Starting phenix.real_space_refine
on Wed Mar  4 09:31:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p0z_13153/03_2026/7p0z_13153.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p0z_13153/03_2026/7p0z_13153.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p0z_13153/03_2026/7p0z_13153.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p0z_13153/03_2026/7p0z_13153.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p0z_13153/03_2026/7p0z_13153.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p0z_13153/03_2026/7p0z_13153.cif"
  }
  resolution = 2.43
  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=   0.246 sd=   1.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    8008      2.51       5
     N    2247      2.21       5
     O    2576      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12873
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1839
          Classifications: {'peptide': 236}
          Link IDs: {'PTRANS': 14, 'TRANS': 221}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E, F, G
  Time building chain proxies: 1.69, per 1000 atoms: 0.13
  Number of scatterers: 12873
  At special positions: 0
  Unit cell: (104.25, 103.416, 104.25, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    2576      8.00
     N    2247      7.00
     C    8008      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.12
  Conformation dependent library (CDL) restraints added in 658.8 milliseconds
  

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3192

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 0 sheets defined
      75.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 22
      removed outlier: 3.553A  pdb=" N   ILE A  14 " --> pdb=" O   ASP A  10 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 80
    Processing helix  chain 'A' and resid 130 through 142
    Processing helix  chain 'A' and resid 146 through 165
    Processing helix  chain 'A' and resid 166 through 171
      removed outlier: 4.168A  pdb=" N   ARG A 169 " --> pdb=" O   ASP A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 223
    Processing helix  chain 'A' and resid 225 through 236
    Processing helix  chain 'A' and resid 241 through 267
      removed outlier: 4.461A  pdb=" N   LYS A 247 " --> pdb=" O   GLU A 243 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 22
      removed outlier: 3.553A  pdb=" N   ILE B  14 " --> pdb=" O   ASP B  10 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU B  22 " --> pdb=" O   ALA B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 80
    Processing helix  chain 'B' and resid 130 through 142
    Processing helix  chain 'B' and resid 146 through 165
    Processing helix  chain 'B' and resid 166 through 171
      removed outlier: 4.168A  pdb=" N   ARG B 169 " --> pdb=" O   ASP B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 223
    Processing helix  chain 'B' and resid 225 through 236
    Processing helix  chain 'B' and resid 241 through 267
      removed outlier: 4.461A  pdb=" N   LYS B 247 " --> pdb=" O   GLU B 243 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 22
      removed outlier: 3.554A  pdb=" N   ILE C  14 " --> pdb=" O   ASP C  10 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU C  22 " --> pdb=" O   ALA C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 39 through 80
    Processing helix  chain 'C' and resid 130 through 142
    Processing helix  chain 'C' and resid 146 through 165
    Processing helix  chain 'C' and resid 166 through 171
      removed outlier: 4.169A  pdb=" N   ARG C 169 " --> pdb=" O   ASP C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 178 through 223
    Processing helix  chain 'C' and resid 225 through 236
    Processing helix  chain 'C' and resid 241 through 267
      removed outlier: 4.461A  pdb=" N   LYS C 247 " --> pdb=" O   GLU C 243 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 10 through 22
      removed outlier: 3.553A  pdb=" N   ILE D  14 " --> pdb=" O   ASP D  10 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU D  22 " --> pdb=" O   ALA D  18 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 39 through 80
    Processing helix  chain 'D' and resid 130 through 142
    Processing helix  chain 'D' and resid 146 through 165
    Processing helix  chain 'D' and resid 166 through 171
      removed outlier: 4.168A  pdb=" N   ARG D 169 " --> pdb=" O   ASP D 166 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 178 through 223
    Processing helix  chain 'D' and resid 225 through 236
    Processing helix  chain 'D' and resid 241 through 267
      removed outlier: 4.460A  pdb=" N   LYS D 247 " --> pdb=" O   GLU D 243 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 10 through 22
      removed outlier: 3.553A  pdb=" N   ILE E  14 " --> pdb=" O   ASP E  10 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU E  22 " --> pdb=" O   ALA E  18 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 39 through 80
    Processing helix  chain 'E' and resid 130 through 142
    Processing helix  chain 'E' and resid 146 through 165
    Processing helix  chain 'E' and resid 166 through 171
      removed outlier: 4.168A  pdb=" N   ARG E 169 " --> pdb=" O   ASP E 166 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 178 through 223
