Starting phenix.real_space_refine
on Wed Feb  4 00:45:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n0b_48780/02_2026/9n0b_48780.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n0b_48780/02_2026/9n0b_48780.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n0b_48780/02_2026/9n0b_48780.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n0b_48780/02_2026/9n0b_48780.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n0b_48780/02_2026/9n0b_48780.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n0b_48780/02_2026/9n0b_48780.cif"
  }
  resolution = 4.1
  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
-------------------------------------------------------------------------------
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=   0.038 sd=   0.328
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       9      5.16       5
     C    5148      2.51       5
     N    1350      2.21       5
     O    1719      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  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: 8226
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 914
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 115}
    Chain: "B"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 914
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 115}
    Chain: "C"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 914
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 115}
    Chain: "D"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 914
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 115}
    Chain: "E"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 914
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 115}
    Chain: "F"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 914
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 115}
    Chain: "G"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 914
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 115}
    Chain: "H"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 914
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 115}
    Chain: "I"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 914
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 115}
  Time building chain proxies: 1.74, per 1000 atoms: 0.21
  Number of scatterers: 8226
  At special positions: 0
  Unit cell: (65.88, 64.8, 240.84, 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       9     16.00
     O    1719      8.00
     N    1350      7.00
     C    5148      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: 0.60
  Conformation dependent library (CDL) restraints added in 310.4 milliseconds
  

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2124

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 27 sheets defined
      1.9% alpha, 41.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 48
      No H-bonds generated for 'chain 'A' and resid 46 through 48'
    Processing helix  chain 'B' and resid 46 through 48
      No H-bonds generated for 'chain 'B' and resid 46 through 48'
    Processing helix  chain 'D' and resid 46 through 48
      No H-bonds generated for 'chain 'D' and resid 46 through 48'
    Processing helix  chain 'E' and resid 80 through 82
      No H-bonds generated for 'chain 'E' and resid 80 through 82'
    Processing helix  chain 'F' and resid 46 through 48
      No H-bonds generated for 'chain 'F' and resid 46 through 48'
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'I' and resid 46 through 48
      No H-bonds generated for 'chain 'I' and resid 46 through 48'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 19
      removed outlier: 3.890A  pdb=" N   SER A  11 " --> pdb=" O   ARG A 123 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 30
    Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 37
      removed outlier: 3.765A  pdb=" N   THR A  40 " --> pdb=" O   THR A  37 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 19
      removed outlier: 3.848A  pdb=" N   SER B  11 " --> pdb=" O   ARG B 123 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 22 through 30
    Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 37
      removed outlier: 3.756A  pdb=" N   THR B  40 " --> pdb=" O   THR B  37 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 19
      removed outlier: 3.960A  pdb=" N   SER C  11 " --> pdb=" O   ARG C 123 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 22 through 30
    Processing sheet with id=AA9, first strand: chain 'C' and resid 36 through 37
      removed outlier: 3.723A  pdb=" N   THR C  40 " --> pdb=" O   THR C  37 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 11 through 19
      removed outlier: 3.501A  pdb=" N   SER D  11 " --> pdb=" O   ARG D 123 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 22 through 30
    Processing sheet with id=AB3, first strand: chain 'D' and resid 36 through 37
      removed outlier: 3.739A  pdb=" N   THR D  40 " --> pdb=" O   THR D  37 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 11 through 19
      removed outlier: 4.016A  pdb=" N   SER E  11 " --> pdb=" O   ARG E 123 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 49 through 50
      removed outlier: 3.582A  pdb=" N   LEU E 107 " --> pdb=" O   TYR E  27 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 36 through 37
      removed outlier: 3.750A  pdb=" N   THR E  40 " --> pdb=" O   THR E  37 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 19
      removed outlier: 3.775A  pdb=" N   SER F  11 " --> pdb=" O   ARG F 123 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 22 through 30
    Processing sheet with id=AB9, first strand: chain 'F' and resid 36 through 37
      removed outlier: 3.752A  pdb=" N   THR F  40 " --> pdb=" O   THR F  37 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'G' and resid 11 through 19
      removed outlier: 3.642A  pdb=" N   SER G  11 " --> pdb=" O   ARG G 123 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'G' and resid 49 through 50
      removed outlier: 3.543A  pdb=" N   LEU G 107 " --> pdb=" O   TYR G  27 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'G' and resid 36 through 37
      removed outlier: 3.733A  pdb=" N   THR G  40 " --> pdb=" O   THR G  37 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'H' and resid 11 through 19
      removed outlier: 3.906A  pdb=" N   SER H  11 " --> pdb=" O   ARG H 123 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'H' and resid 22 through 30
      removed outlier: 3.539A  pdb=" N   ASN H 111 " --> pdb=" O   GLU H  23 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU H 107 " --> pdb=" O   TYR H  27 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'H' and resid 36 through 37
      removed outlier: 3.726A  pdb=" N   THR H  40 " --> pdb=" O   THR H  37 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'I' and resid 11 through 19
      removed outlier: 3.919A  pdb=" N   SER I  11 " --> pdb=" O   ARG I 123 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'I' and resid 22 through 30
    Processing sheet with id=AC9, first strand: chain 'I' and resid 36 through 37
      removed outlier: 3.706A  pdb=" N   THR I  40 " --> pdb=" O   THR I  37 " (cutoff:3.500A)

