Starting phenix.real_space_refine
on Fri Aug 22 15:35:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ur5_42482/08_2025/8ur5_42482.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ur5_42482/08_2025/8ur5_42482.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ur5_42482/08_2025/8ur5_42482.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ur5_42482/08_2025/8ur5_42482.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ur5_42482/08_2025/8ur5_42482.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ur5_42482/08_2025/8ur5_42482.map"
  }
  resolution = 3.7
  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=   0.013 sd=   0.124
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      18      5.16       5
     C    3282      2.51       5
     N     858      2.21       5
     O     831      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4989
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1607
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 84}
          Link IDs: {'PTRANS': 14, 'TRANS': 217}
          Unresolved non-hydrogen bonds: 238
          Unresolved non-hydrogen angles: 293
          Unresolved non-hydrogen dihedrals: 185
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 19, 'ASN:plan1': 11, 'ASP:plan': 4, 'ARG:plan': 3, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 150
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 1.10, per 1000 atoms: 0.22
  Number of scatterers: 4989
  At special positions: 0
  Unit cell: (87.1141, 82.8298, 74.2612, 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      18     16.00
     O     831      8.00
     N     858      7.00
     C    3282      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  59 " - pdb=" SG  CYS A  71 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A  94 " - pdb=" SG  CYS A 139 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 107 " - pdb=" SG  CYS A 271 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B  59 " - pdb=" SG  CYS B  71 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C  59 " - pdb=" SG  CYS C  71 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B  94 " - pdb=" SG  CYS B 139 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  94 " - pdb=" SG  CYS C 139 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 107 " - pdb=" SG  CYS B 271 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 107 " - pdb=" SG  CYS C 271 " distance=2.05

  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
  Links applied
    NAG-ASN
      " NAG A 501 " - " ASN A 163 "
      " NAG A 502 " - " ASN A 129 "
      " NAG A 503 " - " ASN A  58 "
      " NAG A 504 " - " ASN A  91 "
      " NAG B 501 " - " ASN B 163 "
      " NAG B 502 " - " ASN B 129 "
      " NAG B 503 " - " ASN B  58 "
      " NAG B 504 " - " ASN B  91 "
      " NAG C 501 " - " ASN C 163 "
      " NAG C 502 " - " ASN C 129 "
      " NAG C 503 " - " ASN C  58 "
      " NAG C 504 " - " ASN C  91 "
  Time building additional restraints: 0.41
  Conformation dependent library (CDL) restraints added in 163.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1284

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 15 sheets defined
      16.8% alpha, 28.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 67
    Processing helix  chain 'A' and resid 101 through 106
    Processing helix  chain 'A' and resid 122 through 127
      removed outlier: 3.996A  pdb=" N   TRP A 127 " --> pdb=" O   LYS A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 196
    Processing helix  chain 'A' and resid 275 through 283
    Processing helix  chain 'B' and resid 60 through 67
    Processing helix  chain 'B' and resid 101 through 106
    Processing helix  chain 'B' and resid 122 through 127
      removed outlier: 3.996A  pdb=" N   TRP B 127 " --> pdb=" O   LYS B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 196
    Processing helix  chain 'B' and resid 275 through 283
    Processing helix  chain 'C' and resid 60 through 67
    Processing helix  chain 'C' and resid 101 through 106
    Processing helix  chain 'C' and resid 122 through 127
      removed outlier: 3.997A  pdb=" N   TRP C 127 " --> pdb=" O   LYS C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 187 through 196
    Processing helix  chain 'C' and resid 275 through 283
    Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54
    Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 119
      removed outlier: 6.625A  pdb=" N   TYR A 256 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU A 179 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU A 175 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   LEU A 179 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 119
      removed outlier: 6.625A  pdb=" N   TYR A 256 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU A 179 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU A 175 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141
    Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 169
    Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54
    Processing sheet with id=AA7, first strand: chain 'B' and resid 115 through 119
      removed outlier: 6.625A  pdb=" N   TYR B 256 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU B 179 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU B 175 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   LEU B 179 " --> pdb=" O   PRO B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 119
      removed outlier: 6.625A  pdb=" N   TYR B 256 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU B 179 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU B 175 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 141
    Processing sheet with id=AB1, first strand: chain 'B' and resid 164 through 169
    Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AB3, first strand: chain 'C' and resid 115 through 119
      removed outlier: 6.624A  pdb=" N   TYR C 256 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU C 179 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLU C 175 " --> pdb=" O   LEU C 260 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   LEU C 179 " --> pdb=" O   PRO C 254 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 115 through 119
      removed outlier: 6.624A  pdb=" N   TYR C 256 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU C 179 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLU C 175 " --> pdb=" O   LEU C 260 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 140 through 141
    Processing sheet with id=AB6, first strand: chain 'C' and resid 164 through 169

    189 hydrogen bonds defined for protein.
    531 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.65

