Starting phenix.real_space_refine
on Tue Mar  3 12:02:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9oa9_70276/03_2026/9oa9_70276.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9oa9_70276/03_2026/9oa9_70276.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.44
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9oa9_70276/03_2026/9oa9_70276.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9oa9_70276/03_2026/9oa9_70276.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9oa9_70276/03_2026/9oa9_70276.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9oa9_70276/03_2026/9oa9_70276.cif"
  }
  resolution = 3.44
  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=   0.001 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      17      5.16       5
     C    2293      2.51       5
     N     616      2.21       5
     O     750      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3676
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "J"
      Number of atoms: 1836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 1836
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 95}
          Link IDs: {'PTRANS': 22, 'TRANS': 257}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 335
          Unresolved non-hydrogen angles: 420
          Unresolved non-hydrogen dihedrals: 282
          Unresolved non-hydrogen chiralities: 26
          Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 6, 'GLN:plan1': 7, 'ASN:plan1': 4, 'GLU:plan': 8, 'HIS:plan': 5, 'PHE:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 181
    Chain: "K"
      Number of atoms: 1690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 1690
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 103}
          Link IDs: {'PTRANS': 21, 'TRANS': 248}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 416
          Unresolved non-hydrogen angles: 533
          Unresolved non-hydrogen dihedrals: 363
          Unresolved non-hydrogen chiralities: 29
          Planarities with less than four sites: {'TYR:plan': 7, 'GLU:plan': 9, 'TRP:plan': 3, 'PHE:plan': 5, 'ASN:plan1': 4, 'HIS:plan': 6, 'ASP:plan': 5, 'ARG:plan': 4, 'GLN:plan1': 8}
          Unresolved non-hydrogen planarities: 251
    Chain: "X"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 75
          Unusual residues: {'GAL': 1, 'MAN': 2, 'NAG': 3}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "Y"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 75
          Unusual residues: {'GAL': 1, 'MAN': 2, 'NAG': 3}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Residues with excluded nonbonded symmetry interactions: 30
    residue:
      pdb=" N   LEU J 124 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB  LEU J 124 " occ=0.50
    residue:
      pdb=" N   PRO J 126 " occ=0.50
      ... (5 atoms not shown)
      pdb=" CD  PRO J 126 " occ=0.50
    residue:
      pdb=" N   SER J 127 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  SER J 127 " occ=0.00
    residue:
      pdb=" N   LYS J 129 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  LYS J 129 " occ=0.00
    residue:
      pdb=" N   GLY J 139 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY J 139 " occ=0.00
    residue:
      pdb=" N   PRO J 167 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CD  PRO J 167 " occ=0.00
    residue:
      pdb=" N   LEU J 170 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  LEU J 170 " occ=0.00
    residue:
      pdb=" N   GLN J 171 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  GLN J 171 " occ=0.00
    residue:
      pdb=" N   LYS J 209 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB  LYS J 209 " occ=0.50
    residue:
      pdb=" N   LYS J 210 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  LYS J 210 " occ=0.00
    residue:
      pdb=" N   VAL J 211 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  VAL J 211 " occ=0.00
    residue:
      pdb=" N   GLU J 212 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB  GLU J 212 " occ=0.50
    ... (remaining 18 not shown)
  Time building chain proxies: 1.11, per 1000 atoms: 0.30
  Number of scatterers: 3676
  At special positions: 0
  Unit cell: (59.76, 62.25, 109.56, 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      17     16.00
     O     750      8.00
     N     616      7.00
     C    2293      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS J 140 " - pdb=" SG  CYS J 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 222 " - pdb=" SG  CYS K 225 " distance=2.17