    Processing helix  chain 'E' and resid 225 through 236
    Processing helix  chain 'E' and resid 241 through 267
      removed outlier: 4.460A  pdb=" N   LYS E 247 " --> pdb=" O   GLU E 243 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 10 through 22
      removed outlier: 3.553A  pdb=" N   ILE F  14 " --> pdb=" O   ASP F  10 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU F  22 " --> pdb=" O   ALA F  18 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 39 through 80
    Processing helix  chain 'F' and resid 130 through 142
    Processing helix  chain 'F' and resid 146 through 165
    Processing helix  chain 'F' and resid 166 through 171
      removed outlier: 4.169A  pdb=" N   ARG F 169 " --> pdb=" O   ASP F 166 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 178 through 223
    Processing helix  chain 'F' and resid 225 through 236
    Processing helix  chain 'F' and resid 241 through 267
      removed outlier: 4.461A  pdb=" N   LYS F 247 " --> pdb=" O   GLU F 243 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 22
      removed outlier: 3.553A  pdb=" N   ILE G  14 " --> pdb=" O   ASP G  10 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU G  22 " --> pdb=" O   ALA G  18 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 39 through 80
    Processing helix  chain 'G' and resid 130 through 142
    Processing helix  chain 'G' and resid 146 through 165
    Processing helix  chain 'G' and resid 166 through 171
      removed outlier: 4.169A  pdb=" N   ARG G 169 " --> pdb=" O   ASP G 166 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 178 through 223
    Processing helix  chain 'G' and resid 225 through 236
    Processing helix  chain 'G' and resid 241 through 267
      removed outlier: 4.461A  pdb=" N   LYS G 247 " --> pdb=" O   GLU G 243 " (cutoff:3.500A)

    1008 hydrogen bonds defined for protein.
    2982 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.77

  Time building geometry restraints manager: 1.45 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4008
        1.33 -     1.44: 1633
        1.44 -     1.56: 7393
        1.56 -     1.68: 0
        1.68 -     1.80: 77
  Bond restraints: 13111
  Sorted by residual:
  bond pdb=" CB  ARG F 220 "
       pdb=" CG  ARG F 220 "
    ideal  model  delta    sigma   weight residual
    1.520  1.442  0.078 3.00e-02 1.11e+03 6.83e+00
  bond pdb=" CB  ARG C 220 "
       pdb=" CG  ARG C 220 "
    ideal  model  delta    sigma   weight residual
    1.520  1.442  0.078 3.00e-02 1.11e+03 6.80e+00
  bond pdb=" CB  ARG G 220 "
       pdb=" CG  ARG G 220 "
    ideal  model  delta    sigma   weight residual
    1.520  1.442  0.078 3.00e-02 1.11e+03 6.80e+00
  bond pdb=" CB  ARG E 220 "
       pdb=" CG  ARG E 220 "
    ideal  model  delta    sigma   weight residual
    1.520  1.442  0.078 3.00e-02 1.11e+03 6.72e+00
  bond pdb=" CB  ARG B 220 "
       pdb=" CG  ARG B 220 "
    ideal  model  delta    sigma   weight residual
    1.520  1.442  0.078 3.00e-02 1.11e+03 6.70e+00
  ... (remaining 13106 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 16178
        1.52 -     3.04: 1317
        3.04 -     4.56: 257
        4.56 -     6.08: 56
        6.08 -     7.61: 7
  Bond angle restraints: 17815
  Sorted by residual:
  angle pdb=" C   ASN C 264 "
        pdb=" N   THR C 265 "
        pdb=" CA  THR C 265 "
      ideal   model   delta    sigma   weight residual
     120.58  114.74    5.84 1.71e+00 3.42e-01 1.17e+01
  angle pdb=" C   ASN F 264 "
        pdb=" N   THR F 265 "
        pdb=" CA  THR F 265 "
      ideal   model   delta    sigma   weight residual
     120.58  114.74    5.84 1.71e+00 3.42e-01 1.17e+01
  angle pdb=" C   ASN D 264 "
        pdb=" N   THR D 265 "
        pdb=" CA  THR D 265 "
      ideal   model   delta    sigma   weight residual
     120.58  114.76    5.82 1.71e+00 3.42e-01 1.16e+01
  angle pdb=" C   ASN B 264 "
        pdb=" N   THR B 265 "
        pdb=" CA  THR B 265 "
      ideal   model   delta    sigma   weight residual
     120.58  114.77    5.81 1.71e+00 3.42e-01 1.16e+01
  angle pdb=" C   ASN E 264 "
        pdb=" N   THR E 265 "
        pdb=" CA  THR E 265 "
      ideal   model   delta    sigma   weight residual
     120.58  114.78    5.80 1.71e+00 3.42e-01 1.15e+01
  ... (remaining 17810 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.61: 7420
       16.61 -    33.22: 539
       33.22 -    49.83: 77
       49.83 -    66.44: 35
       66.44 -    83.06: 42
  Dihedral angle restraints: 8113
    sinusoidal: 3241
      harmonic: 4872
  Sorted by residual:
  dihedral pdb=" CB  GLU A 270 "
           pdb=" CG  GLU A 270 "
           pdb=" CD  GLU A 270 "
           pdb=" OE1 GLU A 270 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -83.06   83.06     1      3.00e+01 1.11e-03 9.38e+00
  dihedral pdb=" CB  GLU C 270 "
           pdb=" CG  GLU C 270 "
           pdb=" CD  GLU C 270 "
           pdb=" OE1 GLU C 270 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -83.04   83.04     1      3.00e+01 1.11e-03 9.37e+00
  dihedral pdb=" CB  GLU E 270 "
           pdb=" CG  GLU E 270 "
           pdb=" CD  GLU E 270 "
           pdb=" OE1 GLU E 270 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -83.02   83.02     1      3.00e+01 1.11e-03 9.37e+00
  ... (remaining 8110 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 751
