Starting phenix.real_space_refine
on Wed Jul 30 16:01:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p0z_13153/07_2025/7p0z_13153.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p0z_13153/07_2025/7p0z_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_13153/07_2025/7p0z_13153.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p0z_13153/07_2025/7p0z_13153.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p0z_13153/07_2025/7p0z_13153.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p0z_13153/07_2025/7p0z_13153.cif"
  }
  resolution = 2.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.246 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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:
    C, B, E, D, G, F
  Time building chain proxies: 5.00, per 1000 atoms: 0.39
  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: 3.73
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  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: 1.16
  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: 4.00

  Time building geometry restraints manager: 4.34 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: 0.11
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.850
  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:          0.560
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     29.360
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:14.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.050
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.017   0.004   TRP D 156 
 HIS   0.009   0.004   HIS A 223 
 PHE   0.027   0.004   PHE D 159 
 TYR   0.028   0.006   TYR F  81 
 ARG   0.012   0.002   ARG A 165 

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

*********************** 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  : 1.405 
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: 1.5356
  time to fit residues: 655.9416
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  : 1.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 135 optimal weight:    0.9980
   chunk 122 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 126 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 146 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3326 r_free = 0.3326 target = 0.092128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.084390 restraints weight = 20745.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.20
r_work: 0.3055 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  13111  Z= 0.148
  Angle     :  0.539   8.595  17815  Z= 0.280
  Chirality :  0.034   0.128   1967
  Planarity :  0.004   0.036   2401
  Dihedral  :  3.684  13.532   1764
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 13.24 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.81 (0.20), residues: 1624
  helix:  3.10 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop :  0.80 (0.30), residues: 420

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05460 ( 1008)
  hydrogen bonds       : angle       3.50385 ( 2982)
  covalent geometry    : bond        0.00323 (13111)
  covalent geometry    : angle       0.53930 (17815)

*********************** 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
  339 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 300
  time to evaluate  : 2.779 
Fit side-chains
REVERT: B   11 GLN cc_start: 0.8456 (mt0) cc_final: 0.8247 (mt0)
REVERT: E  257 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7400 (mt-10)
REVERT: F  133 LEU cc_start: 0.8967 (mm) cc_final: 0.8701 (mt)
REVERT: F  201 LEU cc_start: 0.9149 (mt) cc_final: 0.8949 (mt)
  outliers start: 39
  outliers final: 12
  residues processed: 313
  average time/residue: 1.7355
  time to fit residues: 592.3031
Evaluate side-chains
  296 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 284
  time to evaluate  : 1.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue  230 VAL
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 134 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 109 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 108 optimal weight:    0.8980
   chunk 68 optimal weight:    4.9990
   chunk 127 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 122 optimal weight:   10.0000
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.091798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.084693 restraints weight = 20948.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.15
r_work: 0.3086 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 2.83 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.2144

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= 0.133
  Angle     :  0.476   5.884  17815  Z= 0.248
  Chirality :  0.033   0.129   1967
  Planarity :  0.004   0.035   2401
  Dihedral  :  3.401  13.196   1764
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 14.58 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.68 (0.20), residues: 1624
  helix:  3.70 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.20 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D 156 
 HIS   0.004   0.001   HIS B 223 
 PHE   0.016   0.002   PHE G 152 
 TYR   0.017   0.002   TYR B  59 
 ARG   0.004   0.000   ARG D  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04918 ( 1008)
  hydrogen bonds       : angle       3.26999 ( 2982)
  covalent geometry    : bond        0.00291 (13111)
  covalent geometry    : angle       0.47553 (17815)

