Starting phenix.real_space_refine
on Wed Mar 12 11:57:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xh7_38343/03_2025/8xh7_38343.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xh7_38343/03_2025/8xh7_38343.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xh7_38343/03_2025/8xh7_38343.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xh7_38343/03_2025/8xh7_38343.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xh7_38343/03_2025/8xh7_38343.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xh7_38343/03_2025/8xh7_38343.cif"
  }
  resolution = 3.52
  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=   0.001 sd=   0.006
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      42      5.16       5
     C    5610      2.51       5
     N    1134      2.21       5
     O    1116      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7902
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 1317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1317
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 1, 'TRANS': 159}
    Chain: "E"
      Number of atoms: 1317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1317
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 1, 'TRANS': 159}
    Chain: "F"
      Number of atoms: 1317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1317
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 1, 'TRANS': 159}
    Chain: "A"
      Number of atoms: 1317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1317
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 1, 'TRANS': 159}
    Chain: "B"
      Number of atoms: 1317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1317
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 1, 'TRANS': 159}
    Chain: "D"
      Number of atoms: 1317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1317
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 1, 'TRANS': 159}
  Time building chain proxies: 7.83, per 1000 atoms: 0.99
  Number of scatterers: 7902
  At special positions: 0
  Unit cell: (125.32, 109.2, 60.32, 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      42     16.00
     O    1116      8.00
     N    1134      7.00
     C    5610      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.16
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1800

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 0 sheets defined
      90.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'C' and resid 24 through 45
    Processing helix  chain 'C' and resid 51 through 72
      removed outlier: 3.932A  pdb=" N   LEU C  55 " --> pdb=" O   ALA C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 77
    Processing helix  chain 'C' and resid 78 through 99
      removed outlier: 4.659A  pdb=" N   ASN C  99 " --> pdb=" O   ILE C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 134
    Processing helix  chain 'C' and resid 136 through 160
    Processing helix  chain 'C' and resid 162 through 180
      removed outlier: 3.612A  pdb=" N   LEU C 168 " --> pdb=" O   TRP C 164 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE C 180 " --> pdb=" O   LEU C 176 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 25 through 44
      removed outlier: 3.826A  pdb=" N   MET E  44 " --> pdb=" O   LEU E  40 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 50 through 72
      removed outlier: 3.926A  pdb=" N   VAL E  54 " --> pdb=" O   GLY E  50 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 79 through 98
      removed outlier: 3.793A  pdb=" N   LEU E  83 " --> pdb=" O   PRO E  79 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 103 through 134
      removed outlier: 3.636A  pdb=" N   LEU E 107 " --> pdb=" O   GLN E 103 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 136 through 160
      removed outlier: 3.550A  pdb=" N   TYR E 159 " --> pdb=" O   ILE E 155 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 164 through 184
      removed outlier: 3.545A  pdb=" N   LEU E 168 " --> pdb=" O   TRP E 164 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   MET E 184 " --> pdb=" O   ILE E 180 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 44
      removed outlier: 3.757A  pdb=" N   MET F  44 " --> pdb=" O   LEU F  40 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 50 through 73
      removed outlier: 3.800A  pdb=" N   VAL F  54 " --> pdb=" O   GLY F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 74 through 77
      removed outlier: 3.898A  pdb=" N   LEU F  77 " --> pdb=" O   ARG F  74 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 74 through 77'
    Processing helix  chain 'F' and resid 78 through 100
      removed outlier: 3.535A  pdb=" N   GLY F  82 " --> pdb=" O   CYS F  78 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ASN F  99 " --> pdb=" O   ILE F  95 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU F 100 " --> pdb=" O   ALA F  96 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 102 through 134