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 753
        1.31 -     1.44: 1533
        1.44 -     1.57: 2841
        1.57 -     1.69: 9
        1.69 -     1.82: 18
  Bond restraints: 5154
  Sorted by residual:
  bond pdb=" C   ARG C 229 "
       pdb=" O   ARG C 229 "
    ideal  model  delta    sigma   weight residual
    1.234  1.185  0.048 1.24e-02 6.50e+03 1.53e+01
  bond pdb=" C   ARG B 229 "
       pdb=" O   ARG B 229 "
    ideal  model  delta    sigma   weight residual
    1.234  1.186  0.048 1.24e-02 6.50e+03 1.47e+01
  bond pdb=" C   ARG A 229 "
       pdb=" O   ARG A 229 "
    ideal  model  delta    sigma   weight residual
    1.234  1.187  0.047 1.24e-02 6.50e+03 1.45e+01
  bond pdb=" CA  ARG B 229 "
       pdb=" CB  ARG B 229 "
    ideal  model  delta    sigma   weight residual
    1.533  1.474  0.059 1.66e-02 3.63e+03 1.26e+01
  bond pdb=" CA  ARG A 229 "
       pdb=" CB  ARG A 229 "
    ideal  model  delta    sigma   weight residual
    1.533  1.474  0.059 1.66e-02 3.63e+03 1.26e+01
  ... (remaining 5149 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 5765
        1.56 -     3.11: 1047
        3.11 -     4.67: 169
        4.67 -     6.23: 93
        6.23 -     7.79: 45
  Bond angle restraints: 7119
  Sorted by residual:
  angle pdb=" C   HIS B 184 "
        pdb=" N   PRO B 185 "
        pdb=" CA  PRO B 185 "
      ideal   model   delta    sigma   weight residual
     119.66  126.85   -7.19 7.30e-01 1.88e+00 9.71e+01
  angle pdb=" C   HIS A 184 "
        pdb=" N   PRO A 185 "
        pdb=" CA  PRO A 185 "
      ideal   model   delta    sigma   weight residual
     119.66  126.82   -7.16 7.30e-01 1.88e+00 9.63e+01
  angle pdb=" C   HIS C 184 "
        pdb=" N   PRO C 185 "
        pdb=" CA  PRO C 185 "
      ideal   model   delta    sigma   weight residual
     119.66  126.80   -7.14 7.30e-01 1.88e+00 9.56e+01
  angle pdb=" C   ASN A  88 "
        pdb=" N   PRO A  89 "
        pdb=" CA  PRO A  89 "
      ideal   model   delta    sigma   weight residual
     119.85  126.77   -6.92 1.01e+00 9.80e-01 4.70e+01
  angle pdb=" C   ASN B  88 "
        pdb=" N   PRO B  89 "
        pdb=" CA  PRO B  89 "
      ideal   model   delta    sigma   weight residual
     119.85  126.76   -6.91 1.01e+00 9.80e-01 4.68e+01
  ... (remaining 7114 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.28: 2852
       12.28 -    24.55: 115
       24.55 -    36.83: 57
       36.83 -    49.10: 18
       49.10 -    61.38: 9
  Dihedral angle restraints: 3051
    sinusoidal: 1038
      harmonic: 2013
  Sorted by residual:
  dihedral pdb=" CB  CYS B  94 "
           pdb=" SG  CYS B  94 "
           pdb=" SG  CYS B 139 "
           pdb=" CB  CYS B 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.41  -37.41     1      1.00e+01 1.00e-02 1.97e+01
  dihedral pdb=" CB  CYS C  94 "
           pdb=" SG  CYS C  94 "
           pdb=" SG  CYS C 139 "
           pdb=" CB  CYS C 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.40  -37.40     1      1.00e+01 1.00e-02 1.97e+01
  dihedral pdb=" CB  CYS A  94 "
           pdb=" SG  CYS A  94 "
           pdb=" SG  CYS A 139 "
           pdb=" CB  CYS A 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.38  -37.38     1      1.00e+01 1.00e-02 1.97e+01
  ... (remaining 3048 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 529
       0.067 -    0.133: 230
       0.133 -    0.200: 27
       0.200 -    0.267: 33
       0.267 -    0.334: 15
  Chirality restraints: 834
  Sorted by residual:
  chirality pdb=" C2  NAG B 501 "
            pdb=" C1  NAG B 501 "
            pdb=" C3  NAG B 501 "
            pdb=" N2  NAG B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.83    0.33 2.00e-01 2.50e+01 2.78e+00
  chirality pdb=" C2  NAG C 501 "
            pdb=" C1  NAG C 501 "
            pdb=" C3  NAG C 501 "
            pdb=" N2  NAG C 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.83    0.33 2.00e-01 2.50e+01 2.78e+00
  chirality pdb=" C2  NAG A 501 "
            pdb=" C1  NAG A 501 "
            pdb=" C3  NAG A 501 "
            pdb=" N2  NAG A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.82    0.33 2.00e-01 2.50e+01 2.76e+00
  ... (remaining 831 not shown)