    288 hydrogen bonds defined for protein.
    804 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: 0.73

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2634
        1.34 -     1.45: 1153
        1.45 -     1.57: 4565
        1.57 -     1.68: 0
        1.68 -     1.80: 18
  Bond restraints: 8370
  Sorted by residual:
  bond pdb=" C   LEU I  31 "
       pdb=" N   ASN I  32 "
    ideal  model  delta    sigma   weight residual
    1.333  1.283  0.049 2.74e-02 1.33e+03 3.25e+00
  bond pdb=" C   LEU H  31 "
       pdb=" N   ASN H  32 "
    ideal  model  delta    sigma   weight residual
    1.333  1.289  0.043 2.74e-02 1.33e+03 2.50e+00
  bond pdb=" C   LEU E  31 "
       pdb=" N   ASN E  32 "
    ideal  model  delta    sigma   weight residual
    1.333  1.290  0.042 2.74e-02 1.33e+03 2.37e+00
  bond pdb=" C   LEU B  31 "
       pdb=" N   ASN B  32 "
    ideal  model  delta    sigma   weight residual
    1.333  1.292  0.041 2.74e-02 1.33e+03 2.20e+00
  bond pdb=" C   LEU F  31 "
       pdb=" N   ASN F  32 "
    ideal  model  delta    sigma   weight residual
    1.333  1.293  0.040 2.74e-02 1.33e+03 2.11e+00
  ... (remaining 8365 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 10803
        1.20 -     2.41: 577
        2.41 -     3.61: 100
        3.61 -     4.81: 22
        4.81 -     6.01: 9
  Bond angle restraints: 11511
  Sorted by residual:
  angle pdb=" CA  ASP B  66 "
        pdb=" CB  ASP B  66 "
        pdb=" CG  ASP B  66 "
      ideal   model   delta    sigma   weight residual
     112.60  115.25   -2.65 1.00e+00 1.00e+00 7.03e+00
  angle pdb=" CA  ASP A  66 "
        pdb=" CB  ASP A  66 "
        pdb=" CG  ASP A  66 "
      ideal   model   delta    sigma   weight residual
     112.60  115.11   -2.51 1.00e+00 1.00e+00 6.28e+00
  angle pdb=" CB  ASP A  66 "
        pdb=" CG  ASP A  66 "
        pdb=" OD1 ASP A  66 "
      ideal   model   delta    sigma   weight residual
     118.40  123.45   -5.05 2.30e+00 1.89e-01 4.82e+00
  angle pdb=" CB  ASP B  66 "
        pdb=" CG  ASP B  66 "
        pdb=" OD1 ASP B  66 "
      ideal   model   delta    sigma   weight residual
     118.40  123.22   -4.82 2.30e+00 1.89e-01 4.39e+00
  angle pdb=" C   GLN F  79 "
        pdb=" N   GLU F  80 "
        pdb=" CA  GLU F  80 "
      ideal   model   delta    sigma   weight residual
     122.07  125.62   -3.55 1.71e+00 3.42e-01 4.30e+00
  ... (remaining 11506 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.08: 4582
       14.08 -    28.17: 318
       28.17 -    42.25: 69
       42.25 -    56.34: 2
       56.34 -    70.42: 24
  Dihedral angle restraints: 4995
    sinusoidal: 1746
      harmonic: 3249
  Sorted by residual:
  dihedral pdb=" CA  PRO I  22 "
           pdb=" C   PRO I  22 "
           pdb=" N   GLU I  23 "
           pdb=" CA  GLU I  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.60   17.40     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CA  PRO A  22 "
           pdb=" C   PRO A  22 "
           pdb=" N   GLU A  23 "
           pdb=" CA  GLU A  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.48   16.52     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  PRO H  22 "
           pdb=" C   PRO H  22 "
           pdb=" N   GLU H  23 "
           pdb=" CA  GLU H  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.44   15.56     0      5.00e+00 4.00e-02 9.69e+00
  ... (remaining 4992 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 899
       0.028 -    0.056: 387
       0.056 -    0.084: 115
       0.084 -    0.112: 67
       0.112 -    0.139: 44
  Chirality restraints: 1512
  Sorted by residual:
  chirality pdb=" CA  VAL E  91 "
            pdb=" N   VAL E  91 "
            pdb=" C   VAL E  91 "
            pdb=" CB  VAL E  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.86e-01
  chirality pdb=" CA  VAL I  91 "
            pdb=" N   VAL I  91 "
            pdb=" C   VAL I  91 "
            pdb=" CB  VAL I  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.72e-01
  chirality pdb=" CA  VAL A  91 "
            pdb=" N   VAL A  91 "
            pdb=" C   VAL A  91 "
            pdb=" CB  VAL A  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.72e-01
  ... (remaining 1509 not shown)