       0.032 -    0.064: 644
       0.064 -    0.097: 378
       0.097 -    0.129: 159
       0.129 -    0.161: 35
  Chirality restraints: 1967
  Sorted by residual:
  chirality pdb=" CA  ASN C 273 "
            pdb=" N   ASN C 273 "
            pdb=" C   ASN C 273 "
            pdb=" CB  ASN C 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.47e-01
  chirality pdb=" CA  ASN E 273 "
            pdb=" N   ASN E 273 "
            pdb=" C   ASN E 273 "
            pdb=" CB  ASN E 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.46e-01
  chirality pdb=" CA  ASN F 273 "
            pdb=" N   ASN F 273 "
            pdb=" C   ASN F 273 "
            pdb=" CB  ASN F 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.37e-01
  ... (remaining 1964 not shown)

  Planarity restraints: 2401
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  81 "   -0.019 2.00e-02 2.50e+03   1.21e-02 2.94e+00
        pdb=" CG  TYR A  81 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  81 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  81 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  81 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  81 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A  81 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  81 "   -0.019 2.00e-02 2.50e+03   1.21e-02 2.93e+00
        pdb=" CG  TYR C  81 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  81 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  81 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  81 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  81 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  81 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C  81 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 273 "    0.009 2.00e-02 2.50e+03   1.71e-02 2.92e+00
        pdb=" CG  ASN A 273 "   -0.030 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 273 "    0.011 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 273 "    0.010 2.00e-02 2.50e+03
  ... (remaining 2398 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 604
        2.69 -     3.24: 13166
        3.24 -     3.80: 22991
        3.80 -     4.35: 25703
        4.35 -     4.90: 42627
  Nonbonded interactions: 105091
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C 257 "
            pdb=" NH1 ARG D 221 "
     model   vdw
     2.141 3.120
  nonbonded pdb=" OE1 GLU E 257 "
            pdb=" NH1 ARG F 221 "
     model   vdw
     2.145 3.120
  nonbonded pdb=" OE1 GLU B 257 "
            pdb=" NH1 ARG C 221 "
     model   vdw
     2.148 3.120
  nonbonded pdb=" OE1 GLU D 257 "
            pdb=" NH1 ARG E 221 "
     model   vdw
     2.148 3.120
  nonbonded pdb=" OE1 GLU A 257 "
            pdb=" NH1 ARG B 221 "
     model   vdw
     2.151 3.120
  ... (remaining 105086 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: 0.03
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'
}

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:                  0.010
  Normalize map: mean=0, sd=1:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.300
  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:6.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
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   0.078  13111  Z= 0.697
  Angle     :  0.943   7.606  17815  Z= 0.523
  Chirality :  0.059   0.161   1967
  Planarity :  0.006   0.041   2401
  Dihedral  : 14.023  83.055   4921
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.90 (0.20), residues: 1624
  helix:  1.71 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop :  0.07 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.002   ARG A 165 
 TYR   0.028   0.006   TYR F  81 
 PHE   0.027   0.004   PHE D 159 
 TRP   0.017   0.004   TRP D 156 
 HIS   0.009   0.004   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.01563 (13111)
  covalent geometry    : angle       0.94254 (17815)
  hydrogen bonds       : bond        0.09803 ( 1008)
  hydrogen bonds       : angle       4.62139 ( 2982)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  399 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 399
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
REVERT: A  221 ARG cc_start: 0.7647 (ptt-90) cc_final: 0.7442 (ptp90)
REVERT: F  133 LEU cc_start: 0.8963 (mm) cc_final: 0.8714 (mt)
REVERT: F  201 LEU cc_start: 0.9089 (mt) cc_final: 0.8878 (mt)
REVERT: G   68 GLN cc_start: 0.8396 (mt0) cc_final: 0.8180 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 399
  average time/residue: 0.6896
  time to fit residues: 294.1956
Evaluate side-chains
  256 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 149 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  55 ASN
D 244 GLN
E 244 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.091949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.084188 restraints weight = 20830.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 1.20
r_work: 0.3057 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  13111  Z= 0.140
  Angle     :  0.536   8.531  17815  Z= 0.280
  Chirality :  0.034   0.130   1967
  Planarity :  0.004   0.034   2401
  Dihedral  :  3.701  13.312   1764
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 13.91 %
    Favored  : 83.63 %