    Processing helix  chain 'F' and resid 136 through 160
    Processing helix  chain 'F' and resid 162 through 180
    Processing helix  chain 'A' and resid 25 through 44
      removed outlier: 3.852A  pdb=" N   MET A  44 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 72
      removed outlier: 3.926A  pdb=" N   VAL A  54 " --> pdb=" O   GLY A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 98
      removed outlier: 3.774A  pdb=" N   LEU A  83 " --> pdb=" O   PRO A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 134
      removed outlier: 3.665A  pdb=" N   LEU A 107 " --> pdb=" O   GLN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 160
      removed outlier: 3.557A  pdb=" N   TYR A 159 " --> pdb=" O   ILE A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 184
      removed outlier: 3.552A  pdb=" N   LEU A 168 " --> pdb=" O   TRP A 164 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   MET A 184 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 44
      removed outlier: 3.502A  pdb=" N   MET B  44 " --> pdb=" O   LEU B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 73
      removed outlier: 3.808A  pdb=" N   VAL B  54 " --> pdb=" O   GLY B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 77
      removed outlier: 3.883A  pdb=" N   LEU B  77 " --> pdb=" O   ARG B  74 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 74 through 77'
    Processing helix  chain 'B' and resid 78 through 100
      removed outlier: 3.540A  pdb=" N   GLY B  82 " --> pdb=" O   CYS B  78 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   ASN B  99 " --> pdb=" O   ILE B  95 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LEU B 100 " --> pdb=" O   ALA B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 134
    Processing helix  chain 'B' and resid 136 through 160
    Processing helix  chain 'B' and resid 162 through 180
    Processing helix  chain 'D' and resid 25 through 45
    Processing helix  chain 'D' and resid 51 through 72
      removed outlier: 3.869A  pdb=" N   LEU D  55 " --> pdb=" O   ALA D  51 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 77
    Processing helix  chain 'D' and resid 78 through 99
      removed outlier: 4.645A  pdb=" N   ASN D  99 " --> pdb=" O   ILE D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 134
    Processing helix  chain 'D' and resid 136 through 160
    Processing helix  chain 'D' and resid 162 through 180
      removed outlier: 3.655A  pdb=" N   LEU D 168 " --> pdb=" O   TRP D 164 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE D 180 " --> pdb=" O   LEU D 176 " (cutoff:3.500A)

    683 hydrogen bonds defined for protein.
    2037 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.30

  Time building geometry restraints manager: 2.52 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1044
        1.29 -     1.43: 2259
        1.43 -     1.57: 4749
        1.57 -     1.70: 0
        1.70 -     1.84: 72
  Bond restraints: 8124
  Sorted by residual:
  bond pdb=" C   MET A  61 "
       pdb=" O   MET A  61 "
    ideal  model  delta    sigma   weight residual
    1.237  1.157  0.080 1.17e-02 7.31e+03 4.66e+01
  bond pdb=" N   ILE E  64 "
       pdb=" CA  ILE E  64 "
    ideal  model  delta    sigma   weight residual
    1.461  1.500 -0.039 1.17e-02 7.31e+03 1.10e+01
  bond pdb=" N   ILE A  64 "
       pdb=" CA  ILE A  64 "
    ideal  model  delta    sigma   weight residual
    1.461  1.500 -0.039 1.17e-02 7.31e+03 1.09e+01
  bond pdb=" N   LEU B 181 "
       pdb=" CA  LEU B 181 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.042 1.29e-02 6.01e+03 1.06e+01
  bond pdb=" N   ILE D  69 "
       pdb=" CA  ILE D  69 "
    ideal  model  delta    sigma   weight residual
    1.461  1.499 -0.038 1.19e-02 7.06e+03 1.04e+01
  ... (remaining 8119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 10134
        1.46 -     2.91: 754
        2.91 -     4.37: 170
        4.37 -     5.83: 53
        5.83 -     7.29: 13
  Bond angle restraints: 11124
  Sorted by residual:
  angle pdb=" CA  MET A  61 "
        pdb=" C   MET A  61 "
        pdb=" O   MET A  61 "
      ideal   model   delta    sigma   weight residual
     120.55  113.26    7.29 1.06e+00 8.90e-01 4.72e+01
  angle pdb=" CA  ILE C 180 "
        pdb=" C   ILE C 180 "
        pdb=" O   ILE C 180 "
      ideal   model   delta    sigma   weight residual
     122.13  116.43    5.70 1.11e+00 8.12e-01 2.64e+01
  angle pdb=" C   ALA F  59 "
        pdb=" N   LEU F  60 "
        pdb=" CA  LEU F  60 "
      ideal   model   delta    sigma   weight residual
     120.31  113.36    6.95 1.52e+00 4.33e-01 2.09e+01
  angle pdb=" O   LEU C  60 "
        pdb=" C   LEU C  60 "
        pdb=" N   MET C  61 "
      ideal   model   delta    sigma   weight residual
     122.12  126.81   -4.69 1.06e+00 8.90e-01 1.96e+01
  angle pdb=" N   MET A  61 "
        pdb=" CA  MET A  61 "
        pdb=" C   MET A  61 "
      ideal   model   delta    sigma   weight residual
     111.28  106.48    4.80 1.09e+00 8.42e-01 1.94e+01