  Planarity restraints: 912
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C  92 "   -0.014 2.00e-02 2.50e+03   2.89e-02 8.38e+00
        pdb=" C   GLY C  92 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLY C  92 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   THR C  93 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  92 "   -0.014 2.00e-02 2.50e+03   2.89e-02 8.35e+00
        pdb=" C   GLY A  92 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLY A  92 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   THR A  93 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B  92 "    0.014 2.00e-02 2.50e+03   2.88e-02 8.31e+00
        pdb=" C   GLY B  92 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   GLY B  92 "    0.019 2.00e-02 2.50e+03
        pdb=" N   THR B  93 "    0.017 2.00e-02 2.50e+03
  ... (remaining 909 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 2582
        2.99 -     3.47: 4265
        3.47 -     3.94: 7952
        3.94 -     4.42: 8647
        4.42 -     4.90: 14219
  Nonbonded interactions: 37665
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 163 "
            pdb=" N2  NAG B 501 "
     model   vdw
     2.510 3.120
  nonbonded pdb=" OD1 ASN A 163 "
            pdb=" N2  NAG A 501 "
     model   vdw
     2.510 3.120
  nonbonded pdb=" OD1 ASN C 163 "
            pdb=" N2  NAG C 501 "
     model   vdw
     2.510 3.120
  nonbonded pdb=" O   ILE A 275 "
            pdb=" N   GLU A 278 "
     model   vdw
     2.541 3.120
  nonbonded pdb=" O   ILE B 275 "
            pdb=" N   GLU B 278 "
     model   vdw
     2.541 3.120
  ... (remaining 37660 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.080
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
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      :  0.011   0.075   5175  Z= 0.662
  Angle     :  1.456   7.787   7173  Z= 1.010
  Chirality :  0.089   0.334    834
  Planarity :  0.005   0.029    900
  Dihedral  :  9.297  51.962   1740
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.35 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  3.42 %
    Favored  : 94.87 %
  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 aren not related in a simple way.
  whole: -0.71 (0.29), residues: 690
  helix: -2.02 (0.42), residues: 117
  sheet:  2.31 (0.34), residues: 171
  loop : -1.32 (0.26), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 229 
 TYR   0.027   0.004   TYR B 195 
 PHE   0.010   0.002   PHE C 115 
 TRP   0.013   0.003   TRP B  80 
 HIS   0.004   0.001   HIS C 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.01061 ( 5154)
  covalent geometry    : angle       1.44711 ( 7119)
  SS BOND              : bond        0.01609 (    9)
  SS BOND              : angle       1.95828 (   18)
  hydrogen bonds       : bond        0.17864 (  168)
  hydrogen bonds       : angle       9.38373 (  531)
  link_NAG-ASN         : bond        0.05884 (   12)
  link_NAG-ASN         : angle       2.50903 (   36)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 166
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A  229 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7726 (mtm110)
REVERT: A  230 ILE cc_start: 0.9278 (tt) cc_final: 0.9013 (tt)
REVERT: A  256 TYR cc_start: 0.8142 (m-80) cc_final: 0.7753 (m-10)
REVERT: B  229 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7723 (mtm110)
REVERT: B  256 TYR cc_start: 0.7999 (m-80) cc_final: 0.7524 (m-10)
REVERT: C  155 THR cc_start: 0.6919 (p) cc_final: 0.6688 (t)
REVERT: C  229 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7594 (mtm110)
REVERT: C  256 TYR cc_start: 0.7957 (m-80) cc_final: 0.7540 (m-10)
  outliers start: 6
  outliers final: 1
  residues processed: 170
  average time/residue: 0.0895
  time to fit residues: 18.2912
Evaluate side-chains
  106 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  229 ARG
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain C residue  229 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    0.0270
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0870
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0470
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.4114

-------------------------------------------------------------------------------
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 = 0.3955 r_free = 0.3955 target = 0.168874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.132575 restraints weight = 8280.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.135632 restraints weight = 5842.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.137701 restraints weight = 4695.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.138641 restraints weight = 4143.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.138641 restraints weight = 3835.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.2778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   5175  Z= 0.147
  Angle     :  0.839  20.632   7173  Z= 0.393
  Chirality :  0.054   0.614    834
  Planarity :  0.005   0.022    900
  Dihedral  :  6.995  57.161   1012
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.04 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 16.81 %
    Favored  : 78.63 %
  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 aren not related in a simple way.
  whole:  0.06 (0.31), residues: 690
  helix: -1.26 (0.49), residues: 117
  sheet:  2.00 (0.35), residues: 180
  loop : -0.48 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 106 
 TYR   0.014   0.002   TYR B  82 
 PHE   0.024   0.002   PHE C 147 
 TRP   0.009   0.001   TRP A 153 
 HIS   0.004   0.001   HIS C 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 5154)
  covalent geometry    : angle       0.69719 ( 7119)
  SS BOND              : bond        0.00656 (    9)
  SS BOND              : angle       2.89765 (   18)
  hydrogen bonds       : bond        0.04817 (  168)
  hydrogen bonds       : angle       7.34813 (  531)
  link_NAG-ASN         : bond        0.00787 (   12)
  link_NAG-ASN         : angle       6.33189 (   36)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8190 (t80) cc_final: 0.7831 (t80)
REVERT: A  224 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.7592 (ttm170)
REVERT: A  229 ARG cc_start: 0.8342 (ttm170) cc_final: 0.7629 (mtm110)
REVERT: A  256 TYR cc_start: 0.8660 (m-80) cc_final: 0.8139 (m-10)
REVERT: B  191 GLN cc_start: 0.7840 (tp40) cc_final: 0.7324 (tp40)
REVERT: B  229 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7754 (mtm110)
REVERT: B  256 TYR cc_start: 0.8526 (m-80) cc_final: 0.7978 (m-10)
REVERT: C  155 THR cc_start: 0.7302 (p) cc_final: 0.6791 (t)
REVERT: C  229 ARG cc_start: 0.8744 (ttm170) cc_final: 0.7569 (mtm110)
REVERT: C  232 TYR cc_start: 0.8496 (m-80) cc_final: 0.8263 (m-10)
REVERT: C  256 TYR cc_start: 0.8373 (m-80) cc_final: 0.8089 (m-10)
  outliers start: 16
  outliers final: 8
  residues processed: 128
  average time/residue: 0.0793
  time to fit residues: 12.6302
Evaluate side-chains
  114 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  236 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 65 optimal weight:    8.9990
   chunk 57 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 21 optimal weight:    9.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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 = 0.3887 r_free = 0.3887 target = 0.163842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.130334 restraints weight = 8056.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.130060 restraints weight = 8675.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.131121 restraints weight = 7112.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.131410 restraints weight = 6099.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.131682 restraints weight = 5495.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.3539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5175  Z= 0.182
  Angle     :  0.797  20.645   7173  Z= 0.372
  Chirality :  0.052   0.533    834
  Planarity :  0.004   0.025    900
  Dihedral  :  6.150  53.514   1003
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.62 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 18.80 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