  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:  3.77 (0.20), residues: 1624
  helix:  3.07 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop :  0.78 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 234 
 TYR   0.017   0.002   TYR E  59 
 PHE   0.016   0.002   PHE E 152 
 TRP   0.014   0.002   TRP D 156 
 HIS   0.003   0.001   HIS G 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (13111)
  covalent geometry    : angle       0.53608 (17815)
  hydrogen bonds       : bond        0.05417 ( 1008)
  hydrogen bonds       : angle       3.52218 ( 2982)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 302
  time to evaluate  : 0.498 
Fit side-chains
REVERT: B   11 GLN cc_start: 0.8455 (mt0) cc_final: 0.8247 (mt0)
REVERT: D  221 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7903 (ptp90)
REVERT: F  133 LEU cc_start: 0.8974 (mm) cc_final: 0.8702 (mt)
  outliers start: 33
  outliers final: 10
  residues processed: 311
  average time/residue: 0.5580
  time to fit residues: 188.7521
Evaluate side-chains
  286 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 275
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain D residue  221 ARG
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain E residue  132 ASP
Chi-restraints excluded: chain E residue  188 MET
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain F residue  132 ASP
Chi-restraints excluded: chain F residue  230 VAL
Chi-restraints excluded: chain G residue  133 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 157 optimal weight:    4.9990
   chunk 77 optimal weight:    5.9990
   chunk 79 optimal weight:    6.9990
   chunk 153 optimal weight:    0.8980
   chunk 125 optimal weight:    5.9990
   chunk 137 optimal weight:    0.0470
   chunk 75 optimal weight:    0.9980
   chunk 140 optimal weight:    0.7980
   chunk 101 optimal weight:    6.9990
   chunk 107 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   overall best weight:    0.9480

-------------------------------------------------------------------------------
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 = 0.3337 r_free = 0.3337 target = 0.092552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.085337 restraints weight = 20979.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.15
r_work: 0.3092 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 2.83 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13111  Z= 0.127
  Angle     :  0.471   5.959  17815  Z= 0.247
  Chirality :  0.033   0.128   1967
  Planarity :  0.003   0.032   2401
  Dihedral  :  3.396  13.141   1764
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 15.25 %
    Favored  : 81.70 %
  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:  4.65 (0.20), residues: 1624
  helix:  3.69 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.19 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  67 
 TYR   0.017   0.002   TYR A  59 
 PHE   0.016   0.002   PHE G 152 
 TRP   0.011   0.002   TRP D 156 
 HIS   0.003   0.001   HIS B 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (13111)
  covalent geometry    : angle       0.47116 (17815)
  hydrogen bonds       : bond        0.04865 ( 1008)
  hydrogen bonds       : angle       3.27876 ( 2982)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 293
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  134 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8490 (mttt)
REVERT: C  141 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7411 (mt-10)
REVERT: C  221 ARG cc_start: 0.7915 (ptp90) cc_final: 0.7658 (ptp90)
REVERT: D  221 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7766 (ptp90)
REVERT: F  133 LEU cc_start: 0.8931 (mm) cc_final: 0.8672 (mt)
REVERT: F  141 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7378 (mt-10)
REVERT: G  134 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8770 (mmtp)
REVERT: G  193 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8123 (mp0)
  outliers start: 41
  outliers final: 15
  residues processed: 308
  average time/residue: 0.5370
  time to fit residues: 181.0139
Evaluate side-chains
  288 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 267
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  251 GLU
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue  141 GLU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain C residue  259 VAL
Chi-restraints excluded: chain D residue  221 ARG
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain E residue  141 GLU
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain F residue  141 GLU
Chi-restraints excluded: chain F residue  205 LEU
Chi-restraints excluded: chain F residue  230 VAL
Chi-restraints excluded: chain G residue  134 LYS
Chi-restraints excluded: chain G residue  193 GLU
Chi-restraints excluded: chain G residue  205 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 144 optimal weight:    4.9990
   chunk 4 optimal weight:    6.9990
   chunk 155 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 106 optimal weight:    3.9990
   chunk 120 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 97 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 146 optimal weight:    3.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