  ... (remaining 11119 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.11: 3883
       16.11 -    32.22: 436
       32.22 -    48.33: 139
       48.33 -    64.44: 22
       64.44 -    80.55: 2
  Dihedral angle restraints: 4482
    sinusoidal: 1692
      harmonic: 2790
  Sorted by residual:
  dihedral pdb=" C   ILE A  71 "
           pdb=" N   ILE A  71 "
           pdb=" CA  ILE A  71 "
           pdb=" CB  ILE A  71 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.43    8.43     0      2.50e+00 1.60e-01 1.14e+01
  dihedral pdb=" CA  ASP B  75 "
           pdb=" CB  ASP B  75 "
           pdb=" CG  ASP B  75 "
           pdb=" OD1 ASP B  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.90   56.90     1      2.00e+01 2.50e-03 1.09e+01
  dihedral pdb=" CA  ASP F  75 "
           pdb=" CB  ASP F  75 "
           pdb=" CG  ASP F  75 "
           pdb=" OD1 ASP F  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.88   56.88     1      2.00e+01 2.50e-03 1.09e+01
  ... (remaining 4479 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1180
       0.067 -    0.134: 146
       0.134 -    0.201: 61
       0.201 -    0.268: 28
       0.268 -    0.335: 7
  Chirality restraints: 1422
  Sorted by residual:
  chirality pdb=" CA  ILE E  64 "
            pdb=" N   ILE E  64 "
            pdb=" C   ILE E  64 "
            pdb=" CB  ILE E  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.77   -0.34 2.00e-01 2.50e+01 2.81e+00
  chirality pdb=" CA  ILE A  64 "
            pdb=" N   ILE A  64 "
            pdb=" C   ILE A  64 "
            pdb=" CB  ILE A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.74   -0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CA  LEU B  88 "
            pdb=" N   LEU B  88 "
            pdb=" C   LEU B  88 "
            pdb=" CB  LEU B  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.98e+00
  ... (remaining 1419 not shown)

  Planarity restraints: 1206
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  47 "   -0.019 2.00e-02 2.50e+03   1.19e-02 3.53e+00
        pdb=" CG  TRP A  47 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  47 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  47 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  47 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E 153 "   -0.009 2.00e-02 2.50e+03   1.86e-02 3.47e+00
        pdb=" C   LEU E 153 "    0.032 2.00e-02 2.50e+03
        pdb=" O   LEU E 153 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LEU E 154 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  62 "   -0.008 2.00e-02 2.50e+03   1.74e-02 3.02e+00
        pdb=" C   LEU A  62 "    0.030 2.00e-02 2.50e+03
        pdb=" O   LEU A  62 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ILE A  63 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1203 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 2753
        2.88 -     3.39: 8491
        3.39 -     3.89: 13348
        3.89 -     4.40: 14230
        4.40 -     4.90: 23282
  Nonbonded interactions: 62104
  Sorted by model distance:
  nonbonded pdb=" O   TRP C  47 "
            pdb=" OG1 THR C  48 "
     model   vdw
     2.376 3.040
  nonbonded pdb=" O   TRP D  47 "
            pdb=" OG1 THR D  48 "
     model   vdw
     2.393 3.040
  nonbonded pdb=" NH1 ARG F  73 "
            pdb=" O   MET F 184 "
     model   vdw
     2.397 3.120
  nonbonded pdb=" O   LEU F 154 "
            pdb=" CD1 LEU F 158 "
     model   vdw
     2.414 3.460
  nonbonded pdb=" O   TRP F  47 "
            pdb=" OG1 THR F  48 "
     model   vdw
     2.460 3.040
  ... (remaining 62099 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 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  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:             9.960
  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:          0.450
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.930
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080   8124  Z= 0.345
  Angle     :  0.913   7.286  11124  Z= 0.631
  Chirality :  0.065   0.335   1422
  Planarity :  0.003   0.021   1206
  Dihedral  : 14.929  80.553   2682
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  4.59 %
    Favored  : 93.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.27), residues: 954
  helix:  2.03 (0.17), residues: 864
  sheet:  None (None), residues: 0
  loop : -2.55 (0.55), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A  47 
 HIS   0.000   0.000   HIS D 101 
 PHE   0.018   0.001   PHE D  58 
 TYR   0.010   0.001   TYR D  41 
 ARG   0.002   0.000   ARG B  73 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 197
  time to evaluate  : 0.804 
Fit side-chains
REVERT: C   40 LEU cc_start: 0.8526 (tp) cc_final: 0.8214 (tp)
REVERT: C   44 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7694 (mpp)
REVERT: F  140 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.7018 (mp)
REVERT: A  178 MET cc_start: 0.6683 (tpp) cc_final: 0.6433 (mmt)
