Starting phenix.real_space_refine
on Tue Feb  3 13:17:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9raw_53880/02_2026/9raw_53880.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9raw_53880/02_2026/9raw_53880.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9raw_53880/02_2026/9raw_53880.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9raw_53880/02_2026/9raw_53880.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9raw_53880/02_2026/9raw_53880.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9raw_53880/02_2026/9raw_53880.cif"
  }
  resolution = 2.79
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.012
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      10      5.16       5
     C    1940      2.51       5
     N     530      2.21       5
     O     580      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3060
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 306
          Classifications: {'peptide': 40}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 39}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 0.51, per 1000 atoms: 0.17
  Number of scatterers: 3060
  At special positions: 0
  Unit cell: (102.9, 122.85, 39.9, 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      10     16.00
     O     580      8.00
     N     530      7.00
     C    1940      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.23
  Conformation dependent library (CDL) restraints added in 121.9 milliseconds
  

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  680

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 7 sheets defined
      0.0% alpha, 35.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13
    Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 22
      removed outlier: 6.311A  pdb=" N   LYS A  16 " --> pdb=" O   LEU C  17 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   PHE C  19 " --> pdb=" O   LYS A  16 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   VAL A  18 " --> pdb=" O   PHE C  19 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   ALA C  21 " --> pdb=" O   VAL A  18 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   PHE A  20 " --> pdb=" O   ALA C  21 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   LYS C  16 " --> pdb=" O   LEU E  17 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   PHE E  19 " --> pdb=" O   LYS C  16 " (cutoff:3.500A)
      removed outlier: 5.959A  pdb=" N   VAL C  18 " --> pdb=" O   PHE E  19 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   ALA E  21 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   PHE C  20 " --> pdb=" O   ALA E  21 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   LYS E  16 " --> pdb=" O   LEU G  17 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   PHE G  19 " --> pdb=" O   LYS E  16 " (cutoff:3.500A)
      removed outlier: 5.959A  pdb=" N   VAL E  18 " --> pdb=" O   PHE G  19 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   ALA G  21 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   PHE E  20 " --> pdb=" O   ALA G  21 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   LYS G  16 " --> pdb=" O   LEU I  17 " (cutoff:3.500A)
      removed outlier: 7.782A  pdb=" N   PHE I  19 " --> pdb=" O   LYS G  16 " (cutoff:3.500A)
      removed outlier: 5.963A  pdb=" N   VAL G  18 " --> pdb=" O   PHE I  19 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   ALA I  21 " --> pdb=" O   VAL G  18 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   PHE G  20 " --> pdb=" O   ALA I  21 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 36
      removed outlier: 6.609A  pdb=" N   LEU A  34 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   MET C  35 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   VAL A  36 " --> pdb=" O   MET C  35 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   LEU C  34 " --> pdb=" O   GLY E  33 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   MET E  35 " --> pdb=" O   LEU C  34 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   VAL C  36 " --> pdb=" O   MET E  35 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   LEU E  34 " --> pdb=" O   GLY G  33 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   MET G  35 " --> pdb=" O   LEU E  34 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   VAL E  36 " --> pdb=" O   MET G  35 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   LEU G  34 " --> pdb=" O   GLY I  33 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   MET I  35 " --> pdb=" O   LEU G  34 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   VAL G  36 " --> pdb=" O   MET I  35 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 13
    Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 22
      removed outlier: 6.308A  pdb=" N   LYS B  16 " --> pdb=" O   LEU D  17 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   PHE D  19 " --> pdb=" O   LYS B  16 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   VAL B  18 " --> pdb=" O   PHE D  19 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   ALA D  21 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   PHE B  20 " --> pdb=" O   ALA D  21 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   LYS D  16 " --> pdb=" O   LEU F  17 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   PHE F  19 " --> pdb=" O   LYS D  16 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   VAL D  18 " --> pdb=" O   PHE F  19 " (cutoff:3.500A)
      removed outlier: 7.803A  pdb=" N   ALA F  21 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   PHE D  20 " --> pdb=" O   ALA F  21 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   LYS F  16 " --> pdb=" O   LEU H  17 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   PHE H  19 " --> pdb=" O   LYS F  16 " (cutoff:3.500A)
      removed outlier: 5.958A  pdb=" N   VAL F  18 " --> pdb=" O   PHE H  19 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   ALA H  21 " --> pdb=" O   VAL F  18 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   PHE F  20 " --> pdb=" O   ALA H  21 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   LYS H  16 " --> pdb=" O   LEU J  17 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   PHE J  19 " --> pdb=" O   LYS H  16 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   VAL H  18 " --> pdb=" O   PHE J  19 " (cutoff:3.500A)
      removed outlier: 7.799A  pdb=" N   ALA J  21 " --> pdb=" O   VAL H  18 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   PHE H  20 " --> pdb=" O   ALA J  21 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 32
    Processing sheet with id=AA7, first strand: chain 'B' and resid 31 through 32
      removed outlier: 6.625A  pdb=" N   LEU D  34 " --> pdb=" O   GLY F  33 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   MET F  35 " --> pdb=" O   LEU D  34 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   VAL D  36 " --> pdb=" O   MET F  35 " (cutoff:3.500A)
      removed outlier: 8.695A  pdb=" N   ILE F  32 " --> pdb=" O   GLY H  33 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   MET H  35 " --> pdb=" O   ILE F  32 " (cutoff:3.500A)
      removed outlier: 8.789A  pdb=" N   LEU F  34 " --> pdb=" O   MET H  35 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   LEU H  34 " --> pdb=" O   GLY J  33 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   MET J  35 " --> pdb=" O   LEU H  34 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   VAL H  36 " --> pdb=" O   MET J  35 " (cutoff:3.500A)

    42 hydrogen bonds defined for protein.
    123 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.28

  Time building geometry restraints manager: 0.31 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 550
        1.31 -     1.43: 840
        1.43 -     1.55: 1690
        1.55 -     1.67: 20
        1.67 -     1.80: 20
  Bond restraints: 3120
  Sorted by residual:
  bond pdb=" C   ALA D  30 "
       pdb=" O   ALA D  30 "
    ideal  model  delta    sigma   weight residual
    1.235  1.190  0.045 1.20e-02 6.94e+03 1.40e+01
  bond pdb=" C   ALA H  30 "
       pdb=" O   ALA H  30 "
    ideal  model  delta    sigma   weight residual
    1.235  1.190  0.045 1.20e-02 6.94e+03 1.40e+01
  bond pdb=" C   ALA G  30 "
       pdb=" O   ALA G  30 "
    ideal  model  delta    sigma   weight residual
    1.235  1.190  0.045 1.20e-02 6.94e+03 1.39e+01
  bond pdb=" C   ALA F  30 "
       pdb=" O   ALA F  30 "
    ideal  model  delta    sigma   weight residual
    1.235  1.190  0.045 1.20e-02 6.94e+03 1.39e+01
  bond pdb=" C   ALA E  30 "
       pdb=" O   ALA E  30 "
    ideal  model  delta    sigma   weight residual
    1.235  1.190  0.045 1.20e-02 6.94e+03 1.38e+01
  ... (remaining 3115 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 3432
        2.50 -     5.00: 608
        5.00 -     7.51: 91
        7.51 -    10.01: 19
       10.01 -    12.51: 40
  Bond angle restraints: 4190
  Sorted by residual:
  angle pdb=" N   MET C  35 "
        pdb=" CA  MET C  35 "
        pdb=" C   MET C  35 "