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 aren not related in a simple way.
  whole: -0.11 (0.31), residues: 690
  helix: -1.16 (0.49), residues: 114
  sheet:  1.29 (0.35), residues: 198
  loop : -0.44 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 106 
 TYR   0.016   0.002   TYR C 168 
 PHE   0.023   0.002   PHE C 118 
 TRP   0.017   0.002   TRP A 153 
 HIS   0.004   0.001   HIS C 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 5154)
  covalent geometry    : angle       0.67710 ( 7119)
  SS BOND              : bond        0.00772 (    9)
  SS BOND              : angle       2.54532 (   18)
  hydrogen bonds       : bond        0.04288 (  168)
  hydrogen bonds       : angle       6.72355 (  531)
  link_NAG-ASN         : bond        0.01631 (   12)
  link_NAG-ASN         : angle       5.72381 (   36)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A  229 ARG cc_start: 0.8309 (ttm170) cc_final: 0.7938 (mtm110)
REVERT: A  237 LEU cc_start: 0.8970 (mt) cc_final: 0.8735 (mt)
REVERT: A  256 TYR cc_start: 0.8546 (m-80) cc_final: 0.7999 (m-10)
REVERT: B   66 LEU cc_start: 0.9168 (mp) cc_final: 0.8931 (mp)
REVERT: B  191 GLN cc_start: 0.8134 (tp40) cc_final: 0.7385 (tp40)
REVERT: B  229 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7489 (mtm110)
REVERT: C   80 TRP cc_start: 0.8875 (p90) cc_final: 0.8263 (p90)
REVERT: C  155 THR cc_start: 0.7389 (p) cc_final: 0.6890 (t)
REVERT: C  229 ARG cc_start: 0.8663 (ttm170) cc_final: 0.7670 (mtm110)
REVERT: C  256 TYR cc_start: 0.8275 (m-80) cc_final: 0.7834 (m-10)
  outliers start: 17
  outliers final: 9
  residues processed: 119
  average time/residue: 0.0775
  time to fit residues: 11.4948
Evaluate side-chains
  114 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  236 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 46 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   chunk 39 optimal weight:    7.9990
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 62 optimal weight:    0.1980
   chunk 60 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    2.2388

-------------------------------------------------------------------------------
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 = 0.3839 r_free = 0.3839 target = 0.159108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.125485 restraints weight = 8188.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.125453 restraints weight = 9376.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.126438 restraints weight = 7171.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.126460 restraints weight = 6977.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.127029 restraints weight = 5939.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.4154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   5175  Z= 0.214
  Angle     :  0.769  19.291   7173  Z= 0.360
  Chirality :  0.053   0.569    834
  Planarity :  0.004   0.031    900
  Dihedral  :  6.181  50.937   1003
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  5.36 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  8.55 %
    Allowed  : 18.23 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