REVERT: B  165 TRP cc_start: 0.7807 (t-100) cc_final: 0.7548 (t-100)
  outliers start: 18
  outliers final: 7
  residues processed: 206
  average time/residue: 0.1445
  time to fit residues: 43.5897
Evaluate side-chains
  165 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 156
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain E residue   42 ILE
Chi-restraints excluded: chain F residue  129 ILE
Chi-restraints excluded: chain F residue  140 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  158 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 75 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0470
   chunk 56 optimal weight:    0.9990
   chunk 87 optimal weight:    0.5980
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
F 101 HIS
B 101 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.209072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.180554 restraints weight = 8923.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.181936 restraints weight = 7167.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.183212 restraints weight = 6291.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.4274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8124  Z= 0.185
  Angle     :  0.578  10.803  11124  Z= 0.271
  Chirality :  0.035   0.161   1422
  Planarity :  0.003   0.023   1206
  Dihedral  :  5.104  47.970   1027
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.79 %
    Favored  : 81.16 %
  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:  3.22 (0.27), residues: 954
  helix:  2.52 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.91 (0.58), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F 164 
 HIS   0.007   0.002   HIS F 101 
 PHE   0.010   0.001   PHE D 112 
 TYR   0.010   0.001   TYR C  41 
 ARG   0.002   0.000   ARG B  73 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 158
  time to evaluate  : 0.972 
Fit side-chains
REVERT: C   44 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7673 (mtp)
REVERT: B  165 TRP cc_start: 0.7944 (t-100) cc_final: 0.7421 (t-100)
  outliers start: 17
  outliers final: 8
  residues processed: 170
  average time/residue: 0.1719
  time to fit residues: 44.1337
Evaluate side-chains
  156 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 147
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  144 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 48 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0980
   chunk 27 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
F 101 HIS
B 101 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4665 r_free = 0.4665 target = 0.217757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.180284 restraints weight = 9697.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.183513 restraints weight = 6621.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.185774 restraints weight = 5290.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.4354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8124  Z= 0.168
  Angle     :  0.549  11.104  11124  Z= 0.257
  Chirality :  0.034   0.171   1422
  Planarity :  0.002   0.023   1206
  Dihedral  :  4.508  52.541   1013
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 18.84 %
    Favored  : 78.50 %
  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:  3.45 (0.27), residues: 954
  helix:  2.67 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.83 (0.60), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 131 
 HIS   0.005   0.001   HIS F 101 
 PHE   0.009   0.001   PHE D 112 
 TYR   0.009   0.001   TYR D  41 
 ARG   0.001   0.000   ARG A 132 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 156
  time to evaluate  : 1.778 
Fit side-chains
REVERT: C  113 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8343 (mp)
REVERT: E  131 TRP cc_start: 0.8301 (t-100) cc_final: 0.8028 (t-100)
REVERT: F  155 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8493 (mt)
REVERT: B  155 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8579 (mt)
REVERT: D  113 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8326 (mp)
  outliers start: 22
  outliers final: 14
  residues processed: 167
  average time/residue: 0.2700
  time to fit residues: 70.7135
Evaluate side-chains
  169 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 1.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   89 MET
Chi-restraints excluded: chain C residue  113 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain F residue  148 PHE
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  164 TRP
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  144 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 93 optimal weight:    0.2980
   chunk 25 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 89 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4655 r_free = 0.4655 target = 0.216657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.178693 restraints weight = 9692.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.182202 restraints weight = 6595.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.184223 restraints weight = 5227.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.4331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8124  Z= 0.174