      ideal   model   delta    sigma   weight residual
     108.90   97.32   11.58 1.63e+00 3.76e-01 5.05e+01
  angle pdb=" N   MET H  35 "
        pdb=" CA  MET H  35 "
        pdb=" C   MET H  35 "
      ideal   model   delta    sigma   weight residual
     108.90   97.33   11.57 1.63e+00 3.76e-01 5.04e+01
  angle pdb=" N   MET I  35 "
        pdb=" CA  MET I  35 "
        pdb=" C   MET I  35 "
      ideal   model   delta    sigma   weight residual
     108.90   97.35   11.55 1.63e+00 3.76e-01 5.02e+01
  angle pdb=" N   MET A  35 "
        pdb=" CA  MET A  35 "
        pdb=" C   MET A  35 "
      ideal   model   delta    sigma   weight residual
     108.90   97.35   11.55 1.63e+00 3.76e-01 5.02e+01
  angle pdb=" N   MET D  35 "
        pdb=" CA  MET D  35 "
        pdb=" C   MET D  35 "
      ideal   model   delta    sigma   weight residual
     108.90   97.36   11.54 1.63e+00 3.76e-01 5.01e+01
  ... (remaining 4185 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     7.98: 1320
        7.98 -    15.95: 260
       15.95 -    23.92: 80
       23.92 -    31.90: 30
       31.90 -    39.87: 60
  Dihedral angle restraints: 1750
    sinusoidal: 670
      harmonic: 1080
  Sorted by residual:
  dihedral pdb=" N   ASN H  27 "
           pdb=" C   ASN H  27 "
           pdb=" CA  ASN H  27 "
           pdb=" CB  ASN H  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  113.90    8.90     0      2.50e+00 1.60e-01 1.27e+01
  dihedral pdb=" N   ASN D  27 "
           pdb=" C   ASN D  27 "
           pdb=" CA  ASN D  27 "
           pdb=" CB  ASN D  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  113.90    8.90     0      2.50e+00 1.60e-01 1.27e+01
  dihedral pdb=" N   ASN G  27 "
           pdb=" C   ASN G  27 "
           pdb=" CA  ASN G  27 "
           pdb=" CB  ASN G  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  113.94    8.86     0      2.50e+00 1.60e-01 1.26e+01
  ... (remaining 1747 not shown)

  Histogram of chiral volume deviations from ideal:
       0.003 -    0.050: 130
       0.050 -    0.098: 158
       0.098 -    0.146: 82
       0.146 -    0.194: 50
       0.194 -    0.242: 20
  Chirality restraints: 440
  Sorted by residual:
  chirality pdb=" CA  ILE D  31 "
            pdb=" N   ILE D  31 "
            pdb=" C   ILE D  31 "
            pdb=" CB  ILE D  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  ILE G  31 "
            pdb=" N   ILE G  31 "
            pdb=" C   ILE G  31 "
            pdb=" CB  ILE G  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  ILE H  31 "
            pdb=" N   ILE H  31 "
            pdb=" C   ILE H  31 "
            pdb=" CB  ILE H  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 437 not shown)

  Planarity restraints: 560
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY H  25 "    0.010 2.00e-02 2.50e+03   2.05e-02 4.20e+00
        pdb=" C   GLY H  25 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   GLY H  25 "    0.013 2.00e-02 2.50e+03
        pdb=" N   SER H  26 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY E  25 "   -0.010 2.00e-02 2.50e+03   2.05e-02 4.20e+00
        pdb=" C   GLY E  25 "    0.035 2.00e-02 2.50e+03
        pdb=" O   GLY E  25 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER E  26 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  25 "   -0.010 2.00e-02 2.50e+03   2.04e-02 4.17e+00
        pdb=" C   GLY A  25 "    0.035 2.00e-02 2.50e+03
        pdb=" O   GLY A  25 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER A  26 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 557 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 1355
        2.91 -     3.41: 2558
        3.41 -     3.91: 5727
        3.91 -     4.40: 5933
        4.40 -     4.90: 11792
  Nonbonded interactions: 27365
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN I  27 "
            pdb=" O   GLY I  29 "
     model   vdw
     2.415 3.040
  nonbonded pdb=" OD1 ASN C  27 "
            pdb=" O   GLY C  29 "
     model   vdw
     2.415 3.040
  nonbonded pdb=" OD1 ASN H  27 "
            pdb=" O   GLY H  29 "
     model   vdw
     2.415 3.040
  nonbonded pdb=" OD1 ASN A  27 "
            pdb=" O   GLY A  29 "
     model   vdw
     2.415 3.040
  nonbonded pdb=" OD1 ASN G  27 "
            pdb=" O   GLY G  29 "
     model   vdw
     2.415 3.040
  ... (remaining 27360 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'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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:             0.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.810