*********************** 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
  333 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 288
  time to evaluate  : 1.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   11 GLN cc_start: 0.8425 (mt0) cc_final: 0.8219 (mt0)
REVERT: C  134 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8499 (mttt)
REVERT: C  141 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7418 (mt-10)
REVERT: C  221 ARG cc_start: 0.7907 (ptp90) cc_final: 0.7571 (ptp90)
REVERT: C  257 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7283 (mt-10)
REVERT: D  221 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7708 (ptp90)
REVERT: E   25 MET cc_start: 0.8818 (mtp) cc_final: 0.8606 (mtm)
REVERT: E  192 LYS cc_start: 0.9125 (ttpt) cc_final: 0.8878 (ttpt)
REVERT: F  133 LEU cc_start: 0.8926 (mm) cc_final: 0.8665 (mt)
REVERT: F  141 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7438 (mt-10)
REVERT: G  193 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8129 (mp0)
  outliers start: 45
  outliers final: 19
  residues processed: 309
  average time/residue: 1.1467
  time to fit residues: 388.7704
Evaluate side-chains
  297 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 273
  time to evaluate  : 1.526 
-------------------------------------------------------------------------------
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  230 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  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  205 LEU
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  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  193 GLU
Chi-restraints excluded: chain G residue  259 VAL
Chi-restraints excluded: chain G residue  276 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 148 optimal weight:    7.9990
   chunk 66 optimal weight:    6.9990
   chunk 151 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 55 optimal weight:    7.9990
   chunk 147 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 68 optimal weight:    0.0270
   chunk 35 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    2.4046

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

Flipped N/Q/H residues before XYZ refinement:
A 253 GLN
** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 264 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.090542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.083452 restraints weight = 20858.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.11
r_work: 0.3059 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  13111  Z= 0.202
  Angle     :  0.546   5.621  17815  Z= 0.284
  Chirality :  0.036   0.130   1967
  Planarity :  0.004   0.036   2401
  Dihedral  :  3.531  13.297   1764
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 15.40 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.59 (0.20), residues: 1624
  helix:  3.60 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.30 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP G 156 
 HIS   0.006   0.002   HIS G 223 
 PHE   0.018   0.002   PHE A 159 
 TYR   0.018   0.003   TYR A  59 
 ARG   0.007   0.000   ARG D  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05486 ( 1008)
  hydrogen bonds       : angle       3.32677 ( 2982)
  covalent geometry    : bond        0.00467 (13111)
  covalent geometry    : angle       0.54571 (17815)

*********************** 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
  335 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 271
  time to evaluate  : 1.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   11 GLN cc_start: 0.8403 (mt0) cc_final: 0.8195 (mt0)
REVERT: C  134 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8466 (mttt)
REVERT: C  141 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7416 (mt-10)
REVERT: C  257 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7283 (mt-10)
REVERT: D  221 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7680 (ptp90)
REVERT: E   11 GLN cc_start: 0.8476 (mt0) cc_final: 0.8253 (mt0)
REVERT: F  133 LEU cc_start: 0.8943 (mm) cc_final: 0.8648 (mt)
REVERT: F  141 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7475 (mt-10)
REVERT: G  193 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8157 (mp0)
  outliers start: 64
  outliers final: 28
  residues processed: 306
  average time/residue: 1.3174
  time to fit residues: 439.3176
Evaluate side-chains
  301 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 268
  time to evaluate  : 1.510 
-------------------------------------------------------------------------------
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  230 VAL
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  133 LEU
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   40 THR
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  207 LYS
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  221 ARG
Chi-restraints excluded: chain D residue  230 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 E residue  281 ILE
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   40 THR
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
Chi-restraints excluded: chain G residue  276 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 106 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 154 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
C 253 GLN
G 264 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.090551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.083441 restraints weight = 20938.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.12
r_work: 0.3058 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  13111  Z= 0.198
  Angle     :  0.542   5.626  17815  Z= 0.282
  Chirality :  0.036   0.131   1967
  Planarity :  0.004   0.036   2401
  Dihedral  :  3.529  13.335   1764
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 17.63 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.60 (0.20), residues: 1624
  helix:  3.60 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.33 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 156 
 HIS   0.005   0.002   HIS G 223 
 PHE   0.017   0.002   PHE G 152 
 TYR   0.019   0.003   TYR A  59 
 ARG   0.005   0.000   ARG D  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05440 ( 1008)
  hydrogen bonds       : angle       3.34875 ( 2982)
  covalent geometry    : bond        0.00458 (13111)
  covalent geometry    : angle       0.54212 (17815)