    Simple disulfide: pdb=" SG  CYS J 225 " - pdb=" SG  CYS K 222 " distance=2.13
    Simple disulfide: pdb=" SG  CYS J 257 " - pdb=" SG  CYS J 317 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 257 " - pdb=" SG  CYS K 317 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 363 " - pdb=" SG  CYS K 421 " distance=2.03

  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
    ALPHA1-3
      " MAN X   3 " - " MAN X   4 "
    ALPHA1-4
      " NAG X   2 " - " MAN X   3 "
      " NAG Y   2 " - " MAN Y   3 "
      " MAN Y   3 " - " MAN Y   4 "
    BETA1-2
      " MAN X   4 " - " NAG X   5 "
      " MAN Y   4 " - " NAG Y   5 "
    BETA1-4
      " NAG X   1 " - " NAG X   2 "
      " NAG X   5 " - " GAL X   6 "
      " NAG Y   1 " - " NAG Y   2 "
      " NAG Y   5 " - " GAL Y   6 "
    NAG-ASN
      " NAG X   1 " - " ASN J 293 "
      " NAG Y   1 " - " ASN K 293 "
  Time building additional restraints: 0.48
  Conformation dependent library (CDL) restraints added in 150.3 milliseconds
  

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1042

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 7 sheets defined
      3.3% alpha, 11.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'J' and resid 186 through 191
      removed outlier: 3.595A  pdb=" N   THR J 191 " --> pdb=" O   SER J 187 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 410 through 415
    Processing helix  chain 'K' and resid 242 through 247
      removed outlier: 4.105A  pdb=" N   ASP K 245 " --> pdb=" O   LYS K 242 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   THR K 246 " --> pdb=" O   PRO K 243 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU K 247 " --> pdb=" O   LYS K 244 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 242 through 247'
    Processing sheet with id=AA1, first strand: chain 'J' and resid 235 through 239
    Processing sheet with id=AA2, first strand: chain 'J' and resid 283 through 286
    Processing sheet with id=AA3, first strand: chain 'J' and resid 315 through 317
    Processing sheet with id=AA4, first strand: chain 'J' and resid 343 through 347
      removed outlier: 6.286A  pdb=" N   PHE J 400 " --> pdb=" O   GLY J 367 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'K' and resid 317 through 319
      removed outlier: 3.542A  pdb=" N   CYS K 317 " --> pdb=" O   LYS K 330 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'K' and resid 343 through 347
    Processing sheet with id=AA7, first strand: chain 'K' and resid 374 through 376
      removed outlier: 3.706A  pdb=" N   ALA K 374 " --> pdb=" O   MET K 424 " (cutoff:3.500A)

    50 hydrogen bonds defined for protein.
    117 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: 0.46

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 805
        1.33 -     1.45: 810
        1.45 -     1.58: 2107
        1.58 -     1.70: 0
        1.70 -     1.82: 18
  Bond restraints: 3740
  Sorted by residual:
  bond pdb=" C   GLU J 229 "
       pdb=" N   ALA J 230 "
    ideal  model  delta    sigma   weight residual
    1.332  1.426 -0.094 1.40e-02 5.10e+03 4.48e+01
  bond pdb=" C   GLU K 229 "
       pdb=" N   ALA K 230 "
    ideal  model  delta    sigma   weight residual
    1.332  1.393 -0.061 1.40e-02 5.10e+03 1.90e+01
  bond pdb=" N   ASP J 266 "
       pdb=" CA  ASP J 266 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.031 7.40e-03 1.83e+04 1.71e+01
  bond pdb=" C   SER J 333 "
       pdb=" O   SER J 333 "
    ideal  model  delta    sigma   weight residual
    1.235  1.278 -0.042 1.26e-02 6.30e+03 1.13e+01
  bond pdb=" N   GLU K 229 "
       pdb=" CA  GLU K 229 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 1.13e-02 7.83e+03 1.10e+01
  ... (remaining 3735 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 4666
        1.99 -     3.98: 390
        3.98 -     5.97: 56
        5.97 -     7.96: 26
        7.96 -     9.96: 12
  Bond angle restraints: 5150
  Sorted by residual:
  angle pdb=" N   PRO J 223 "
        pdb=" CA  PRO J 223 "
        pdb=" C   PRO J 223 "
      ideal   model   delta    sigma   weight residual
     110.70  118.91   -8.21 1.22e+00 6.72e-01 4.53e+01
  angle pdb=" C   CYS K 225 "
        pdb=" CA  CYS K 225 "
        pdb=" CB  CYS K 225 "
      ideal   model   delta    sigma   weight residual
     109.38  101.24    8.14 1.44e+00 4.82e-01 3.20e+01
  angle pdb=" N   THR K 246 "
        pdb=" CA  THR K 246 "
        pdb=" C   THR K 246 "
      ideal   model   delta    sigma   weight residual