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:6.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
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      :  0.016   0.048   3120  Z= 1.170
  Angle     :  2.284  12.511   4190  Z= 1.563
  Chirality :  0.102   0.242    440
  Planarity :  0.006   0.020    560
  Dihedral  : 13.279  39.871   1070
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.37), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.05 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H   5 
 TYR   0.006   0.002   TYR F  10 
 PHE   0.018   0.003   PHE D  20 
 HIS   0.004   0.002   HIS C  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.01559 ( 3120)
  covalent geometry    : angle       2.28372 ( 4190)
  hydrogen bonds       : bond        0.03380 (   40)
  hydrogen bonds       : angle       6.22200 (  123)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LEU cc_start: 0.9088 (mt) cc_final: 0.8782 (mt)
REVERT: D   23 ASP cc_start: 0.8517 (m-30) cc_final: 0.8201 (m-30)
REVERT: D   28 LYS cc_start: 0.8889 (mttt) cc_final: 0.8405 (mttp)
REVERT: E    5 ARG cc_start: 0.7527 (mtp180) cc_final: 0.7325 (mtp85)
REVERT: E   28 LYS cc_start: 0.8970 (mttt) cc_final: 0.8616 (mttp)
REVERT: F    5 ARG cc_start: 0.7451 (mtp180) cc_final: 0.6903 (ttt-90)
REVERT: F   15 GLN cc_start: 0.8792 (tt0) cc_final: 0.8550 (tt0)
REVERT: F   28 LYS cc_start: 0.8918 (mttt) cc_final: 0.8599 (mttp)
REVERT: H   35 MET cc_start: 0.8224 (mtp) cc_final: 0.8002 (mtp)
REVERT: I    5 ARG cc_start: 0.7457 (mtp180) cc_final: 0.6596 (mmp-170)
REVERT: I   28 LYS cc_start: 0.8899 (mttt) cc_final: 0.8690 (mttp)
REVERT: J    5 ARG cc_start: 0.7583 (mtp180) cc_final: 0.6613 (mmp-170)
REVERT: J   20 PHE cc_start: 0.8464 (t80) cc_final: 0.8242 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.6112
  time to fit residues: 85.5530
Evaluate side-chains
  109 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
D  27 ASN
E  15 GLN
I  15 GLN
J   6 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.141179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.112391 restraints weight = 3721.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3812 rms_B_bonded: 2.11
r_work: 0.3675 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3550 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.2936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3120  Z= 0.177
  Angle     :  0.589   9.881   4190  Z= 0.295
  Chirality :  0.051   0.130    440
  Planarity :  0.002   0.008    560
  Dihedral  :  6.546  22.107    420
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 19.03 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.11 (0.23), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C   5 
 TYR   0.004   0.001   TYR B  10 
 PHE   0.009   0.001   PHE C  20 
 HIS   0.003   0.001   HIS D   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 3120)
  covalent geometry    : angle       0.58917 ( 4190)
  hydrogen bonds       : bond        0.02520 (   40)
  hydrogen bonds       : angle       4.96967 (  123)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A   20 PHE cc_start: 0.8506 (t80) cc_final: 0.8240 (t80)
REVERT: D   28 LYS cc_start: 0.9196 (mttt) cc_final: 0.8890 (mttm)
REVERT: E   28 LYS cc_start: 0.9209 (mttt) cc_final: 0.8948 (mttp)
REVERT: F   28 LYS cc_start: 0.9267 (mttt) cc_final: 0.9051 (mttp)
REVERT: G   15 GLN cc_start: 0.9105 (tt0) cc_final: 0.8900 (tt0)
REVERT: G   35 MET cc_start: 0.8617 (mtp) cc_final: 0.8336 (mtp)
REVERT: I   28 LYS cc_start: 0.9245 (mttt) cc_final: 0.8975 (mttp)
REVERT: J   28 LYS cc_start: 0.9157 (mttm) cc_final: 0.8920 (mttt)
  outliers start: 11
  outliers final: 4
  residues processed: 89
  average time/residue: 0.4994
  time to fit residues: 45.6570
Evaluate side-chains
  79 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain H residue   34 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 22 optimal weight:   10.0000
   chunk 32 optimal weight:   20.0000
   chunk 34 optimal weight:    0.0970
   chunk 4 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 2 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0770
   chunk 8 optimal weight:   10.0000
   chunk 26 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   overall best weight:    4.4342

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
B   6 HIS
F  15 GLN
I  15 GLN