*********************** 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
  329 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 272
  time to evaluate  : 6.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  134 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8491 (mttt)
REVERT: C  141 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7384 (mt-10)
REVERT: C  257 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7311 (mt-10)
REVERT: D  221 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7661 (ptp90)
REVERT: E   11 GLN cc_start: 0.8490 (mt0) cc_final: 0.8262 (mt0)
REVERT: F  141 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7451 (mt-10)
REVERT: G  193 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8166 (mp0)
  outliers start: 57
  outliers final: 31
  residues processed: 302
  average time/residue: 1.5789
  time to fit residues: 521.9465
Evaluate side-chains
  301 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 265
  time to evaluate  : 1.532 
-------------------------------------------------------------------------------
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  230 VAL
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  133 LEU
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   40 THR
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  193 GLU
Chi-restraints excluded: chain D residue  221 ARG
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain D residue  276 LYS
Chi-restraints excluded: chain E residue   21 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 E residue  281 ILE
Chi-restraints excluded: chain F residue  132 ASP
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   40 THR
Chi-restraints excluded: chain G residue  193 GLU
Chi-restraints excluded: chain G residue  205 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 87 optimal weight:    0.0060
   chunk 130 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 94 optimal weight:    0.0870
   chunk 24 optimal weight:    0.9990
   chunk 151 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 58 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 102 optimal weight:    1.9990
   overall best weight:    0.4174

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

Flipped N/Q/H residues before XYZ refinement:
A  55 ASN
G 264 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.093860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.086745 restraints weight = 21260.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 1.16
r_work: 0.3117 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  13111  Z= 0.108
  Angle     :  0.447   5.338  17815  Z= 0.234
  Chirality :  0.032   0.124   1967
  Planarity :  0.003   0.036   2401
  Dihedral  :  3.165  11.949   1764
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 19.27 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.28 (0.20), residues: 1624
  helix:  4.14 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.43 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 156 
 HIS   0.001   0.000   HIS B 223 
 PHE   0.017   0.002   PHE G 152 
 TYR   0.013   0.001   TYR E  59 
 ARG   0.005   0.000   ARG D  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04251 ( 1008)
  hydrogen bonds       : angle       3.18527 ( 2982)
  covalent geometry    : bond        0.00225 (13111)
  covalent geometry    : angle       0.44657 (17815)

*********************** 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
  348 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 309
  time to evaluate  : 2.021 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  134 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8480 (mttt)
REVERT: E   11 GLN cc_start: 0.8396 (mt0) cc_final: 0.8179 (mt0)
REVERT: E  141 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7329 (mt-10)
REVERT: F  141 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7320 (mt-10)
  outliers start: 39
  outliers final: 14
  residues processed: 327
  average time/residue: 1.1674
  time to fit residues: 420.0659
Evaluate side-chains
  297 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 280
  time to evaluate  : 1.468 
-------------------------------------------------------------------------------
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  260 LEU
Chi-restraints excluded: chain B residue  141 GLU
Chi-restraints excluded: chain B residue  205 LEU
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  141 GLU
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain F residue  133 LEU
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 F residue  254 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 141 optimal weight:    5.9990
   chunk 159 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 101 optimal weight:    7.9990
   chunk 130 optimal weight:    1.9990
   chunk 84 optimal weight:    6.9990
   chunk 142 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    1.7990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.091060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.084033 restraints weight = 20913.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.15
r_work: 0.3075 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13111  Z= 0.168
  Angle     :  0.516   5.913  17815  Z= 0.268
  Chirality :  0.035   0.173   1967
  Planarity :  0.004   0.035   2401
  Dihedral  :  3.303  12.514   1764
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.31 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.07 (0.20), residues: 1624
  helix:  3.97 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.41 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP G 156 
 HIS   0.005   0.002   HIS B 223 
 PHE   0.017   0.002   PHE G 152 
 TYR   0.018   0.002   TYR E  59 
 ARG   0.003   0.000   ARG E 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04898 ( 1008)
  hydrogen bonds       : angle       3.21710 ( 2982)
  covalent geometry    : bond        0.00389 (13111)
  covalent geometry    : angle       0.51559 (17815)