  Angle     :  0.547  10.595  11124  Z= 0.254
  Chirality :  0.034   0.170   1422
  Planarity :  0.002   0.023   1206
  Dihedral  :  4.566  56.578   1013
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 20.41 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.59 (0.27), residues: 954
  helix:  2.76 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.74 (0.62), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 131 
 HIS   0.001   0.000   HIS C 101 
 PHE   0.008   0.001   PHE E 112 
 TYR   0.009   0.001   TYR D  41 
 ARG   0.001   0.000   ARG F  73 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 157
  time to evaluate  : 0.877 
Fit side-chains
REVERT: C  113 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8309 (mp)
REVERT: E  131 TRP cc_start: 0.8289 (t-100) cc_final: 0.8034 (t-100)
REVERT: F  155 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8522 (mt)
REVERT: B  155 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8542 (mt)
REVERT: D  113 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8260 (mp)
  outliers start: 29
  outliers final: 19
  residues processed: 171
  average time/residue: 0.1521
  time to fit residues: 39.0138
Evaluate side-chains
  177 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 154
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   89 MET
Chi-restraints excluded: chain C residue  113 ILE
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain F residue  111 LEU
Chi-restraints excluded: chain F residue  148 PHE
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  164 TRP
Chi-restraints excluded: chain F residue  181 LEU
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  144 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0370
   chunk 1 optimal weight:    0.9980
   chunk 85 optimal weight:   10.0000
   chunk 13 optimal weight:    0.0980
   chunk 15 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
F 101 HIS
B 101 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.217308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.179412 restraints weight = 9646.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.182658 restraints weight = 6622.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.184956 restraints weight = 5289.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.4342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8124  Z= 0.164
  Angle     :  0.541  10.246  11124  Z= 0.254
  Chirality :  0.034   0.173   1422
  Planarity :  0.002   0.022   1206
  Dihedral  :  4.584  56.855   1013
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 21.74 %
    Favored  : 74.40 %
  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:  3.64 (0.27), residues: 954
  helix:  2.78 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.63 (0.65), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  39 
 HIS   0.005   0.001   HIS F 101 
 PHE   0.008   0.001   PHE D  58 
 TYR   0.016   0.001   TYR E 125 
 ARG   0.002   0.000   ARG F  73 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 156
  time to evaluate  : 0.832 
Fit side-chains
REVERT: C  113 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8299 (mp)
REVERT: E  131 TRP cc_start: 0.8290 (t-100) cc_final: 0.8076 (t-100)
REVERT: F  155 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8521 (mt)
REVERT: B  113 ILE cc_start: 0.8178 (tp) cc_final: 0.7706 (pt)
REVERT: B  155 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8549 (mt)
REVERT: D   44 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7323 (mpp)
REVERT: D  113 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8253 (mp)
  outliers start: 32
  outliers final: 18
  residues processed: 172
  average time/residue: 0.1467
  time to fit residues: 37.3661
Evaluate side-chains
  172 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 149
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   89 MET
Chi-restraints excluded: chain C residue  113 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain F residue  148 PHE
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  164 TRP
Chi-restraints excluded: chain F residue  181 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  144 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   chunk 82 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.4618 r_free = 0.4618 target = 0.213560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.175747 restraints weight = 9748.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.179202 restraints weight = 6552.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.181354 restraints weight = 5186.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.4306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8124  Z= 0.214
  Angle     :  0.594   9.743  11124  Z= 0.273
  Chirality :  0.034   0.170   1422