J  15 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.130132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.102592 restraints weight = 3879.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 2.11
r_work: 0.3509 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.3468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   3120  Z= 0.327
  Angle     :  0.649  11.264   4190  Z= 0.320
  Chirality :  0.051   0.145    440
  Planarity :  0.002   0.006    560
  Dihedral  :  6.569  24.344    420
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  6.45 %
    Allowed  : 18.39 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.08 (0.30), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.58 (0.23), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I   5 
 TYR   0.009   0.002   TYR E  10 
 PHE   0.013   0.001   PHE B  20 
 HIS   0.003   0.001   HIS G  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00717 ( 3120)
  covalent geometry    : angle       0.64892 ( 4190)
  hydrogen bonds       : bond        0.03729 (   40)
  hydrogen bonds       : angle       4.75430 (  123)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A   20 PHE cc_start: 0.8553 (t80) cc_final: 0.8194 (t80)
REVERT: C   22 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8414 (tt0)
REVERT: D   28 LYS cc_start: 0.9184 (mttt) cc_final: 0.8960 (mttm)
REVERT: E   23 ASP cc_start: 0.9089 (m-30) cc_final: 0.8803 (m-30)
REVERT: E   28 LYS cc_start: 0.9224 (mttt) cc_final: 0.9014 (mttp)
REVERT: G   15 GLN cc_start: 0.9083 (tt0) cc_final: 0.8842 (tt0)
  outliers start: 20
  outliers final: 3
  residues processed: 95
  average time/residue: 0.5408
  time to fit residues: 52.7172
Evaluate side-chains
  78 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 GLU
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain H residue   34 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 6 optimal weight:    6.9990
   chunk 8 optimal weight:   20.0000
   chunk 17 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   chunk 24 optimal weight:   20.0000
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.4191 r_free = 0.4191 target = 0.139480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.111868 restraints weight = 3754.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3830 rms_B_bonded: 2.10
r_work: 0.3690 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3567 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.3869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3120  Z= 0.109
  Angle     :  0.474   6.896   4190  Z= 0.241
  Chirality :  0.050   0.126    440
  Planarity :  0.002   0.015    560
  Dihedral  :  5.811  23.225    420
  Min Nonbonded Distance : 2.678

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 24.52 %
    Favored  : 73.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.28 (0.30), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.23), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H   5 
 TYR   0.013   0.001   TYR G  10 
 PHE   0.011   0.001   PHE F  20 
 HIS   0.002   0.000   HIS I   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 3120)
  covalent geometry    : angle       0.47444 ( 4190)
  hydrogen bonds       : bond        0.01708 (   40)
  hydrogen bonds       : angle       4.50874 (  123)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.076 
Fit side-chains
REVERT: A   20 PHE cc_start: 0.8460 (t80) cc_final: 0.8173 (t80)
REVERT: D   28 LYS cc_start: 0.9224 (mttt) cc_final: 0.8974 (mttp)
REVERT: E   28 LYS cc_start: 0.9237 (mttt) cc_final: 0.9035 (mttp)
REVERT: G   15 GLN cc_start: 0.9103 (tt0) cc_final: 0.8857 (tt0)
REVERT: G   32 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8967 (mt)
REVERT: H   32 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8982 (mt)
  outliers start: 6
  outliers final: 1
  residues processed: 78
  average time/residue: 0.4994
  time to fit residues: 39.9635
Evaluate side-chains
  70 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain H residue   32 ILE
Chi-restraints excluded: chain H residue   34 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 39 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 37 optimal weight:    7.9990
   chunk 32 optimal weight:   20.0000
   chunk 14 optimal weight:    9.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
I  15 GLN
** J  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.129852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.101454 restraints weight = 3697.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 2.12
r_work: 0.3496 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3368 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.051   3120  Z= 0.342