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 aren not related in a simple way.
  whole: -0.37 (0.31), residues: 690
  helix: -1.42 (0.48), residues: 114
  sheet:  0.78 (0.35), residues: 195
  loop : -0.35 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 106 
 TYR   0.022   0.002   TYR C 232 
 PHE   0.028   0.002   PHE C 118 
 TRP   0.014   0.001   TRP C 153 
 HIS   0.005   0.001   HIS C 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 5154)
  covalent geometry    : angle       0.64428 ( 7119)
  SS BOND              : bond        0.00571 (    9)
  SS BOND              : angle       1.95276 (   18)
  hydrogen bonds       : bond        0.04029 (  168)
  hydrogen bonds       : angle       6.51226 (  531)
  link_NAG-ASN         : bond        0.01439 (   12)
  link_NAG-ASN         : angle       5.81547 (   36)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  237 LEU cc_start: 0.8981 (mt) cc_final: 0.8697 (mt)
REVERT: B   66 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8894 (mp)
REVERT: B  191 GLN cc_start: 0.8407 (tp40) cc_final: 0.7526 (tp40)
REVERT: B  229 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7131 (mtm110)
REVERT: C   80 TRP cc_start: 0.8905 (p90) cc_final: 0.8323 (p90)
REVERT: C   82 TYR cc_start: 0.6222 (m-80) cc_final: 0.5826 (m-80)
REVERT: C  152 LEU cc_start: 0.8028 (mt) cc_final: 0.7690 (mt)
REVERT: C  191 GLN cc_start: 0.8549 (tp40) cc_final: 0.7620 (tp40)
REVERT: C  229 ARG cc_start: 0.8655 (ttm170) cc_final: 0.7700 (mtm110)
REVERT: C  256 TYR cc_start: 0.8349 (m-80) cc_final: 0.8127 (m-10)
  outliers start: 30
  outliers final: 18
  residues processed: 124
  average time/residue: 0.0789
  time to fit residues: 12.0567
Evaluate side-chains
  117 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  118 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  164 LEU
Chi-restraints excluded: chain C residue  182 VAL
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  244 ILE
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 10 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 34 optimal weight:   10.0000
   chunk 18 optimal weight:    0.8980
   chunk 52 optimal weight:    9.9990
   chunk 31 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 13 optimal weight:    0.0170
   overall best weight:    1.5222

-------------------------------------------------------------------------------
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 = 0.3835 r_free = 0.3835 target = 0.159236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.123895 restraints weight = 8296.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.124368 restraints weight = 8224.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.127217 restraints weight = 5980.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.126705 restraints weight = 4794.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.126901 restraints weight = 4711.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.4425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5175  Z= 0.163
  Angle     :  0.731  18.121   7173  Z= 0.339
  Chirality :  0.051   0.484    834
  Planarity :  0.004   0.027    900
  Dihedral  :  6.166  47.202   1003
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.93 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  6.27 %
    Allowed  : 22.79 %
    Favored  : 70.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.46 %

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 aren not related in a simple way.
  whole: -0.36 (0.31), residues: 690
  helix: -1.10 (0.51), residues: 114
  sheet:  0.60 (0.35), residues: 195
  loop : -0.34 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 106 
 TYR   0.031   0.002   TYR C 232 
 PHE   0.023   0.002   PHE C 118 
 TRP   0.010   0.001   TRP C  64 
 HIS   0.005   0.001   HIS C 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 5154)
  covalent geometry    : angle       0.62086 ( 7119)
  SS BOND              : bond        0.00316 (    9)
  SS BOND              : angle       1.86287 (   18)
  hydrogen bonds       : bond        0.03746 (  168)
  hydrogen bonds       : angle       6.31330 (  531)
  link_NAG-ASN         : bond        0.01257 (   12)
  link_NAG-ASN         : angle       5.33057 (   36)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  237 LEU cc_start: 0.9005 (mt) cc_final: 0.8674 (mt)
REVERT: B   66 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8919 (mp)
REVERT: B  118 PHE cc_start: 0.6661 (OUTLIER) cc_final: 0.6344 (p90)
REVERT: B  168 TYR cc_start: 0.8013 (t80) cc_final: 0.7705 (t80)
REVERT: B  191 GLN cc_start: 0.8531 (tp40) cc_final: 0.7662 (tp40)
REVERT: B  229 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.6877 (mtm110)
REVERT: B  256 TYR cc_start: 0.8409 (m-80) cc_final: 0.7577 (m-80)
REVERT: C   80 TRP cc_start: 0.8816 (p90) cc_final: 0.8388 (p90)
REVERT: C  152 LEU cc_start: 0.8010 (mt) cc_final: 0.7669 (mt)
REVERT: C  229 ARG cc_start: 0.8667 (ttm170) cc_final: 0.7643 (mtm110)
  outliers start: 22
  outliers final: 12
  residues processed: 112
  average time/residue: 0.0894
  time to fit residues: 12.2636
Evaluate side-chains
  111 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  118 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 42 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0370
   chunk 32 optimal weight:    7.9990
   chunk 64 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0870
   chunk 11 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.9640

-------------------------------------------------------------------------------
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 = 0.3843 r_free = 0.3843 target = 0.160082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.126885 restraints weight = 8328.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.128258 restraints weight = 8502.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.128995 restraints weight = 5749.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.128408 restraints weight = 5084.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.128495 restraints weight = 5007.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.4675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5175  Z= 0.126
  Angle     :  0.708  16.734   7173  Z= 0.325
  Chirality :  0.049   0.448    834
  Planarity :  0.004   0.026    900
  Dihedral  :  6.025  43.274   1003
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  4.35 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  6.27 %
    Allowed  : 24.22 %
    Favored  : 69.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