  Planarity :  0.002   0.023   1206
  Dihedral  :  4.611  54.770   1013
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 22.58 %
    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 (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:  3.55 (0.27), residues: 954
  helix:  2.72 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.57 (0.67), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  39 
 HIS   0.001   0.000   HIS D 101 
 PHE   0.011   0.001   PHE E 112 
 TYR   0.019   0.001   TYR E 125 
 ARG   0.002   0.000   ARG F  73 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 157
  time to evaluate  : 0.800 
Fit side-chains
REVERT: C  113 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8320 (mp)
REVERT: F  113 ILE cc_start: 0.8168 (tp) cc_final: 0.7671 (pt)
REVERT: F  155 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8565 (mt)
REVERT: B  113 ILE cc_start: 0.8165 (tp) cc_final: 0.7694 (pt)
REVERT: B  155 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8584 (mt)
REVERT: D   44 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.7304 (mpp)
REVERT: D  113 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8329 (mp)
  outliers start: 35
  outliers final: 25
  residues processed: 174
  average time/residue: 0.1592
  time to fit residues: 41.1284
Evaluate side-chains
  183 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 153
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   89 MET
Chi-restraints excluded: chain C residue  113 ILE
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain F residue  111 LEU
Chi-restraints excluded: chain F residue  148 PHE
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  164 TRP
Chi-restraints excluded: chain F residue  181 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   98 TRP
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  143 PHE
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  129 ILE
Chi-restraints excluded: chain D residue  144 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 73 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   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 = 0.4635 r_free = 0.4635 target = 0.214452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.176148 restraints weight = 9659.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.179583 restraints weight = 6596.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.181648 restraints weight = 5239.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.4287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8124  Z= 0.196
  Angle     :  0.578   9.848  11124  Z= 0.269
  Chirality :  0.035   0.181   1422
  Planarity :  0.002   0.022   1206
  Dihedral  :  4.584  54.343   1013
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 23.19 %
    Favored  : 72.58 %
  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:  3.50 (0.27), residues: 954
  helix:  2.68 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.49 (0.69), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D  39 
 HIS   0.001   0.000   HIS C 101 
 PHE   0.009   0.001   PHE E 112 
 TYR   0.017   0.001   TYR E 125 
 ARG   0.002   0.000   ARG F  73 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 158
  time to evaluate  : 1.725 
Fit side-chains
REVERT: C  113 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8284 (mp)
REVERT: F  113 ILE cc_start: 0.8142 (tp) cc_final: 0.7642 (pt)
REVERT: F  155 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8544 (mt)
REVERT: B  113 ILE cc_start: 0.8133 (tp) cc_final: 0.7671 (pt)
REVERT: B  155 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8573 (mt)
REVERT: D   44 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.7294 (mpp)
REVERT: D  113 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8312 (mp)
REVERT: D  158 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7401 (mm)
  outliers start: 35
  outliers final: 23
  residues processed: 176
  average time/residue: 0.1774
  time to fit residues: 47.0457
Evaluate side-chains
  186 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 157
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   89 MET
Chi-restraints excluded: chain C residue  113 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain F residue  111 LEU
Chi-restraints excluded: chain F residue  148 PHE
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  164 TRP
Chi-restraints excluded: chain F residue  181 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   98 TRP
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  143 PHE
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain D residue  158 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 69 optimal weight:    0.1980
   chunk 55 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 83 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 34 optimal weight:    0.4980