G 264 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.091170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.084040 restraints weight = 20943.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 1.14
r_work: 0.3061 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 2.80 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13111  Z= 0.175
  Angle     :  0.521   5.347  17815  Z= 0.272
  Chirality :  0.035   0.129   1967
  Planarity :  0.004   0.034   2401
  Dihedral  :  3.439  12.899   1764
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 15.25 %
    Favored  : 80.58 %
  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:  4.78 (0.20), residues: 1624
  helix:  3.74 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.37 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  67 
 TYR   0.017   0.002   TYR A  59 
 PHE   0.016   0.002   PHE G 152 
 TRP   0.012   0.002   TRP G 156 
 HIS   0.005   0.002   HIS G 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (13111)
  covalent geometry    : angle       0.52142 (17815)
  hydrogen bonds       : bond        0.05226 ( 1008)
  hydrogen bonds       : angle       3.27793 ( 2982)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 272
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  134 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8477 (mttt)
REVERT: C  141 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7414 (mt-10)
REVERT: D  221 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7747 (ptp90)
REVERT: E   11 GLN cc_start: 0.8480 (mt0) cc_final: 0.8253 (mt0)
REVERT: F  133 LEU cc_start: 0.8950 (mm) cc_final: 0.8651 (mt)
REVERT: F  141 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7480 (mt-10)
REVERT: G  193 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8128 (mp0)
  outliers start: 56
  outliers final: 23
  residues processed: 300
  average time/residue: 0.5160
  time to fit residues: 169.6912
Evaluate side-chains
  298 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 270
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  251 GLU
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue  141 GLU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  221 ARG
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain C residue  259 VAL
Chi-restraints excluded: chain D residue  221 ARG
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain E residue  132 ASP
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  141 GLU
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain F residue  132 ASP
Chi-restraints excluded: chain F residue  141 GLU
Chi-restraints excluded: chain F residue  230 VAL
Chi-restraints excluded: chain G residue  193 GLU
Chi-restraints excluded: chain G residue  207 LYS
Chi-restraints excluded: chain G residue  232 LEU
Chi-restraints excluded: chain G residue  259 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 120 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0970
   chunk 73 optimal weight:    5.9990
   chunk 109 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 138 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
F 197 HIS
G 264 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.092746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.085562 restraints weight = 21128.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 1.16
r_work: 0.3095 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13111  Z= 0.124
  Angle     :  0.468   5.125  17815  Z= 0.244
  Chirality :  0.032   0.124   1967
  Planarity :  0.003   0.033   2401
  Dihedral  :  3.239  12.060   1764
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 17.26 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  5.13 (0.20), residues: 1624
  helix:  4.02 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.41 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 221 
 TYR   0.016   0.002   TYR A  59 
 PHE   0.017   0.002   PHE G 152 
 TRP   0.012   0.002   TRP C 156 
 HIS   0.003   0.001   HIS B 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (13111)
  covalent geometry    : angle       0.46804 (17815)
  hydrogen bonds       : bond        0.04604 ( 1008)
  hydrogen bonds       : angle       3.19209 ( 2982)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 287
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  134 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8515 (mttt)
REVERT: C  141 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7389 (mt-10)
REVERT: D  221 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7698 (ptp90)
REVERT: E   11 GLN cc_start: 0.8443 (mt0) cc_final: 0.8217 (mt0)
REVERT: F  133 LEU cc_start: 0.8967 (mm) cc_final: 0.8687 (mt)
REVERT: F  141 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7369 (mt-10)
  outliers start: 47
  outliers final: 18
  residues processed: 310
  average time/residue: 0.5492
  time to fit residues: 185.7009
Evaluate side-chains
  300 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 278
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  251 GLU
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue  141 GLU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain D residue  193 GLU
Chi-restraints excluded: chain D residue  221 ARG
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain E residue  132 ASP
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  141 GLU