  Planarity restraints: 1449
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A  66 "    0.012 2.00e-02 2.50e+03   2.47e-02 6.12e+00
        pdb=" CG  ASP A  66 "   -0.043 2.00e-02 2.50e+03
        pdb=" OD1 ASP A  66 "    0.016 2.00e-02 2.50e+03
        pdb=" OD2 ASP A  66 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A  66 "   -0.012 2.00e-02 2.50e+03   2.47e-02 6.10e+00
        pdb=" C   ASP A  66 "    0.043 2.00e-02 2.50e+03
        pdb=" O   ASP A  66 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ASN A  67 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B  66 "    0.012 2.00e-02 2.50e+03   2.44e-02 5.96e+00
        pdb=" C   ASP B  66 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   ASP B  66 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ASN B  67 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1446 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.66: 180
        2.66 -     3.22: 7837
        3.22 -     3.78: 11791
        3.78 -     4.34: 15845
        4.34 -     4.90: 26704
  Nonbonded interactions: 62357
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B  67 "
            pdb=" OG1 THR D  20 "
     model   vdw
     2.094 3.040
  nonbonded pdb=" OD1 ASN C  67 "
            pdb=" OG1 THR F  20 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" OD1 ASN E  67 "
            pdb=" OG1 THR H  20 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" OD1 ASN D  67 "
            pdb=" OG1 THR G  20 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" OD1 ASN A  67 "
            pdb=" OG1 THR E  20 "
     model   vdw
     2.181 3.040
  ... (remaining 62352 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: 0.00
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'
}