  Angle     :  0.593   8.961   4190  Z= 0.298
  Chirality :  0.050   0.140    440
  Planarity :  0.002   0.015    560
  Dihedral  :  6.136  26.812    420
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 22.90 %
    Favored  : 72.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.45 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.86 (0.23), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG G   5 
 TYR   0.011   0.002   TYR I  10 
 PHE   0.013   0.001   PHE B  20 
 HIS   0.003   0.001   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00757 ( 3120)
  covalent geometry    : angle       0.59323 ( 4190)
  hydrogen bonds       : bond        0.03379 (   40)
  hydrogen bonds       : angle       4.52338 (  123)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.073 
Fit side-chains
REVERT: A   20 PHE cc_start: 0.8418 (t80) cc_final: 0.8048 (t80)
REVERT: D   28 LYS cc_start: 0.9204 (mttt) cc_final: 0.8997 (mttp)
REVERT: E   23 ASP cc_start: 0.9127 (m-30) cc_final: 0.8870 (m-30)
REVERT: E   28 LYS cc_start: 0.9251 (mttt) cc_final: 0.9014 (mttm)
REVERT: E   34 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8795 (mt)
REVERT: F   28 LYS cc_start: 0.9283 (mttm) cc_final: 0.8996 (mttp)
REVERT: G   15 GLN cc_start: 0.9069 (tt0) cc_final: 0.8835 (tt0)
REVERT: H   32 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8935 (mt)
  outliers start: 13
  outliers final: 2
  residues processed: 85
  average time/residue: 0.5313
  time to fit residues: 46.2956
Evaluate side-chains
  77 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain E residue   34 LEU
Chi-restraints excluded: chain H residue   32 ILE
Chi-restraints excluded: chain H residue   34 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 20 optimal weight:   20.0000
   chunk 39 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
B  15 GLN
F  15 GLN
J  15 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.135186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.107628 restraints weight = 3761.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 2.08
r_work: 0.3615 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3492 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.3914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3120  Z= 0.129
  Angle     :  0.450   6.602   4190  Z= 0.235
  Chirality :  0.050   0.129    440
  Planarity :  0.001   0.013    560
  Dihedral  :  5.575  23.884    420
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 25.16 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.61 (0.30), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.23), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I   5 
 TYR   0.004   0.001   TYR D  10 
 PHE   0.006   0.001   PHE G  20 
 HIS   0.002   0.000   HIS D  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3120)
  covalent geometry    : angle       0.45006 ( 4190)
  hydrogen bonds       : bond        0.01977 (   40)
  hydrogen bonds       : angle       4.26703 (  123)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A   20 PHE cc_start: 0.8478 (t80) cc_final: 0.8148 (t80)
REVERT: D   28 LYS cc_start: 0.9155 (mttt) cc_final: 0.8951 (mttp)
REVERT: E   28 LYS cc_start: 0.9258 (mttt) cc_final: 0.9039 (mttp)
REVERT: F   28 LYS cc_start: 0.9300 (mttm) cc_final: 0.8991 (mttp)
REVERT: G   15 GLN cc_start: 0.9085 (tt0) cc_final: 0.8871 (tt0)
REVERT: H   32 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8964 (mt)
  outliers start: 5
  outliers final: 1
  residues processed: 76
  average time/residue: 0.4966
  time to fit residues: 38.6929
Evaluate side-chains
  71 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 69
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   32 ILE
Chi-restraints excluded: chain J residue   15 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 14 optimal weight:    7.9990
   chunk 10 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 22 optimal weight:    3.9990
   chunk 30 optimal weight:    9.9990
   chunk 25 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** J  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.129448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.101749 restraints weight = 3852.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 2.10
r_work: 0.3516 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.3898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   3120  Z= 0.292