*********************** 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
  321 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 282
  time to evaluate  : 1.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 THR cc_start: 0.8968 (p) cc_final: 0.8748 (p)
REVERT: A  160 ASN cc_start: 0.9280 (OUTLIER) cc_final: 0.9024 (t0)
REVERT: C  134 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8513 (mttt)
REVERT: F  141 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7462 (mt-10)
  outliers start: 39
  outliers final: 20
  residues processed: 307
  average time/residue: 1.0721
  time to fit residues: 361.4825
Evaluate side-chains
  298 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 275
  time to evaluate  : 1.439 
-------------------------------------------------------------------------------
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  160 ASN
Chi-restraints excluded: chain A residue  281 ILE
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 B residue  265 THR
Chi-restraints excluded: chain C residue  134 LYS
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  141 GLU
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain E residue  265 THR
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain F residue  133 LEU
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 146 optimal weight:    5.9990
   chunk 102 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 95 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 132 optimal weight:    6.9990
   chunk 158 optimal weight:    0.8980
   chunk 144 optimal weight:    1.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
F 253 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.090188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.083090 restraints weight = 20999.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 1.15
r_work: 0.3051 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  13111  Z= 0.212
  Angle     :  0.567   7.371  17815  Z= 0.294
  Chirality :  0.037   0.169   1967
  Planarity :  0.005   0.035   2401
  Dihedral  :  3.498  13.088   1764
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.54 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.72 (0.20), residues: 1624
  helix:  3.69 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.39 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP G 156 
 HIS   0.006   0.002   HIS B 223 
 PHE   0.018   0.003   PHE A 159 
 TYR   0.017   0.003   TYR A  59 
 ARG   0.005   0.001   ARG D  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05405 ( 1008)
  hydrogen bonds       : angle       3.32773 ( 2982)
  covalent geometry    : bond        0.00494 (13111)
  covalent geometry    : angle       0.56719 (17815)

*********************** 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
  316 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 276
  time to evaluate  : 1.431 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7322 (mt-10)
REVERT: A  160 ASN cc_start: 0.9319 (OUTLIER) cc_final: 0.9018 (t0)
REVERT: C  134 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8470 (mttt)
REVERT: C  226 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8426 (tt)
REVERT: C  257 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7402 (tt0)
REVERT: F  141 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7453 (mt-10)
  outliers start: 40
  outliers final: 22
  residues processed: 297
  average time/residue: 1.0796
  time to fit residues: 352.6680
Evaluate side-chains
  300 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 273
  time to evaluate  : 1.596 
-------------------------------------------------------------------------------
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  160 ASN
Chi-restraints excluded: chain A residue  281 ILE
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 B residue  265 THR
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  207 LYS
Chi-restraints excluded: chain C residue  226 LEU
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain C residue  276 LYS
Chi-restraints excluded: chain D residue   13 GLU
Chi-restraints excluded: chain D residue  193 GLU
Chi-restraints excluded: chain D residue  230 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 E residue  265 THR
Chi-restraints excluded: chain F residue  133 LEU
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  276 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 113 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 154 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 128 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0070
   chunk 18 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.5604

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

Flipped N/Q/H residues before XYZ refinement:
A  55 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.091365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.084292 restraints weight = 20989.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 1.16
r_work: 0.3069 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13111  Z= 0.155
  Angle     :  0.519   5.930  17815  Z= 0.269
  Chirality :  0.034   0.174   1967
  Planarity :  0.004   0.038   2401
  Dihedral  :  3.376  12.715   1764
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 21.28 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.91 (0.20), residues: 1624
  helix:  3.83 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.42 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 156 
 HIS   0.004   0.001   HIS B 223 
 PHE   0.017   0.002   PHE G 152 
 TYR   0.018   0.002   TYR A  59 
 ARG   0.016   0.000   ARG E 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04931 ( 1008)
  hydrogen bonds       : angle       3.28159 ( 2982)
  covalent geometry    : bond        0.00357 (13111)
  covalent geometry    : angle       0.51906 (17815)