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:             2.140
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.880
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
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   0.052   8370  Z= 0.211
  Angle     :  0.649   6.014  11511  Z= 0.357
  Chirality :  0.041   0.139   1512
  Planarity :  0.005   0.043   1449
  Dihedral  : 11.932  70.422   2871
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  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:  1.50 (0.27), residues: 1080
  helix:  None (None), residues: 0
  sheet:  2.84 (0.24), residues: 441
  loop : -0.43 (0.26), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG H  92 
 TYR   0.016   0.002   TYR F  27 
 PHE   0.023   0.002   PHE C  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 8370)
  covalent geometry    : angle       0.64907 (11511)
  hydrogen bonds       : bond        0.28501 (  288)
  hydrogen bonds       : angle       9.63591 (  804)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: F   10 MET cc_start: 0.8939 (mtp) cc_final: 0.8346 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1235
  time to fit residues: 9.4403
Evaluate side-chains
  44 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    8.9990
   chunk 106 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
C  95 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2542 r_free = 0.2542 target = 0.029064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2399 r_free = 0.2399 target = 0.025921 restraints weight = 78343.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2430 r_free = 0.2430 target = 0.026659 restraints weight = 37371.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2452 r_free = 0.2452 target = 0.027155 restraints weight = 22052.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2468 r_free = 0.2468 target = 0.027507 restraints weight = 14537.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2480 r_free = 0.2480 target = 0.027772 restraints weight = 10484.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.2481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8750
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   8370  Z= 0.277
  Angle     :  0.678   9.441  11511  Z= 0.367
  Chirality :  0.046   0.157   1512
  Planarity :  0.005   0.038   1449
  Dihedral  :  5.021  19.093   1179
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  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:  1.46 (0.28), residues: 1080
  helix:  None (None), residues: 0
  sheet:  2.49 (0.25), residues: 450
  loop : -0.22 (0.27), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 123 
 TYR   0.014   0.002   TYR E  69 
 PHE   0.021   0.002   PHE C  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00610 ( 8370)
  covalent geometry    : angle       0.67827 (11511)
  hydrogen bonds       : bond        0.04777 (  288)
  hydrogen bonds       : angle       6.92804 (  804)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.314 
Fit side-chains
REVERT: B   23 GLU cc_start: 0.8148 (pm20) cc_final: 0.7931 (pm20)
REVERT: D   23 GLU cc_start: 0.8080 (pm20) cc_final: 0.7741 (pm20)
REVERT: F   10 MET cc_start: 0.8765 (mtp) cc_final: 0.8246 (mtp)
REVERT: I   23 GLU cc_start: 0.8219 (pm20) cc_final: 0.7805 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1316
  time to fit residues: 9.0974
Evaluate side-chains
  44 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 59 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 100 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 65 optimal weight:    8.9990
   chunk 28 optimal weight:    7.9990
   chunk 97 optimal weight:   10.0000
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
D  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2538 r_free = 0.2538 target = 0.029076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2399 r_free = 0.2399 target = 0.025935 restraints weight = 77550.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2429 r_free = 0.2429 target = 0.026676 restraints weight = 36706.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2450 r_free = 0.2450 target = 0.027179 restraints weight = 21449.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2467 r_free = 0.2467 target = 0.027541 restraints weight = 14140.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2477 r_free = 0.2477 target = 0.027793 restraints weight = 10148.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.2477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8756
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   8370  Z= 0.247
  Angle     :  0.638   9.495  11511  Z= 0.343
  Chirality :  0.044   0.164   1512
  Planarity :  0.005   0.033   1449
  Dihedral  :  5.032  19.451   1179
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  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:  1.29 (0.28), residues: 1080
  helix:  None (None), residues: 0
  sheet:  2.27 (0.25), residues: 450
  loop : -0.24 (0.27), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  36 
 TYR   0.012   0.002   TYR C  70 
 PHE   0.013   0.002   PHE D  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 ( 8370)
  covalent geometry    : angle       0.63769 (11511)
  hydrogen bonds       : bond        0.04059 (  288)
  hydrogen bonds       : angle       6.39907 (  804)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.333 
Fit side-chains
REVERT: D   23 GLU cc_start: 0.8214 (pm20) cc_final: 0.7817 (pm20)
REVERT: E   23 GLU cc_start: 0.7459 (mp0) cc_final: 0.7096 (mp0)
REVERT: F   10 MET cc_start: 0.8641 (mtp) cc_final: 0.7857 (mtp)
REVERT: I   23 GLU cc_start: 0.8305 (pm20) cc_final: 0.7930 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1439
  time to fit residues: 9.7820
Evaluate side-chains
  45 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 67 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 92 optimal weight:    7.9990
   chunk 77 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    3.5788