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 aren not related in a simple way.
  whole: -0.22 (0.31), residues: 690
  helix: -0.79 (0.53), residues: 114
  sheet:  0.95 (0.37), residues: 180
  loop : -0.43 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 224 
 TYR   0.024   0.001   TYR C 168 
 PHE   0.026   0.002   PHE C 118 
 TRP   0.007   0.001   TRP B 180 
 HIS   0.006   0.001   HIS C 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 5154)
  covalent geometry    : angle       0.60789 ( 7119)
  SS BOND              : bond        0.00305 (    9)
  SS BOND              : angle       1.71042 (   18)
  hydrogen bonds       : bond        0.03524 (  168)
  hydrogen bonds       : angle       6.13879 (  531)
  link_NAG-ASN         : bond        0.00989 (   12)
  link_NAG-ASN         : angle       5.02547 (   36)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8910 (OUTLIER) cc_final: 0.8477 (t-100)
REVERT: A  237 LEU cc_start: 0.8993 (mt) cc_final: 0.8653 (mt)
REVERT: B   66 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8917 (mp)
REVERT: B  106 ARG cc_start: 0.8680 (ttm110) cc_final: 0.8445 (ttm-80)
REVERT: B  168 TYR cc_start: 0.8253 (t80) cc_final: 0.7992 (t80)
REVERT: B  172 LYS cc_start: 0.8590 (mtpp) cc_final: 0.8366 (mtmm)
REVERT: B  191 GLN cc_start: 0.8598 (tp40) cc_final: 0.7724 (tp40)
REVERT: B  229 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.6662 (mtm110)
REVERT: B  237 LEU cc_start: 0.9058 (mt) cc_final: 0.8739 (mt)
REVERT: C   80 TRP cc_start: 0.8807 (p90) cc_final: 0.8375 (p90)
REVERT: C  152 LEU cc_start: 0.7822 (mt) cc_final: 0.7496 (mt)
REVERT: C  191 GLN cc_start: 0.8526 (tp40) cc_final: 0.7531 (tp40)
REVERT: C  229 ARG cc_start: 0.8595 (ttm170) cc_final: 0.7594 (mtm110)
REVERT: C  274 HIS cc_start: 0.8191 (OUTLIER) cc_final: 0.7821 (t-90)
  outliers start: 22
  outliers final: 14
  residues processed: 115
  average time/residue: 0.0809
  time to fit residues: 11.5292
Evaluate side-chains
  115 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 TRP
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue  164 LEU
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  203 LEU
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  274 HIS
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 7 optimal weight:    0.4980
   chunk 11 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 67 optimal weight:   10.0000
   chunk 66 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.3841 r_free = 0.3841 target = 0.159924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.126907 restraints weight = 8103.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.126867 restraints weight = 9443.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.129589 restraints weight = 7285.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.129162 restraints weight = 5773.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.129270 restraints weight = 5185.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.4766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5175  Z= 0.134
  Angle     :  0.739  20.040   7173  Z= 0.340
  Chirality :  0.051   0.467    834
  Planarity :  0.004   0.043    900
  Dihedral  :  6.307  57.666   1003
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  3.62 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 25.93 %
    Favored  : 68.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.61 %

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 aren not related in a simple way.
  whole: -0.25 (0.31), residues: 690
  helix: -0.73 (0.52), residues: 114
  sheet:  0.94 (0.37), residues: 180
  loop : -0.48 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 224 
 TYR   0.028   0.002   TYR C 232 
 PHE   0.029   0.002   PHE C 118 
 TRP   0.013   0.001   TRP B 127 
 HIS   0.006   0.001   HIS C 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 5154)
  covalent geometry    : angle       0.63204 ( 7119)
  SS BOND              : bond        0.00496 (    9)
  SS BOND              : angle       1.89518 (   18)
  hydrogen bonds       : bond        0.03599 (  168)
  hydrogen bonds       : angle       6.08212 (  531)
  link_NAG-ASN         : bond        0.00459 (   12)
  link_NAG-ASN         : angle       5.28235 (   36)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8920 (OUTLIER) cc_final: 0.8512 (t-100)
REVERT: A  237 LEU cc_start: 0.9007 (mt) cc_final: 0.8667 (mt)
REVERT: B   66 LEU cc_start: 0.9114 (mp) cc_final: 0.8774 (mp)
REVERT: B  106 ARG cc_start: 0.8661 (ttm110) cc_final: 0.8432 (ttm-80)
REVERT: B  168 TYR cc_start: 0.8324 (t80) cc_final: 0.7855 (t80)
REVERT: B  191 GLN cc_start: 0.8655 (tp40) cc_final: 0.7718 (tp40)
REVERT: B  229 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.6562 (mtm110)
REVERT: B  232 TYR cc_start: 0.8773 (m-80) cc_final: 0.8498 (m-10)
REVERT: C   80 TRP cc_start: 0.8795 (p90) cc_final: 0.8405 (p90)
REVERT: C  152 LEU cc_start: 0.7850 (mt) cc_final: 0.7553 (mt)
REVERT: C  191 GLN cc_start: 0.8618 (tp40) cc_final: 0.7537 (tp40)
REVERT: C  229 ARG cc_start: 0.8613 (ttm170) cc_final: 0.7616 (mtm110)
REVERT: C  274 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7865 (t-90)
  outliers start: 20
  outliers final: 14
  residues processed: 108
  average time/residue: 0.0761
  time to fit residues: 10.3226
Evaluate side-chains
  111 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ASN
Chi-restraints excluded: chain A residue   64 TRP
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  274 HIS
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 1 optimal weight:    0.1980
   chunk 4 optimal weight:    0.0470
   chunk 25 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 54 optimal weight:    9.9990
   chunk 44 optimal weight:    5.9990
   chunk 49 optimal weight:    7.9990
   overall best weight:    2.0082