  Angle     :  0.548   7.882   4190  Z= 0.277
  Chirality :  0.050   0.133    440
  Planarity :  0.002   0.014    560
  Dihedral  :  5.858  26.742    420
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 25.16 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG I   5 
 TYR   0.014   0.001   TYR G  10 
 PHE   0.015   0.001   PHE B  20 
 HIS   0.004   0.001   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00644 ( 3120)
  covalent geometry    : angle       0.54756 ( 4190)
  hydrogen bonds       : bond        0.03073 (   40)
  hydrogen bonds       : angle       4.42790 (  123)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.073 
Fit side-chains
REVERT: A   20 PHE cc_start: 0.8437 (t80) cc_final: 0.8074 (t80)
REVERT: E   28 LYS cc_start: 0.9257 (mttt) cc_final: 0.9055 (mttm)
REVERT: F   28 LYS cc_start: 0.9308 (mttm) cc_final: 0.9012 (mttp)
REVERT: G   15 GLN cc_start: 0.9054 (tt0) cc_final: 0.8748 (tt0)
REVERT: H   32 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8956 (mt)
REVERT: J   15 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8880 (tt0)
  outliers start: 7
  outliers final: 1
  residues processed: 83
  average time/residue: 0.5128
  time to fit residues: 43.5928
Evaluate side-chains
  76 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain H residue   32 ILE
Chi-restraints excluded: chain J residue   15 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:   20.0000
   chunk 16 optimal weight:   20.0000
   chunk 15 optimal weight:    5.9990
   chunk 20 optimal weight:    9.9990
   chunk 37 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 36 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
B  15 GLN
J  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.131980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.104612 restraints weight = 3806.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 2.08
r_work: 0.3577 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3455 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.4006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3120  Z= 0.178
  Angle     :  0.479   6.862   4190  Z= 0.246
  Chirality :  0.050   0.129    440
  Planarity :  0.001   0.011    560
  Dihedral  :  5.604  25.193    420
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 26.13 %
    Favored  : 72.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.71 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I   5 
 TYR   0.005   0.001   TYR I  10 
 PHE   0.012   0.001   PHE F  20 
 HIS   0.002   0.001   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 3120)
  covalent geometry    : angle       0.47875 ( 4190)
  hydrogen bonds       : bond        0.02341 (   40)
  hydrogen bonds       : angle       4.25163 (  123)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A   20 PHE cc_start: 0.8446 (t80) cc_final: 0.8088 (t80)
REVERT: E   28 LYS cc_start: 0.9259 (mttt) cc_final: 0.9058 (mttm)
REVERT: F   28 LYS cc_start: 0.9316 (mttm) cc_final: 0.9008 (mttp)
REVERT: G   15 GLN cc_start: 0.9066 (tt0) cc_final: 0.8763 (tt0)
REVERT: H   32 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8964 (mt)
  outliers start: 5
  outliers final: 1
  residues processed: 78
  average time/residue: 0.5426
  time to fit residues: 43.3350
Evaluate side-chains
  73 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain H residue   32 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 28 optimal weight:   20.0000
   chunk 21 optimal weight:    0.4980
   chunk 9 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 38 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 10 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    2.4786

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

Flipped N/Q/H residues before XYZ refinement:
I  15 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.131020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.103726 restraints weight = 3824.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 2.07
r_work: 0.3561 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3436 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.4115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3120  Z= 0.197
  Angle     :  0.497   9.780   4190  Z= 0.252
  Chirality :  0.050   0.144    440
  Planarity :  0.002   0.009    560
  Dihedral  :  5.640  27.000    420
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 27.74 %