   chunk 77 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4645 r_free = 0.4645 target = 0.215810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.177686 restraints weight = 9696.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.181094 restraints weight = 6564.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.183046 restraints weight = 5237.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.4316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8124  Z= 0.178
  Angle     :  0.583   9.795  11124  Z= 0.270
  Chirality :  0.034   0.185   1422
  Planarity :  0.002   0.022   1206
  Dihedral  :  4.547  53.932   1013
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 23.55 %
    Favored  : 71.98 %
  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:  3.55 (0.27), residues: 954
  helix:  2.72 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.52 (0.69), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D  39 
 HIS   0.001   0.000   HIS C 101 
 PHE   0.008   0.001   PHE E 112 
 TYR   0.016   0.001   TYR E 125 
 ARG   0.002   0.000   ARG F  73 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 164
  time to evaluate  : 0.772 
Fit side-chains
REVERT: C  113 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8299 (mp)
REVERT: C  158 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7429 (mm)
REVERT: E  158 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7682 (mm)
REVERT: F  113 ILE cc_start: 0.8125 (tp) cc_final: 0.7638 (pt)
REVERT: F  155 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8552 (mt)
REVERT: B  113 ILE cc_start: 0.8112 (tp) cc_final: 0.7662 (pt)
REVERT: B  155 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8578 (mt)
REVERT: D   44 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7318 (mpp)
REVERT: D  113 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8296 (mp)
  outliers start: 37
  outliers final: 24
  residues processed: 181
  average time/residue: 0.1407
  time to fit residues: 37.8657
Evaluate side-chains
  189 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 158
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   89 MET
Chi-restraints excluded: chain C residue  113 ILE
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  158 LEU
Chi-restraints excluded: chain F residue  111 LEU
Chi-restraints excluded: chain F residue  148 PHE
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  164 TRP
Chi-restraints excluded: chain F residue  181 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   98 TRP
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain D residue   40 LEU
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  144 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 83 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0870
   chunk 73 optimal weight:    0.4980
   chunk 85 optimal weight:   20.0000
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.4649 r_free = 0.4649 target = 0.216515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.178603 restraints weight = 9866.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.182252 restraints weight = 6599.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.184337 restraints weight = 5180.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.4336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8124  Z= 0.179
  Angle     :  0.602  10.380  11124  Z= 0.276
  Chirality :  0.034   0.194   1422
  Planarity :  0.002   0.021   1206
  Dihedral  :  4.517  53.856   1013
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 24.15 %
    Favored  : 71.86 %
  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:  3.60 (0.27), residues: 954
  helix:  2.75 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.53 (0.69), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP E 131 
 HIS   0.001   0.000   HIS E 101 
 PHE   0.009   0.001   PHE D  58 
 TYR   0.018   0.001   TYR A 125 
 ARG   0.002   0.000   ARG F  73 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 160
  time to evaluate  : 0.798 
Fit side-chains
REVERT: C  113 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8265 (mp)
REVERT: C  158 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7391 (mm)
REVERT: E  178 MET cc_start: 0.7326 (tpp) cc_final: 0.6969 (mmt)
REVERT: F  113 ILE cc_start: 0.8080 (tp) cc_final: 0.7597 (pt)
REVERT: F  155 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8528 (mt)
REVERT: B  113 ILE cc_start: 0.8103 (tp) cc_final: 0.7657 (pt)
REVERT: B  155 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8555 (mt)
REVERT: D   44 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7308 (mpp)
REVERT: D  113 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8247 (mp)
REVERT: D  158 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7372 (mm)
  outliers start: 33
  outliers final: 23
  residues processed: 175
  average time/residue: 0.1454
  time to fit residues: 37.3992
Evaluate side-chains
  183 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 153
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   89 MET
Chi-restraints excluded: chain C residue  113 ILE
Chi-restraints excluded: chain C residue  144 ILE