-------------------------------------------------------------------------------
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 = 0.2524 r_free = 0.2524 target = 0.028814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2387 r_free = 0.2387 target = 0.025736 restraints weight = 78771.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2418 r_free = 0.2418 target = 0.026474 restraints weight = 37002.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2439 r_free = 0.2439 target = 0.026965 restraints weight = 21372.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2454 r_free = 0.2454 target = 0.027309 restraints weight = 14006.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2464 r_free = 0.2464 target = 0.027516 restraints weight = 10043.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.2462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8769
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.075   8370  Z= 0.302
  Angle     :  0.679  10.601  11511  Z= 0.361
  Chirality :  0.045   0.167   1512
  Planarity :  0.005   0.030   1449
  Dihedral  :  5.190  20.101   1179
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.10 (0.28), residues: 1080
  helix:  None (None), residues: 0
  sheet:  2.05 (0.25), residues: 450
  loop : -0.29 (0.27), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG I  26 
 TYR   0.013   0.002   TYR A  70 
 PHE   0.014   0.002   PHE D  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00669 ( 8370)
  covalent geometry    : angle       0.67877 (11511)
  hydrogen bonds       : bond        0.03959 (  288)
  hydrogen bonds       : angle       6.12371 (  804)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.199 
Fit side-chains
REVERT: B   10 MET cc_start: 0.8952 (mtp) cc_final: 0.8590 (mtp)
REVERT: C   10 MET cc_start: 0.8535 (mtp) cc_final: 0.8260 (mtp)
REVERT: D   23 GLU cc_start: 0.8407 (pm20) cc_final: 0.8020 (pm20)
REVERT: F   10 MET cc_start: 0.8608 (mtp) cc_final: 0.7943 (mtp)
REVERT: I   23 GLU cc_start: 0.8353 (pm20) cc_final: 0.7940 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.1396
  time to fit residues: 8.5056
Evaluate side-chains
  42 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 88 optimal weight:    0.0020
   chunk 91 optimal weight:    1.9990
   chunk 96 optimal weight:    0.3980
   chunk 80 optimal weight:    7.9990
   chunk 41 optimal weight:    0.0870
   chunk 87 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 69 optimal weight:    5.9990
   chunk 33 optimal weight:    0.0060
   chunk 70 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0570
   overall best weight:    0.1100

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

Flipped N/Q/H residues before XYZ refinement:
D  21 ASN
E  21 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2575 r_free = 0.2575 target = 0.029981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2431 r_free = 0.2431 target = 0.026663 restraints weight = 75709.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2464 r_free = 0.2464 target = 0.027453 restraints weight = 36076.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2487 r_free = 0.2487 target = 0.027984 restraints weight = 21040.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2502 r_free = 0.2502 target = 0.028344 restraints weight = 13878.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2514 r_free = 0.2514 target = 0.028612 restraints weight = 10022.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.2514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8711
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8370  Z= 0.115
  Angle     :  0.558   7.901  11511  Z= 0.302
  Chirality :  0.044   0.161   1512
  Planarity :  0.005   0.038   1449
  Dihedral  :  4.677  15.307   1179
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  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:  1.21 (0.28), residues: 1080
  helix:  None (None), residues: 0
  sheet:  2.16 (0.25), residues: 450
  loop : -0.25 (0.28), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 123 
 TYR   0.012   0.002   TYR A  70 
 PHE   0.009   0.001   PHE B  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8370)
  covalent geometry    : angle       0.55846 (11511)
  hydrogen bonds       : bond        0.02688 (  288)
  hydrogen bonds       : angle       5.82352 (  804)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.238 
Fit side-chains
REVERT: C   10 MET cc_start: 0.8494 (mtp) cc_final: 0.8268 (mtp)
REVERT: E   95 GLN cc_start: 0.8441 (mp10) cc_final: 0.8219 (mp10)
REVERT: F   10 MET cc_start: 0.8526 (mtp) cc_final: 0.7893 (mtp)
REVERT: F  123 ARG cc_start: 0.8990 (ptt-90) cc_final: 0.8698 (pmt-80)
REVERT: G   10 MET cc_start: 0.8885 (mtp) cc_final: 0.8501 (mtp)
REVERT: I   23 GLU cc_start: 0.8067 (pm20) cc_final: 0.7629 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1275
  time to fit residues: 9.4823
Evaluate side-chains
  44 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 84 optimal weight:    0.0770
   chunk 64 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 92 optimal weight:    8.9990
   chunk 21 optimal weight:    7.9990
   chunk 50 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 6 optimal weight:    0.5980
   chunk 94 optimal weight:    8.9990
   chunk 61 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    2.3342