    Favored  : 70.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.73 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I   5 
 TYR   0.015   0.002   TYR G  10 
 PHE   0.016   0.001   PHE B  20 
 HIS   0.002   0.001   HIS D  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 3120)
  covalent geometry    : angle       0.49691 ( 4190)
  hydrogen bonds       : bond        0.02521 (   40)
  hydrogen bonds       : angle       4.26290 (  123)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A   20 PHE cc_start: 0.8442 (t80) cc_final: 0.8059 (t80)
REVERT: E   28 LYS cc_start: 0.9246 (mttt) cc_final: 0.9037 (mttm)
REVERT: F   28 LYS cc_start: 0.9312 (mttm) cc_final: 0.9004 (mttp)
REVERT: G   15 GLN cc_start: 0.9060 (tt0) cc_final: 0.8859 (tt0)
REVERT: G   17 LEU cc_start: 0.9198 (mt) cc_final: 0.8980 (mt)
REVERT: H   32 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8952 (mt)
  outliers start: 5
  outliers final: 1
  residues processed: 77
  average time/residue: 0.4562
  time to fit residues: 36.0433
Evaluate side-chains
  71 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 69
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain H residue   32 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 2 optimal weight:    0.2980
   chunk 1 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.4195 r_free = 0.4195 target = 0.137264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.109410 restraints weight = 3688.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3799 rms_B_bonded: 2.13
r_work: 0.3645 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3518 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.4226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3120  Z= 0.107
  Angle     :  0.442   8.860   4190  Z= 0.230
  Chirality :  0.050   0.127    440
  Planarity :  0.001   0.007    560
  Dihedral  :  5.322  24.814    420
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 29.03 %
    Favored  : 70.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.72 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E   5 
 TYR   0.005   0.001   TYR D  10 
 PHE   0.007   0.001   PHE D   4 
 HIS   0.002   0.000   HIS G   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 3120)
  covalent geometry    : angle       0.44194 ( 4190)
  hydrogen bonds       : bond        0.01584 (   40)
  hydrogen bonds       : angle       4.10319 (  123)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A   20 PHE cc_start: 0.8499 (t80) cc_final: 0.8167 (t80)
REVERT: C   28 LYS cc_start: 0.9370 (mttm) cc_final: 0.9110 (mttp)
REVERT: E   28 LYS cc_start: 0.9204 (mttt) cc_final: 0.8978 (mttm)
REVERT: G   15 GLN cc_start: 0.9121 (tt0) cc_final: 0.8872 (tt0)
REVERT: H   32 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8979 (mt)
  outliers start: 2
  outliers final: 0
  residues processed: 72
  average time/residue: 0.4188
  time to fit residues: 30.9752
Evaluate side-chains
  69 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   32 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 39 optimal weight:    0.6980
   chunk 24 optimal weight:   20.0000
   chunk 19 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 13 optimal weight:   10.0000
   chunk 23 optimal weight:    0.7980
   overall best weight:    1.6784

-------------------------------------------------------------------------------
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 = 0.4168 r_free = 0.4168 target = 0.135606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.107323 restraints weight = 3689.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3768 rms_B_bonded: 2.13
r_work: 0.3605 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.4332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3120  Z= 0.147
  Angle     :  0.464   8.935   4190  Z= 0.237
  Chirality :  0.050   0.134    440
  Planarity :  0.001   0.008    560
  Dihedral  :  5.370  25.004    420
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 29.03 %
    Favored  : 70.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.72 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A   5 
 TYR   0.015   0.002   TYR G  10 
 PHE   0.017   0.001   PHE B  20 
 HIS   0.002   0.001   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3120)
  covalent geometry    : angle       0.46377 ( 4190)
  hydrogen bonds       : bond        0.02076 (   40)
  hydrogen bonds       : angle       4.09076 (  123)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1379.53 seconds
wall clock time: 24 minutes 11.06 seconds (1451.06 seconds total)