     114.04  107.03    7.01 1.24e+00 6.50e-01 3.19e+01
  angle pdb=" N   PRO K 223 "
        pdb=" CA  PRO K 223 "
        pdb=" C   PRO K 223 "
      ideal   model   delta    sigma   weight residual
     110.70  117.10   -6.40 1.22e+00 6.72e-01 2.75e+01
  angle pdb=" C   ASN K 430 "
        pdb=" CA  ASN K 430 "
        pdb=" CB  ASN K 430 "
      ideal   model   delta    sigma   weight residual
     117.23  110.10    7.13 1.36e+00 5.41e-01 2.75e+01
  ... (remaining 5145 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.75: 2180
       27.75 -    55.51: 124
       55.51 -    83.26: 35
       83.26 -   111.01: 40
      111.01 -   138.77: 28
  Dihedral angle restraints: 2407
    sinusoidal: 823
      harmonic: 1584
  Sorted by residual:
  dihedral pdb=" CB  CYS J 225 "
           pdb=" SG  CYS J 225 "
           pdb=" SG  CYS K 222 "
           pdb=" CB  CYS K 222 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.72  -80.72     1      1.00e+01 1.00e-02 8.05e+01
  dihedral pdb=" C   CYS K 225 "
           pdb=" N   CYS K 225 "
           pdb=" CA  CYS K 225 "
           pdb=" CB  CYS K 225 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -107.20  -15.40     0      2.50e+00 1.60e-01 3.79e+01
  dihedral pdb=" CA  VAL K 269 "
           pdb=" C   VAL K 269 "
           pdb=" N   LYS K 270 "
           pdb=" CA  LYS K 270 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.17  -28.83     0      5.00e+00 4.00e-02 3.33e+01
  ... (remaining 2404 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.115: 625
       0.115 -    0.229: 44
       0.229 -    0.344: 8
       0.344 -    0.458: 1
       0.458 -    0.573: 5
  Chirality restraints: 683
  Sorted by residual:
  chirality pdb=" C1  GAL Y   6 "
            pdb=" O4  NAG Y   5 "
            pdb=" C2  GAL Y   6 "
            pdb=" O5  GAL Y   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.86   -0.54 2.00e-02 2.50e+03 7.25e+02
  chirality pdb=" C1  MAN X   4 "
            pdb=" O3  MAN X   3 "
            pdb=" C2  MAN X   4 "
            pdb=" O5  MAN X   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    1.91    0.49 2.00e-02 2.50e+03 6.01e+02
  chirality pdb=" C1  NAG X   5 "
            pdb=" O2  MAN X   4 "
            pdb=" C2  NAG X   5 "
            pdb=" O5  NAG X   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.92   -0.48 2.00e-02 2.50e+03 5.81e+02
  ... (remaining 680 not shown)

  Planarity restraints: 655
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG X   5 "   -0.328 2.00e-02 2.50e+03   2.85e-01 1.01e+03
        pdb=" C7  NAG X   5 "    0.082 2.00e-02 2.50e+03
        pdb=" C8  NAG X   5 "   -0.048 2.00e-02 2.50e+03
        pdb=" N2  NAG X   5 "    0.497 2.00e-02 2.50e+03
        pdb=" O7  NAG X   5 "   -0.204 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG Y   1 "   -0.321 2.00e-02 2.50e+03   2.77e-01 9.59e+02
        pdb=" C7  NAG Y   1 "    0.071 2.00e-02 2.50e+03
        pdb=" C8  NAG Y   1 "   -0.021 2.00e-02 2.50e+03
        pdb=" N2  NAG Y   1 "    0.481 2.00e-02 2.50e+03
        pdb=" O7  NAG Y   1 "   -0.210 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG Y   2 "   -0.229 2.00e-02 2.50e+03   1.95e-01 4.76e+02
        pdb=" C7  NAG Y   2 "    0.049 2.00e-02 2.50e+03
        pdb=" C8  NAG Y   2 "    0.036 2.00e-02 2.50e+03
        pdb=" N2  NAG Y   2 "    0.321 2.00e-02 2.50e+03
        pdb=" O7  NAG Y   2 "   -0.177 2.00e-02 2.50e+03
  ... (remaining 652 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 87
        2.58 -     3.16: 3353
        3.16 -     3.74: 5720
        3.74 -     4.32: 7040
        4.32 -     4.90: 10982
  Nonbonded interactions: 27182
  Sorted by model distance:
  nonbonded pdb=" O3  MAN X   3 "
            pdb=" O6  MAN X   3 "
     model   vdw
     2.002 3.040
  nonbonded pdb=" N   ASP J 217 "
            pdb=" OD1 ASP J 217 "
     model   vdw
     2.161 3.120
  nonbonded pdb=" O   SER J 396 "
            pdb=" OG  SER J 396 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" O   PHE J 239 "
            pdb=" CB  THR J 256 "
     model   vdw
     2.200 2.776
  nonbonded pdb=" O   LEU K 170 "
            pdb=" OG  SER K 179 "
     model   vdw
     2.220 3.040
  ... (remaining 27177 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'J' and ((resid 127 through 130 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 131 through 134 or (resid 135 through 137 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 138 through 140 or (resid 1 \ 