-------------------------------------------------------------------------------
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 = 0.2545 r_free = 0.2545 target = 0.029177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2406 r_free = 0.2406 target = 0.026055 restraints weight = 78351.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2437 r_free = 0.2437 target = 0.026788 restraints weight = 37269.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2458 r_free = 0.2458 target = 0.027282 restraints weight = 21676.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2472 r_free = 0.2472 target = 0.027616 restraints weight = 14281.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2484 r_free = 0.2484 target = 0.027875 restraints weight = 10345.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.2483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8370  Z= 0.210
  Angle     :  0.586   9.624  11511  Z= 0.311
  Chirality :  0.043   0.164   1512
  Planarity :  0.005   0.032   1449
  Dihedral  :  4.786  17.482   1179
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  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:  1.22 (0.28), residues: 1080
  helix:  None (None), residues: 0
  sheet:  2.07 (0.25), residues: 450
  loop : -0.15 (0.28), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 123 
 TYR   0.010   0.002   TYR B  70 
 PHE   0.013   0.001   PHE B  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 8370)
  covalent geometry    : angle       0.58586 (11511)
  hydrogen bonds       : bond        0.03252 (  288)
  hydrogen bonds       : angle       5.73232 (  804)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.333 
Fit side-chains
REVERT: C   10 MET cc_start: 0.8502 (mtp) cc_final: 0.8253 (mtp)
REVERT: C   66 ASP cc_start: 0.8876 (t70) cc_final: 0.8645 (t0)
REVERT: D   66 ASP cc_start: 0.8687 (t70) cc_final: 0.8372 (t0)
REVERT: F   10 MET cc_start: 0.8497 (mtp) cc_final: 0.7690 (mtp)
REVERT: F  123 ARG cc_start: 0.9039 (ptt-90) cc_final: 0.8713 (pmt-80)
REVERT: I   23 GLU cc_start: 0.8293 (pm20) cc_final: 0.7829 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1467
  time to fit residues: 9.3431
Evaluate side-chains
  43 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    6.9990
   chunk 72 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   chunk 50 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
E  21 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2532 r_free = 0.2532 target = 0.029049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2392 r_free = 0.2392 target = 0.025877 restraints weight = 77549.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2423 r_free = 0.2423 target = 0.026615 restraints weight = 37033.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2444 r_free = 0.2444 target = 0.027106 restraints weight = 21736.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2459 r_free = 0.2459 target = 0.027450 restraints weight = 14364.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2470 r_free = 0.2470 target = 0.027693 restraints weight = 10405.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.2470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8752
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   8370  Z= 0.207
  Angle     :  0.589   9.973  11511  Z= 0.313
  Chirality :  0.043   0.163   1512
  Planarity :  0.005   0.030   1449
  Dihedral  :  4.821  15.839   1179
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  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:  1.14 (0.28), residues: 1080
  helix:  None (None), residues: 0
  sheet:  2.02 (0.25), residues: 450
  loop : -0.22 (0.28), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 123 
 TYR   0.010   0.002   TYR B  70 
 PHE   0.010   0.001   PHE I  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 8370)
  covalent geometry    : angle       0.58935 (11511)
  hydrogen bonds       : bond        0.03137 (  288)
  hydrogen bonds       : angle       5.63765 (  804)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.306 
Fit side-chains
REVERT: B   10 MET cc_start: 0.9068 (mtp) cc_final: 0.8637 (mtp)
REVERT: C   10 MET cc_start: 0.8503 (mtp) cc_final: 0.8251 (mtp)
REVERT: C   66 ASP cc_start: 0.8823 (t70) cc_final: 0.8569 (t0)
REVERT: D   66 ASP cc_start: 0.8704 (t70) cc_final: 0.8427 (t0)
REVERT: F   10 MET cc_start: 0.8472 (mtp) cc_final: 0.7610 (mtp)
REVERT: I   23 GLU cc_start: 0.8295 (pm20) cc_final: 0.7810 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.1597
  time to fit residues: 9.8248
Evaluate side-chains
  43 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 90 optimal weight:    0.0770
   chunk 3 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0980
   chunk 11 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 12 optimal weight:    6.9990
   chunk 103 optimal weight:    0.0000
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.3942

