REVERT: H   15 ARG cc_start: 0.8437 (mtt180) cc_final: 0.7255 (mpp-170)
REVERT: I   26 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8787 (mt-10)
REVERT: G   26 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8861 (mt-10)
  outliers start: 5
  outliers final: 4
  residues processed: 132
  average time/residue: 1.6889
  time to fit residues: 229.4053
Evaluate side-chains
  131 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 127
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 SER
Chi-restraints excluded: chain F residue    2 SER
Chi-restraints excluded: chain K residue    2 SER
Chi-restraints excluded: chain L residue    2 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 = 0.3283 r_free = 0.3283 target = 0.089173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.074026 restraints weight = 6523.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 1.76
r_work: 0.2862 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2736 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8862
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   5340  Z= 0.196
  Angle     :  0.496   5.598   7164  Z= 0.290
  Chirality :  0.040   0.114    600
  Planarity :  0.004   0.027    960
  Dihedral  :  4.522  16.509    744
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 12.50 %
    Favored  : 86.40 %
  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: -3.67 (0.21), residues: 624
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.79 (0.16), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  18 
 HIS   0.001   0.000   HIS D  37 
 PHE   0.012   0.001   PHE D   3 
 TYR   0.028   0.002   TYR C  42 
 ARG   0.007   0.000   ARG I  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02694 (   65)
  hydrogen bonds       : angle       4.32528 (  195)
  covalent geometry    : bond        0.00442 ( 5340)
  covalent geometry    : angle       0.49632 ( 7164)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 129
  time to evaluate  : 0.572 
Fit side-chains
REVERT: A    2 SER cc_start: 0.9103 (t) cc_final: 0.8758 (t)
REVERT: A   15 ARG cc_start: 0.8724 (mtt180) cc_final: 0.8287 (mtm180)
REVERT: A   34 LYS cc_start: 0.8954 (mttt) cc_final: 0.8740 (mttp)
REVERT: B   12 ASP cc_start: 0.8707 (t70) cc_final: 0.8487 (t70)
REVERT: B   39 ARG cc_start: 0.8838 (ttt90) cc_final: 0.8537 (tmm-80)
REVERT: C   12 ASP cc_start: 0.8903 (t70) cc_final: 0.8614 (t70)
REVERT: C   15 ARG cc_start: 0.8542 (mtt180) cc_final: 0.7368 (mtm-85)
REVERT: C   17 MET cc_start: 0.9251 (ttp) cc_final: 0.9037 (ttp)
REVERT: C   34 LYS cc_start: 0.8964 (mttt) cc_final: 0.8722 (mttp)
REVERT: C   39 ARG cc_start: 0.8710 (ttt180) cc_final: 0.8115 (ttp-170)
REVERT: C   46 LYS cc_start: 0.8296 (ttmm) cc_final: 0.7360 (tmtm)
REVERT: E   15 ARG cc_start: 0.8532 (mtt180) cc_final: 0.7142 (mpp-170)
REVERT: D   39 ARG cc_start: 0.8873 (ttm-80) cc_final: 0.8482 (ttp-170)
REVERT: D   46 LYS cc_start: 0.8476 (mttm) cc_final: 0.7757 (tttt)
REVERT: F   39 ARG cc_start: 0.8704 (ttt90) cc_final: 0.7997 (ttp-170)
REVERT: F   46 LYS cc_start: 0.8356 (mttt) cc_final: 0.8120 (ttmm)
REVERT: H   12 ASP cc_start: 0.8922 (t70) cc_final: 0.8630 (t0)
REVERT: H   15 ARG cc_start: 0.8427 (mtt180) cc_final: 0.7282 (mpp-170)
REVERT: I   26 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8789 (mt-10)
REVERT: G   26 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8856 (mt-10)
  outliers start: 5
  outliers final: 4
  residues processed: 133
  average time/residue: 1.6237
  time to fit residues: 222.5091
Evaluate side-chains
  129 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 125
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 SER
Chi-restraints excluded: chain F residue    2 SER
Chi-restraints excluded: chain K residue    2 SER
Chi-restraints excluded: chain L residue    2 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 24 optimal weight:    0.1980
   chunk 36 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0050
   chunk 13 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.9798

-------------------------------------------------------------------------------
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 = 0.3287 r_free = 0.3287 target = 0.089409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.074288 restraints weight = 6569.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 1.77
r_work: 0.2870 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2746 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8853
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   5340  Z= 0.179
  Angle     :  0.489   5.476   7164  Z= 0.286
  Chirality :  0.040   0.113    600
  Planarity :  0.003   0.026    960
  Dihedral  :  4.493  16.595    744
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 13.38 %
    Favored  : 85.75 %
  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: -3.66 (0.21), residues: 624
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.79 (0.16), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  18 
 HIS   0.001   0.000   HIS I  37 
 PHE   0.011   0.001   PHE D   3 
 TYR   0.028   0.002   TYR F  42 
 ARG   0.007   0.000   ARG B  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02763 (   65)
  hydrogen bonds       : angle       4.24443 (  195)
  covalent geometry    : bond        0.00401 ( 5340)
  covalent geometry    : angle       0.48930 ( 7164)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5560.77 seconds
wall clock time: 98 minutes 47.99 seconds (5927.99 seconds total)