41 through 151 and (name N or name CA or name C or name O or name CB )) or resid \ 
 152 through 153 or (resid 154 and (name N or name CA or name C or name O or nam \ 
e CB )) or resid 162 through 165 or (resid 166 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 167 through 174 or (resid 175 through 176 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 177 through 188 or  \ 
(resid 189 and (name N or name CA or name C or name O or name CB )) or resid 190 \ 
 or (resid 191 through 192 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 193 through 207 or (resid 208 through 212 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 213 or (resid 214 and (name N or name C \ 
A or name C or name O or name CB )) or resid 215 through 216 or (resid 217 throu \ 
gh 218 and (name N or name CA or name C or name O or name CB )) or resid 219 thr \ 
ough 220 or (resid 221 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 222 through 237 or (resid 238 through 239 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 240 through 244 or (resid 245 through 246 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 247 through 249 \ 
 or (resid 250 through 251 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 252 through 253 or (resid 254 through 256 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 257 through 264 or (resid 265 through 2 \ 
66 and (name N or name CA or name C or name O or name CB )) or resid 267 through \ 
 269 or (resid 270 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 271 through 273 or (resid 274 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 275 through 276 or (resid 282 through 286 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 287 through 288 or (resid 291 t \ 
hrough 292 and (name N or name CA or name C or name O or name CB )) or resid 293 \ 
 through 294 or (resid 295 through 301 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 302 through 306 or (resid 307 through 310 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 311 through 313 or resid 31 \ 
7 through 331 or (resid 332 through 336 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 337 through 342 or (resid 343 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 344 through 372 or (resid 373 through  \ 
376 and (name N or name CA or name C or name O or name CB )) or resid 377 throug \ 
h 379 or (resid 400 through 401 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 402 or (resid 403 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 404 through 406 or (resid 407 through 408 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 409 through 410 or (resid 411  \ 
through 420 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 
1 through 435))
  selection = (chain 'K' and ((resid 127 through 130 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 131 through 141 or (resid 142 through 145 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 150 through 154 or resid 16 \ 
2 through 170 or (resid 171 and (name N or name CA or name C or name O or name C \ 
B )) or resid 172 through 182 or (resid 183 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 184 through 186 or (resid 187 through 189 and (nam \ 
e N or name CA or name C or name O or name CB )) or (resid 190 through 192 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 193 through 194 or  \ 
(resid 195 and (name N or name CA or name C or name O or name CB )) or resid 196 \ 
 through 197 or resid 199 or resid 205 through 208 or (resid 209 through 212 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 213 through 228 o \ 
r (resid 229 through 231 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 232 through 235 or (resid 236 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 237 through 257 or (resid 258 through 261 and (name N \ 
 or name CA or name C or name O or name CB )) or resid 262 or (resid 263 through \ 
 266 and (name N or name CA or name C or name O or name CB )) or resid 267 throu \ 
gh 288 or resid 291 through 297 or (resid 298 through 301 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 302 through 312 or (resid 316 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 317 through 321 or ( \ 
resid 322 through 324 and (name N or name CA or name C or name O or name CB )) o \ 
r resid 325 through 330 or (resid 331 through 336 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 337 through 349 or (resid 356 through 358 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 359 through 367  \ 