*********************** 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
  307 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 274
  time to evaluate  : 1.549 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 THR cc_start: 0.8968 (p) cc_final: 0.8731 (p)
REVERT: A  141 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7309 (mt-10)
REVERT: A  160 ASN cc_start: 0.9277 (OUTLIER) cc_final: 0.8987 (t0)
REVERT: B  237 LYS cc_start: 0.7262 (tppt) cc_final: 0.7032 (tptt)
REVERT: C  134 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8476 (mttt)
REVERT: C  226 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8392 (tt)
REVERT: F  141 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7440 (mt-10)
REVERT: F  262 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7984 (tp30)
  outliers start: 33
  outliers final: 21
  residues processed: 291
  average time/residue: 1.0954
  time to fit residues: 350.4172
Evaluate side-chains
  297 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 270
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
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  160 ASN
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  281 ILE
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  226 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  230 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 E residue  281 ILE
Chi-restraints excluded: chain F residue  132 ASP
Chi-restraints excluded: chain F residue  133 LEU
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  262 GLU
Chi-restraints excluded: chain G residue  207 LYS
Chi-restraints excluded: chain G residue  276 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 28 optimal weight:    0.7980
   chunk 101 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 112 optimal weight:    0.8980
   chunk 148 optimal weight:    5.9990
   chunk 139 optimal weight:    0.9980
   chunk 7 optimal weight:    8.9990
   chunk 137 optimal weight:    2.9990
   chunk 120 optimal weight:    3.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A  55 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.092625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.085552 restraints weight = 20891.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.15
r_work: 0.3099 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.2688

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= 0.123
  Angle     :  0.488   5.623  17815  Z= 0.253
  Chirality :  0.033   0.164   1967
  Planarity :  0.004   0.040   2401
  Dihedral  :  3.233  13.831   1764
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 22.02 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.19 (0.20), residues: 1624
  helix:  4.06 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.46 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 156 
 HIS   0.003   0.001   HIS B 223 
 PHE   0.017   0.002   PHE G 152 
 TYR   0.016   0.002   TYR A  59 
 ARG   0.013   0.000   ARG E 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04445 ( 1008)
  hydrogen bonds       : angle       3.20950 ( 2982)
  covalent geometry    : bond        0.00278 (13111)
  covalent geometry    : angle       0.48774 (17815)

********************** 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
  308 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 282
  time to evaluate  : 1.444 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 THR cc_start: 0.8948 (p) cc_final: 0.8711 (p)
REVERT: C  134 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8494 (mttt)
REVERT: E  141 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7405 (mt-10)
REVERT: F  141 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7360 (mt-10)
  outliers start: 26
  outliers final: 15
  residues processed: 298
  average time/residue: 1.1350
  time to fit residues: 370.5871
Evaluate side-chains
  290 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 272
  time to evaluate  : 1.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 LEU
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  230 VAL
Chi-restraints excluded: chain C residue  276 LYS
Chi-restraints excluded: chain D residue   13 GLU
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  141 GLU
Chi-restraints excluded: chain E residue  230 VAL
Chi-restraints excluded: chain F residue  133 LEU
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  276 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 126 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 119 optimal weight:    4.9990
   chunk 112 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 152 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 144 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
C  11 GLN
D 160 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.092303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.085358 restraints weight = 20933.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.14
r_work: 0.3101 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13111  Z= 0.125
  Angle     :  0.496   6.525  17815  Z= 0.255
  Chirality :  0.033   0.161   1967
  Planarity :  0.004   0.042   2401
  Dihedral  :  3.216  13.944   1764
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 22.17 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.21 (0.20), residues: 1624
  helix:  4.07 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop :  1.49 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 156 
 HIS   0.003   0.001   HIS B 223 
 PHE   0.017   0.002   PHE G 152 
 TYR   0.015   0.002   TYR A  59 
 ARG   0.012   0.000   ARG E 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04400 ( 1008)
  hydrogen bonds       : angle       3.18854 ( 2982)
  covalent geometry    : bond        0.00283 (13111)
  covalent geometry    : angle       0.49579 (17815)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10214.99 seconds
wall clock time: 182 minutes 11.42 seconds (10931.42 seconds total)