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain F residue  141 GLU
Chi-restraints excluded: chain F residue  205 LEU
Chi-restraints excluded: chain F residue  230 VAL
Chi-restraints excluded: chain G residue  232 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 133 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 20 optimal weight:    6.9990
   chunk 84 optimal weight:    6.9990
   chunk 53 optimal weight:    0.0570
   chunk 88 optimal weight:    0.9990
   chunk 30 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.6900

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

Flipped N/Q/H residues before XYZ refinement:
B 160 ASN
D  11 GLN
G 264 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.093760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.086711 restraints weight = 20791.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.13
r_work: 0.3118 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  13111  Z= 0.113
  Angle     :  0.453   4.863  17815  Z= 0.236
  Chirality :  0.032   0.122   1967
  Planarity :  0.003   0.031   2401
  Dihedral  :  3.113  11.148   1764
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 19.42 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  5.33 (0.20), residues: 1624
  helix:  4.18 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.47 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  67 
 TYR   0.015   0.001   TYR E  59 
 PHE   0.016   0.002   PHE G 152 
 TRP   0.011   0.001   TRP C 156 
 HIS   0.002   0.001   HIS B 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (13111)
  covalent geometry    : angle       0.45310 (17815)
  hydrogen bonds       : bond        0.04240 ( 1008)
  hydrogen bonds       : angle       3.11056 ( 2982)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 296
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  134 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8514 (mttt)
REVERT: C  141 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7372 (mt-10)
REVERT: D   59 TYR cc_start: 0.8570 (m-80) cc_final: 0.8361 (m-80)
REVERT: E   11 GLN cc_start: 0.8411 (mt0) cc_final: 0.8199 (mt0)
REVERT: F  133 LEU cc_start: 0.8957 (mm) cc_final: 0.8677 (mt)
REVERT: F  141 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7353 (mt-10)
REVERT: F  262 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8232 (tt0)
  outliers start: 38
  outliers final: 18
  residues processed: 318
  average time/residue: 0.4942
  time to fit residues: 172.3772
Evaluate side-chains
  304 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 282
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue  141 GLU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain C residue  259 VAL
Chi-restraints excluded: chain D residue  193 GLU
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain F residue  141 GLU
Chi-restraints excluded: chain F residue  160 ASN
Chi-restraints excluded: chain F residue  230 VAL
Chi-restraints excluded: chain F residue  254 GLU
Chi-restraints excluded: chain F residue  262 GLU
Chi-restraints excluded: chain G residue  134 LYS
Chi-restraints excluded: chain G residue  207 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 105 optimal weight:    6.9990
   chunk 137 optimal weight:    1.9990
   chunk 144 optimal weight:    3.9990
   chunk 96 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   chunk 101 optimal weight:    7.9990
   chunk 117 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0870
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.7160

-------------------------------------------------------------------------------
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 = 0.3360 r_free = 0.3360 target = 0.093837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.086763 restraints weight = 21012.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 1.14
r_work: 0.3122 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13111  Z= 0.113
  Angle     :  0.457   5.313  17815  Z= 0.237
  Chirality :  0.032   0.169   1967
  Planarity :  0.003   0.036   2401
  Dihedral  :  3.076  11.843   1764
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 19.87 %
    Favored  : 77.23 %
  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:  5.42 (0.20), residues: 1624
  helix:  4.24 (0.13), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.51 (0.33), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  67 
 TYR   0.014   0.002   TYR E  59 
 PHE   0.017   0.002   PHE G 152 
 TRP   0.010   0.001   TRP C 156 
 HIS   0.002   0.001   HIS B 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (13111)
  covalent geometry    : angle       0.45676 (17815)
  hydrogen bonds       : bond        0.04133 ( 1008)
  hydrogen bonds       : angle       3.07582 ( 2982)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 295
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
REVERT: C  134 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8501 (mttt)
REVERT: E   11 GLN cc_start: 0.8397 (mt0) cc_final: 0.8186 (mt0)
REVERT: F  133 LEU cc_start: 0.8954 (mm) cc_final: 0.8666 (mt)
REVERT: F  141 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7418 (mt-10)
  outliers start: 39
  outliers final: 17
  residues processed: 315
  average time/residue: 0.4935
  time to fit residues: 170.2993
Evaluate side-chains