or (resid 368 through 369 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 370 or (resid 371 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 372 through 377 or (resid 378 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 379 through 407 or (resid 408 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 409 or (resid 410 through 415 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 419 through 421  \ 
or (resid 422 through 429 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 432 through 435))
}
ncs_group {
  reference = chain 'X'
  selection = chain 'Y'
}

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=0.00 max=1.00 mean=0.97
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.770
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4618
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      :  0.009   0.142   3758  Z= 0.514
  Angle     :  1.468  26.720   5198  Z= 0.783
  Chirality :  0.082   0.573    683
  Planarity :  0.022   0.285    653
  Dihedral  : 30.584 138.765   1347
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 38.87
  Ramachandran Plot:
    Outliers :  2.90 %
    Allowed  : 28.19 %
    Favored  : 68.92 %
  Rotamer:
    Outliers : 19.87 %
    Allowed  : 15.49 %
    Favored  : 64.65 %
  Cbeta Deviations :  0.58 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.89 (0.28), residues: 518
  helix: -2.16 (1.50), residues: 12
  sheet: -3.50 (0.41), residues: 104
  loop : -4.50 (0.24), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG J 412 
 TYR   0.014   0.002   TYR K 369 
 PHE   0.013   0.003   PHE J 271 
 TRP   0.022   0.003   TRP J 309 
 HIS   0.008   0.002   HIS K 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00834 ( 3740)
  covalent geometry    : angle       1.30248 ( 5150)
  SS BOND              : bond        0.07126 (    6)
  SS BOND              : angle       3.52587 (   12)
  hydrogen bonds       : bond        0.19236 (   50)
  hydrogen bonds       : angle       9.22882 (  117)
  link_ALPHA1-3        : bond        0.00802 (    1)
  link_ALPHA1-3        : angle       4.53393 (    3)
  link_ALPHA1-4        : bond        0.02425 (    3)
  link_ALPHA1-4        : angle      10.07446 (    9)
  link_BETA1-2         : bond        0.00470 (    2)
  link_BETA1-2         : angle       1.79156 (    6)
  link_BETA1-4         : bond        0.00710 (    4)
  link_BETA1-4         : angle       2.72006 (   12)
  link_NAG-ASN         : bond        0.04614 (    2)
  link_NAG-ASN         : angle      14.34133 (    6)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 33
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: J  377 TRP cc_start: 0.6077 (OUTLIER) cc_final: 0.5200 (p90)
REVERT: K  328 ILE cc_start: 0.1175 (OUTLIER) cc_final: 0.0804 (tp)
REVERT: K  345 TYR cc_start: 0.5783 (OUTLIER) cc_final: 0.5410 (m-80)
REVERT: K  369 TYR cc_start: 0.4772 (OUTLIER) cc_final: 0.2517 (p90)
  outliers start: 59
  outliers final: 26
  residues processed: 85
  average time/residue: 0.0518
  time to fit residues: 5.7381
Evaluate side-chains
  49 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 19
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  175 LEU
Chi-restraints excluded: chain J residue  181 VAL
Chi-restraints excluded: chain J residue  186 SER
Chi-restraints excluded: chain J residue  214 LYS
Chi-restraints excluded: chain J residue  217 ASP
Chi-restraints excluded: chain J residue  219 THR
Chi-restraints excluded: chain J residue  237 PHE
Chi-restraints excluded: chain J residue  238 LEU
Chi-restraints excluded: chain J residue  245 ASP
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  278 VAL
Chi-restraints excluded: chain J residue  281 HIS
Chi-restraints excluded: chain J residue  295 THR
Chi-restraints excluded: chain J residue  319 VAL
Chi-restraints excluded: chain J residue  377 TRP
Chi-restraints excluded: chain J residue  394 LEU
Chi-restraints excluded: chain K residue  131 THR
Chi-restraints excluded: chain K residue  164 HIS
Chi-restraints excluded: chain K residue  228 PRO
Chi-restraints excluded: chain K residue  229 GLU
Chi-restraints excluded: chain K residue  260 VAL
Chi-restraints excluded: chain K residue  269 VAL
Chi-restraints excluded: chain K residue  302 LEU
Chi-restraints excluded: chain K residue  322 LYS
Chi-restraints excluded: chain K residue  328 ILE
Chi-restraints excluded: chain K residue  345 TYR
Chi-restraints excluded: chain K residue  361 LEU
Chi-restraints excluded: chain K residue  364 LEU
Chi-restraints excluded: chain K residue  369 TYR