-------------------------------------------------------------------------------
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 = 0.3818 r_free = 0.3818 target = 0.157913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.124258 restraints weight = 8340.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.126452 restraints weight = 7910.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.126620 restraints weight = 5457.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.126010 restraints weight = 5384.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.126010 restraints weight = 5530.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.5117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5175  Z= 0.189
  Angle     :  0.708  12.627   7173  Z= 0.341
  Chirality :  0.048   0.237    834
  Planarity :  0.004   0.044    900
  Dihedral  :  6.210  49.930   1003
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  4.35 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  6.27 %
    Allowed  : 24.79 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.61 %

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 aren not related in a simple way.
  whole: -0.51 (0.31), residues: 690
  helix: -0.75 (0.54), residues: 105
  sheet:  0.77 (0.38), residues: 180
  loop : -0.72 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 224 
 TYR   0.030   0.002   TYR C 168 
 PHE   0.030   0.002   PHE C 118 
 TRP   0.012   0.001   TRP C 153 
 HIS   0.006   0.001   HIS C 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 5154)
  covalent geometry    : angle       0.64235 ( 7119)
  SS BOND              : bond        0.00322 (    9)
  SS BOND              : angle       2.48782 (   18)
  hydrogen bonds       : bond        0.04026 (  168)
  hydrogen bonds       : angle       6.23114 (  531)
  link_NAG-ASN         : bond        0.00381 (   12)
  link_NAG-ASN         : angle       3.89552 (   36)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ARG cc_start: 0.8352 (ttm170) cc_final: 0.7152 (mtm-85)
REVERT: A  237 LEU cc_start: 0.9075 (mt) cc_final: 0.8716 (mt)
REVERT: B   66 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8900 (mp)
REVERT: B  168 TYR cc_start: 0.8396 (t80) cc_final: 0.7683 (t80)
REVERT: B  191 GLN cc_start: 0.8559 (tp40) cc_final: 0.7549 (tp40)
REVERT: B  229 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.6539 (mtm110)
REVERT: B  232 TYR cc_start: 0.8762 (m-80) cc_final: 0.8373 (m-10)
REVERT: C  152 LEU cc_start: 0.7885 (mt) cc_final: 0.7528 (mt)
REVERT: C  229 ARG cc_start: 0.8677 (ttm170) cc_final: 0.7314 (mtm-85)
REVERT: C  274 HIS cc_start: 0.7895 (OUTLIER) cc_final: 0.6832 (t70)
  outliers start: 22
  outliers final: 14
  residues processed: 108
  average time/residue: 0.0802
  time to fit residues: 10.7549
Evaluate side-chains
  106 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  182 VAL
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  274 HIS
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 63 optimal weight:    0.4980
   chunk 17 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0470
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.8482

-------------------------------------------------------------------------------
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 = 0.3847 r_free = 0.3847 target = 0.159468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.121815 restraints weight = 8457.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.121985 restraints weight = 7195.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.123896 restraints weight = 5471.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.125453 restraints weight = 4711.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.126032 restraints weight = 4309.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.5240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5175  Z= 0.114
  Angle     :  0.649   9.828   7173  Z= 0.308
  Chirality :  0.045   0.172    834
  Planarity :  0.004   0.041    900
  Dihedral  :  5.602  41.020   1003
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  3.91 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 26.78 %
    Favored  : 68.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.61 %

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 aren not related in a simple way.
  whole: -0.48 (0.31), residues: 690
  helix: -0.70 (0.54), residues: 105
  sheet:  0.82 (0.38), residues: 180
  loop : -0.74 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 224 
 TYR   0.029   0.001   TYR C 168 
 PHE   0.027   0.002   PHE C 118 
 TRP   0.012   0.001   TRP C  80 
 HIS   0.005   0.001   HIS C 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 5154)
  covalent geometry    : angle       0.60279 ( 7119)
  SS BOND              : bond        0.00260 (    9)
  SS BOND              : angle       1.85286 (   18)
  hydrogen bonds       : bond        0.03489 (  168)
  hydrogen bonds       : angle       5.99026 (  531)
  link_NAG-ASN         : bond        0.00357 (   12)
  link_NAG-ASN         : angle       3.20868 (   36)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8847 (OUTLIER) cc_final: 0.8460 (t-100)
REVERT: A  229 ARG cc_start: 0.8442 (ttm170) cc_final: 0.7359 (mtm110)
REVERT: A  237 LEU cc_start: 0.9186 (mt) cc_final: 0.8836 (mt)
REVERT: B   66 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8850 (mp)
REVERT: B  168 TYR cc_start: 0.8567 (t80) cc_final: 0.7844 (t80)
REVERT: B  191 GLN cc_start: 0.8362 (tp40) cc_final: 0.7534 (tp40)
REVERT: B  229 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.6110 (mtm110)
REVERT: B  232 TYR cc_start: 0.8760 (m-80) cc_final: 0.8470 (m-10)
REVERT: C  152 LEU cc_start: 0.7760 (mt) cc_final: 0.7334 (mt)
REVERT: C  172 LYS cc_start: 0.9000 (mtpp) cc_final: 0.8592 (mttp)
REVERT: C  229 ARG cc_start: 0.8720 (ttm170) cc_final: 0.7111 (mtm-85)
REVERT: C  274 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.6704 (t70)
  outliers start: 18
  outliers final: 11
  residues processed: 103
  average time/residue: 0.0695
  time to fit residues: 8.9162
Evaluate side-chains
  99 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 TRP
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  203 LEU
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  274 HIS
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 1 optimal weight:    0.4980
   chunk 7 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 60 optimal weight:    9.9990
   chunk 21 optimal weight:   10.0000
   chunk 54 optimal weight:    8.9990
   chunk 4 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0970
   chunk 44 optimal weight:    9.9990
   overall best weight:    0.6578