  307 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 288
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue  141 GLU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain C residue  259 VAL
Chi-restraints excluded: chain D residue  193 GLU
Chi-restraints excluded: chain D residue  200 LYS
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain F residue  141 GLU
Chi-restraints excluded: chain F residue  160 ASN
Chi-restraints excluded: chain F residue  230 VAL
Chi-restraints excluded: chain G residue  134 LYS
Chi-restraints excluded: chain G residue  207 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 120 optimal weight:    1.9990
   chunk 48 optimal weight:    0.4980
   chunk 128 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9990
   chunk 79 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0370
   chunk 119 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 142 optimal weight:    0.7980
   chunk 91 optimal weight:    5.9990
   overall best weight:    0.6460

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

Flipped N/Q/H residues before XYZ refinement:
E 160 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.094351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.087322 restraints weight = 20897.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 1.14
r_work: 0.3132 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 2.83 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  13111  Z= 0.110
  Angle     :  0.465   7.355  17815  Z= 0.239
  Chirality :  0.032   0.164   1967
  Planarity :  0.003   0.040   2401
  Dihedral  :  3.046  12.143   1764
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 21.21 %
    Favored  : 76.56 %
  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:  5.51 (0.20), residues: 1624
  helix:  4.31 (0.13), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.53 (0.33), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  67 
 TYR   0.014   0.001   TYR E  59 
 PHE   0.017   0.002   PHE G 152 
 TRP   0.010   0.001   TRP C 156 
 HIS   0.002   0.001   HIS B 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (13111)
  covalent geometry    : angle       0.46544 (17815)
  hydrogen bonds       : bond        0.03993 ( 1008)
  hydrogen bonds       : angle       3.04540 ( 2982)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 298
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 THR cc_start: 0.8940 (p) cc_final: 0.8714 (p)
REVERT: C  134 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8494 (mttt)
REVERT: E   11 GLN cc_start: 0.8375 (mt0) cc_final: 0.8168 (mt0)
REVERT: F  133 LEU cc_start: 0.8961 (mm) cc_final: 0.8669 (mt)
REVERT: F  141 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7426 (mt-10)
  outliers start: 30
  outliers final: 14
  residues processed: 313
  average time/residue: 0.5041
  time to fit residues: 173.1108
Evaluate side-chains
  302 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 286
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue  141 GLU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain D residue  193 GLU
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain F residue  141 GLU
Chi-restraints excluded: chain F residue  160 ASN
Chi-restraints excluded: chain F residue  230 VAL
Chi-restraints excluded: chain F residue  254 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 148 optimal weight:    6.9990
   chunk 78 optimal weight:    0.0980
   chunk 4 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 139 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 128 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 56 optimal weight:    6.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
C  11 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.093094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.086060 restraints weight = 20987.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.14
r_work: 0.3108 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13111  Z= 0.132
  Angle     :  0.489   6.167  17815  Z= 0.253
  Chirality :  0.033   0.165   1967
  Planarity :  0.004   0.040   2401
  Dihedral  :  3.128  12.216   1764
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 20.91 %
    Favored  : 76.79 %
  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:  5.40 (0.20), residues: 1624
  helix:  4.22 (0.13), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.51 (0.33), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  67 
 TYR   0.017   0.002   TYR D  59 
 PHE   0.017   0.002   PHE B 152 
 TRP   0.012   0.002   TRP G 156 
 HIS   0.003   0.001   HIS B 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (13111)
  covalent geometry    : angle       0.48870 (17815)
  hydrogen bonds       : bond        0.04325 ( 1008)
  hydrogen bonds       : angle       3.07583 ( 2982)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 291
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 THR cc_start: 0.8943 (p) cc_final: 0.8710 (p)
REVERT: A  160 ASN cc_start: 0.9239 (OUTLIER) cc_final: 0.9006 (t0)
REVERT: C  134 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8515 (mttt)
REVERT: E   11 GLN cc_start: 0.8451 (mt0) cc_final: 0.8250 (mt0)
REVERT: F  141 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7437 (mt-10)
  outliers start: 31
  outliers final: 19
  residues processed: 304