-------------------------------------------------------------------------------
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 = 0.2576 r_free = 0.2576 target = 0.029948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2436 r_free = 0.2436 target = 0.026698 restraints weight = 75776.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2468 r_free = 0.2468 target = 0.027475 restraints weight = 36034.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2490 r_free = 0.2490 target = 0.027995 restraints weight = 20954.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2504 r_free = 0.2504 target = 0.028346 restraints weight = 13776.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2515 r_free = 0.2515 target = 0.028596 restraints weight = 9919.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.2517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8370  Z= 0.109
  Angle     :  0.542   8.482  11511  Z= 0.290
  Chirality :  0.043   0.155   1512
  Planarity :  0.004   0.035   1449
  Dihedral  :  4.556  15.867   1179
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  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:  1.20 (0.28), residues: 1080
  helix:  None (None), residues: 0
  sheet:  2.14 (0.25), residues: 450
  loop : -0.24 (0.28), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 123 
 TYR   0.010   0.002   TYR A  27 
 PHE   0.008   0.001   PHE A   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8370)
  covalent geometry    : angle       0.54151 (11511)
  hydrogen bonds       : bond        0.02473 (  288)
  hydrogen bonds       : angle       5.50026 (  804)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A   10 MET cc_start: 0.8764 (mtp) cc_final: 0.8322 (mtp)
REVERT: B   10 MET cc_start: 0.8959 (mtp) cc_final: 0.8566 (mtp)
REVERT: C   10 MET cc_start: 0.8511 (mtp) cc_final: 0.8235 (mtp)
REVERT: C   66 ASP cc_start: 0.8779 (t70) cc_final: 0.8522 (t0)
REVERT: D   66 ASP cc_start: 0.8671 (t70) cc_final: 0.8363 (t0)
REVERT: D   67 ASN cc_start: 0.9193 (m-40) cc_final: 0.8838 (m-40)
REVERT: F   10 MET cc_start: 0.8412 (mtp) cc_final: 0.7709 (mtp)
REVERT: F  123 ARG cc_start: 0.8984 (ptt-90) cc_final: 0.8701 (pmt-80)
REVERT: I   23 GLU cc_start: 0.8115 (pm20) cc_final: 0.7627 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1515
  time to fit residues: 11.0312
Evaluate side-chains
  47 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 65 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 61 optimal weight:   10.0000
   chunk 71 optimal weight:    3.9990
   chunk 8 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 = 0.2560 r_free = 0.2560 target = 0.029615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2423 r_free = 0.2423 target = 0.026429 restraints weight = 76829.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2452 r_free = 0.2452 target = 0.027164 restraints weight = 36353.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2473 r_free = 0.2473 target = 0.027665 restraints weight = 21317.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2488 r_free = 0.2488 target = 0.028032 restraints weight = 13980.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2499 r_free = 0.2499 target = 0.028283 restraints weight = 10035.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.2501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8730
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8370  Z= 0.144
  Angle     :  0.548   9.046  11511  Z= 0.293
  Chirality :  0.043   0.157   1512
  Planarity :  0.004   0.035   1449
  Dihedral  :  4.563  17.481   1179
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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:  1.25 (0.28), residues: 1080
  helix:  None (None), residues: 0
  sheet:  1.59 (0.23), residues: 540
  loop :  0.07 (0.31), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 123 
 TYR   0.012   0.002   TYR G  27 
 PHE   0.014   0.001   PHE I  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 8370)
  covalent geometry    : angle       0.54838 (11511)
  hydrogen bonds       : bond        0.02678 (  288)
  hydrogen bonds       : angle       5.40069 (  804)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.320 
Fit side-chains
REVERT: B   10 MET cc_start: 0.8998 (mtp) cc_final: 0.8663 (mtp)
REVERT: C   10 MET cc_start: 0.8528 (mtp) cc_final: 0.8312 (mtp)
REVERT: C   66 ASP cc_start: 0.8815 (t70) cc_final: 0.8551 (t0)
REVERT: D   66 ASP cc_start: 0.8708 (t70) cc_final: 0.8399 (t0)
REVERT: F   10 MET cc_start: 0.8457 (mtp) cc_final: 0.7654 (mtp)
REVERT: F  123 ARG cc_start: 0.9008 (ptt-90) cc_final: 0.8720 (pmt-80)
REVERT: G   10 MET cc_start: 0.9019 (mtp) cc_final: 0.8818 (mtp)
REVERT: H   10 MET cc_start: 0.9055 (mtp) cc_final: 0.8666 (mtp)
REVERT: H  123 ARG cc_start: 0.9035 (ptt-90) cc_final: 0.8627 (pmt-80)
REVERT: I   23 GLU cc_start: 0.8129 (pm20) cc_final: 0.7638 (pm20)
REVERT: I  123 ARG cc_start: 0.9065 (ptt-90) cc_final: 0.8445 (pmt-80)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1512
  time to fit residues: 9.7746
Evaluate side-chains
  45 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 96 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 107 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   chunk 5 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 52 optimal weight:    7.9990
   chunk 70 optimal weight:    8.9990
   chunk 86 optimal weight:    4.9990
   overall best weight:    3.9388