-------------------------------------------------------------------------------
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 = 0.3862 r_free = 0.3862 target = 0.160572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 94)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.122965 restraints weight = 8367.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.125204 restraints weight = 6261.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.126736 restraints weight = 5327.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.127314 restraints weight = 4851.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.127554 restraints weight = 4609.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.5418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   5175  Z= 0.109
  Angle     :  0.640   7.722   7173  Z= 0.307
  Chirality :  0.046   0.189    834
  Planarity :  0.004   0.050    900
  Dihedral  :  5.403  42.987   1003
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  3.91 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 26.78 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.61 %

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 aren not related in a simple way.
  whole: -0.45 (0.31), residues: 690
  helix: -0.55 (0.55), residues: 105
  sheet:  0.84 (0.38), residues: 180
  loop : -0.75 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 224 
 TYR   0.036   0.001   TYR C 168 
 PHE   0.029   0.002   PHE C 118 
 TRP   0.033   0.001   TRP C  80 
 HIS   0.006   0.001   HIS C 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 5154)
  covalent geometry    : angle       0.60442 ( 7119)
  SS BOND              : bond        0.00197 (    9)
  SS BOND              : angle       1.62027 (   18)
  hydrogen bonds       : bond        0.03437 (  168)
  hydrogen bonds       : angle       5.90185 (  531)
  link_NAG-ASN         : bond        0.00445 (   12)
  link_NAG-ASN         : angle       2.81816 (   36)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ARG cc_start: 0.8419 (ttm170) cc_final: 0.7379 (mtm110)
REVERT: A  237 LEU cc_start: 0.9164 (mt) cc_final: 0.8828 (mt)
REVERT: B   66 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8869 (mp)
REVERT: B  168 TYR cc_start: 0.8573 (t80) cc_final: 0.7751 (t80)
REVERT: B  191 GLN cc_start: 0.8369 (tp40) cc_final: 0.7533 (tp40)
REVERT: B  229 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.5991 (mtm110)
REVERT: B  232 TYR cc_start: 0.8790 (m-80) cc_final: 0.8546 (m-10)
REVERT: C  152 LEU cc_start: 0.7733 (mt) cc_final: 0.7305 (mt)
REVERT: C  229 ARG cc_start: 0.8693 (ttm170) cc_final: 0.7096 (mtm-85)
REVERT: C  274 HIS cc_start: 0.7639 (OUTLIER) cc_final: 0.6738 (t70)
  outliers start: 15
  outliers final: 12
  residues processed: 98
  average time/residue: 0.0716
  time to fit residues: 8.6649
Evaluate side-chains
  101 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  203 LEU
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  274 HIS
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 8 optimal weight:    9.9990
   chunk 30 optimal weight:    0.2980
   chunk 28 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 21 optimal weight:    9.9990
   chunk 23 optimal weight:    5.9990
   chunk 2 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3863 r_free = 0.3863 target = 0.160845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.126442 restraints weight = 8498.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 82)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.123517 restraints weight = 8350.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.125395 restraints weight = 6307.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.126848 restraints weight = 5372.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.127124 restraints weight = 4963.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.5478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   5175  Z= 0.108
  Angle     :  0.640   9.379   7173  Z= 0.303
  Chirality :  0.046   0.212    834
  Planarity :  0.004   0.048    900
  Dihedral  :  5.179  39.792   1003
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  3.48 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 27.07 %
    Favored  : 68.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.61 %

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 aren not related in a simple way.
  whole: -0.37 (0.32), residues: 690
  helix: -0.41 (0.56), residues: 105
  sheet:  0.91 (0.39), residues: 180
  loop : -0.73 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 224 
 TYR   0.019   0.001   TYR A 168 
 PHE   0.028   0.002   PHE C 118 
 TRP   0.029   0.001   TRP C  80 
 HIS   0.006   0.001   HIS C 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 5154)
  covalent geometry    : angle       0.60028 ( 7119)
  SS BOND              : bond        0.00200 (    9)
  SS BOND              : angle       1.74194 (   18)
  hydrogen bonds       : bond        0.03387 (  168)
  hydrogen bonds       : angle       5.87224 (  531)
  link_NAG-ASN         : bond        0.00416 (   12)
  link_NAG-ASN         : angle       2.97808 (   36)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 962.56 seconds
wall clock time: 17 minutes 7.46 seconds (1027.46 seconds total)