  average time/residue: 0.5041
  time to fit residues: 167.8864
Evaluate side-chains
  301 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 279
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  160 ASN
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue  141 GLU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain C residue  259 VAL
Chi-restraints excluded: chain D residue   13 GLU
Chi-restraints excluded: chain D residue  193 GLU
Chi-restraints excluded: chain D residue  200 LYS
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain F residue  141 GLU
Chi-restraints excluded: chain F residue  160 ASN
Chi-restraints excluded: chain F residue  230 VAL
Chi-restraints excluded: chain F residue  254 GLU
Chi-restraints excluded: chain G residue  207 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 109 optimal weight:    6.9990
   chunk 77 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 152 optimal weight:    3.9990
   chunk 134 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 63 optimal weight:    0.6980
   chunk 150 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 143 optimal weight:    0.6980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
C 160 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.093811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.086784 restraints weight = 21058.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 1.15
r_work: 0.3122 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13111  Z= 0.116
  Angle     :  0.482   6.372  17815  Z= 0.249
  Chirality :  0.032   0.157   1967
  Planarity :  0.004   0.054   2401
  Dihedral  :  3.086  12.033   1764
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 21.65 %
    Favored  : 76.41 %
  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:  5.48 (0.20), residues: 1624
  helix:  4.28 (0.13), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.54 (0.33), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.000   ARG D 234 
 TYR   0.015   0.002   TYR E  59 
 PHE   0.016   0.002   PHE B 152 
 TRP   0.011   0.001   TRP C 156 
 HIS   0.002   0.001   HIS B 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (13111)
  covalent geometry    : angle       0.48203 (17815)
  hydrogen bonds       : bond        0.04108 ( 1008)
  hydrogen bonds       : angle       3.06279 ( 2982)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 292
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 THR cc_start: 0.8940 (p) cc_final: 0.8695 (p)
REVERT: C  134 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8516 (mttt)
REVERT: E   11 GLN cc_start: 0.8413 (mt0) cc_final: 0.8201 (mt0)
REVERT: F  141 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7424 (mt-10)
  outliers start: 26
  outliers final: 19
  residues processed: 302
  average time/residue: 0.5044
  time to fit residues: 166.9977
Evaluate side-chains
  307 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 286
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue  141 GLU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain D residue   13 GLU
Chi-restraints excluded: chain D residue  193 GLU
Chi-restraints excluded: chain D residue  200 LYS
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain F residue  141 GLU
Chi-restraints excluded: chain F residue  160 ASN
Chi-restraints excluded: chain F residue  230 VAL
Chi-restraints excluded: chain F residue  254 GLU
Chi-restraints excluded: chain F residue  257 GLU
Chi-restraints excluded: chain G residue  134 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 2 optimal weight:    0.0000
   chunk 12 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 69 optimal weight:   10.0000
   chunk 156 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 159 optimal weight:    3.9990
   chunk 93 optimal weight:    0.5980
   chunk 117 optimal weight:    0.2980
   overall best weight:    0.5784

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

Flipped N/Q/H residues before XYZ refinement:
C 244 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.094537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.087591 restraints weight = 20850.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 1.14
r_work: 0.3140 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 2.83 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  13111  Z= 0.109
  Angle     :  0.469   6.230  17815  Z= 0.242
  Chirality :  0.032   0.150   1967
  Planarity :  0.004   0.044   2401
  Dihedral  :  3.050  12.562   1764
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 21.88 %
    Favored  : 76.26 %
  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:  5.57 (0.20), residues: 1624
  helix:  4.34 (0.13), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.58 (0.33), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG D 234 
 TYR   0.015   0.001   TYR D  59 
 PHE   0.017   0.002   PHE B 152 
 TRP   0.010   0.001   TRP C 156 
 HIS   0.002   0.001   HIS B 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (13111)
  covalent geometry    : angle       0.46912 (17815)
  hydrogen bonds       : bond        0.03898 ( 1008)
  hydrogen bonds       : angle       3.03582 ( 2982)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4535.10 seconds
wall clock time: 77 minutes 48.97 seconds (4668.97 seconds total)