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain F residue  111 LEU
Chi-restraints excluded: chain F residue  148 PHE
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  164 TRP
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   98 TRP
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  143 PHE
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain D residue   40 LEU
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain D residue  158 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    0.4980
   chunk 44 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 18 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9990
   chunk 80 optimal weight:    0.0670
   chunk 69 optimal weight:    0.2980
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.4918

-------------------------------------------------------------------------------
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 = 0.4664 r_free = 0.4664 target = 0.217563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.179981 restraints weight = 9719.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.183524 restraints weight = 6529.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.185689 restraints weight = 5160.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.4355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.2475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8124  Z= 0.171
  Angle     :  0.595  10.259  11124  Z= 0.270
  Chirality :  0.034   0.192   1422
  Planarity :  0.002   0.022   1206
  Dihedral  :  4.230  52.651   1011
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 25.12 %
    Favored  : 71.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.69 (0.27), residues: 954
  helix:  2.81 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.52 (0.68), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 131 
 HIS   0.001   0.000   HIS C 101 
 PHE   0.007   0.001   PHE D  58 
 TYR   0.018   0.001   TYR A 125 
 ARG   0.002   0.000   ARG F  73 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 159
  time to evaluate  : 0.799 
Fit side-chains
REVERT: C  113 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8223 (mp)
REVERT: C  158 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7409 (mm)
REVERT: F  113 ILE cc_start: 0.8069 (tp) cc_final: 0.7593 (pt)
REVERT: F  155 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8588 (mt)
REVERT: B  113 ILE cc_start: 0.8065 (tp) cc_final: 0.7633 (pt)
REVERT: B  155 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8548 (mt)
REVERT: D   44 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7461 (mpp)
REVERT: D  113 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8254 (mp)
REVERT: D  158 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7351 (mm)
  outliers start: 29
  outliers final: 20
  residues processed: 172
  average time/residue: 0.1411
  time to fit residues: 36.2608
Evaluate side-chains
  182 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   89 MET
Chi-restraints excluded: chain C residue  113 ILE
Chi-restraints excluded: chain C residue  144 ILE
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain F residue  148 PHE
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  164 TRP
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   98 TRP
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  143 PHE
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain D residue   40 LEU
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain D residue  158 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0870
   chunk 95 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 36 optimal weight:    0.2980
   overall best weight:    0.6160

-------------------------------------------------------------------------------
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 = 0.4654 r_free = 0.4654 target = 0.216523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.178078 restraints weight = 9791.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.181708 restraints weight = 6572.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.183780 restraints weight = 5145.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.4307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8124  Z= 0.181
  Angle     :  0.601  11.551  11124  Z= 0.272
  Chirality :  0.034   0.187   1422
  Planarity :  0.002   0.023   1206
  Dihedral  :  4.254  53.193   1011
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 24.64 %
    Favored  : 71.86 %
  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:  3.61 (0.27), residues: 954
  helix:  2.76 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.52 (0.69), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 131 
 HIS   0.001   0.000   HIS D 101 
 PHE   0.008   0.001   PHE E 112 
 TYR   0.018   0.001   TYR A 125 
 ARG   0.002   0.000   ARG F  73 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3560.07 seconds
wall clock time: 64 minutes 35.68 seconds (3875.68 seconds total)