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

Flipped N/Q/H residues before XYZ refinement:
D  21 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2518 r_free = 0.2518 target = 0.028671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2384 r_free = 0.2384 target = 0.025680 restraints weight = 79543.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2415 r_free = 0.2415 target = 0.026395 restraints weight = 37051.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2435 r_free = 0.2435 target = 0.026865 restraints weight = 21321.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2449 r_free = 0.2449 target = 0.027189 restraints weight = 13999.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2458 r_free = 0.2458 target = 0.027393 restraints weight = 10105.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.2458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8771
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.081   8370  Z= 0.325
  Angle     :  0.662  11.338  11511  Z= 0.352
  Chirality :  0.045   0.162   1512
  Planarity :  0.005   0.043   1449
  Dihedral  :  5.066  18.132   1179
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  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:  1.06 (0.27), residues: 1080
  helix:  None (None), residues: 0
  sheet:  2.03 (0.24), residues: 450
  loop : -0.33 (0.27), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 123 
 TYR   0.010   0.002   TYR F  70 
 PHE   0.021   0.002   PHE F  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00729 ( 8370)
  covalent geometry    : angle       0.66195 (11511)
  hydrogen bonds       : bond        0.03600 (  288)
  hydrogen bonds       : angle       5.61170 (  804)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.276 
Fit side-chains
REVERT: C   66 ASP cc_start: 0.8865 (t70) cc_final: 0.8611 (t0)
REVERT: D   66 ASP cc_start: 0.8730 (t70) cc_final: 0.8433 (t0)
REVERT: F   10 MET cc_start: 0.8539 (mtp) cc_final: 0.7677 (mtp)
REVERT: F  123 ARG cc_start: 0.9047 (ptt-90) cc_final: 0.8649 (pmt-80)
REVERT: I   23 GLU cc_start: 0.8314 (pm20) cc_final: 0.7828 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1429
  time to fit residues: 8.6911
Evaluate side-chains
  44 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 77 optimal weight:    9.9990
   chunk 18 optimal weight:    0.3980
   chunk 100 optimal weight:    3.9990
   chunk 81 optimal weight:    7.9990
   chunk 93 optimal weight:    7.9990
   chunk 24 optimal weight:    6.9990
   chunk 84 optimal weight:    3.9990
   chunk 78 optimal weight:    0.6980
   overall best weight:    1.7984

-------------------------------------------------------------------------------
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 = 0.2548 r_free = 0.2548 target = 0.029226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2411 r_free = 0.2411 target = 0.026155 restraints weight = 78636.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2442 r_free = 0.2442 target = 0.026889 restraints weight = 37038.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2463 r_free = 0.2463 target = 0.027372 restraints weight = 21424.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2476 r_free = 0.2476 target = 0.027687 restraints weight = 14109.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2486 r_free = 0.2486 target = 0.027934 restraints weight = 10358.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.2490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8756
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8370  Z= 0.176
  Angle     :  0.578  10.039  11511  Z= 0.310
  Chirality :  0.043   0.159   1512
  Planarity :  0.005   0.038   1449
  Dihedral  :  4.842  15.763   1179
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  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:  1.08 (0.27), residues: 1080
  helix:  None (None), residues: 0
  sheet:  2.06 (0.24), residues: 450
  loop : -0.32 (0.27), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 123 
 TYR   0.010   0.002   TYR G  27 
 PHE   0.012   0.001   PHE F  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 8370)
  covalent geometry    : angle       0.57757 (11511)
  hydrogen bonds       : bond        0.02892 (  288)
  hydrogen bonds       : angle       5.47115 (  804)

===============================================================================
Job complete
usr+sys time: 1002.20 seconds
wall clock time: 18 minutes 20.48 seconds (1100.48 seconds total)