Chi-restraints excluded: chain K residue  424 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:   20.0000
   chunk 31 optimal weight:    0.0980
   chunk 25 optimal weight:   20.0000
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
J 164 HIS
K 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4955 r_free = 0.4955 target = 0.177904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4820 r_free = 0.4820 target = 0.168113 restraints weight = 12196.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.4808 rms_B_bonded: 2.83
r_work: 0.4731 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.4731
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4745
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4745 r_free = 0.4745    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4741 r_free = 0.4741    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
r_final: 0.4741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4458
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080   3758  Z= 0.213
  Angle     :  1.172  14.831   5198  Z= 0.535
  Chirality :  0.059   0.366    683
  Planarity :  0.010   0.119    653
  Dihedral  : 28.312 131.033    842
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 24.23
  Ramachandran Plot:
    Outliers :  1.16 %
    Allowed  : 25.10 %
    Favored  : 73.75 %
  Rotamer:
    Outliers : 13.47 %
    Allowed  : 21.55 %
    Favored  : 64.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.72 (0.29), residues: 518
  helix: -1.77 (1.24), residues: 18
  sheet: -3.14 (0.39), residues: 109
  loop : -4.51 (0.25), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG J 288 
 TYR   0.015   0.001   TYR K 369 
 PHE   0.018   0.003   PHE K 271 
 TRP   0.017   0.003   TRP J 154 
 HIS   0.005   0.002   HIS J 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 3740)
  covalent geometry    : angle       1.10155 ( 5150)
  SS BOND              : bond        0.00311 (    6)
  SS BOND              : angle       1.24996 (   12)
  hydrogen bonds       : bond        0.04655 (   50)
  hydrogen bonds       : angle       8.38074 (  117)
  link_ALPHA1-3        : bond        0.00432 (    1)
  link_ALPHA1-3        : angle       5.27028 (    3)
  link_ALPHA1-4        : bond        0.01560 (    3)
  link_ALPHA1-4        : angle       3.72068 (    9)
  link_BETA1-2         : bond        0.00744 (    2)
  link_BETA1-2         : angle       2.81881 (    6)
  link_BETA1-4         : bond        0.01826 (    4)
  link_BETA1-4         : angle       4.62629 (   12)
  link_NAG-ASN         : bond        0.00449 (    2)
  link_NAG-ASN         : angle       7.72996 (    6)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 26
  time to evaluate  : 0.137 
Fit side-chains
REVERT: J  238 LEU cc_start: -0.1425 (OUTLIER) cc_final: -0.3283 (mp)
REVERT: J  377 TRP cc_start: 0.6012 (OUTLIER) cc_final: 0.5113 (p90)
REVERT: K  345 TYR cc_start: 0.4893 (OUTLIER) cc_final: 0.4691 (m-80)
REVERT: K  369 TYR cc_start: 0.5214 (OUTLIER) cc_final: 0.4079 (p90)
  outliers start: 40
  outliers final: 28
  residues processed: 57
  average time/residue: 0.0417
  time to fit residues: 3.3251
Evaluate side-chains
  52 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 20
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  164 HIS
Chi-restraints excluded: chain J residue  181 VAL
Chi-restraints excluded: chain J residue  214 LYS
Chi-restraints excluded: chain J residue  219 THR
Chi-restraints excluded: chain J residue  237 PHE
Chi-restraints excluded: chain J residue  238 LEU
Chi-restraints excluded: chain J residue  245 ASP
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  275 VAL
Chi-restraints excluded: chain J residue  278 VAL
Chi-restraints excluded: chain J residue  281 HIS
Chi-restraints excluded: chain J residue  319 VAL
Chi-restraints excluded: chain J residue  347 LEU
Chi-restraints excluded: chain J residue  375 VAL
Chi-restraints excluded: chain J residue  377 TRP
Chi-restraints excluded: chain K residue  153 SER
Chi-restraints excluded: chain K residue  164 HIS
Chi-restraints excluded: chain K residue  184 VAL
Chi-restraints excluded: chain K residue  229 GLU
Chi-restraints excluded: chain K residue  235 SER
Chi-restraints excluded: chain K residue  252 THR
Chi-restraints excluded: chain K residue  260 VAL
Chi-restraints excluded: chain K residue  302 LEU
Chi-restraints excluded: chain K residue  322 LYS
Chi-restraints excluded: chain K residue  328 ILE
Chi-restraints excluded: chain K residue  345 TYR
Chi-restraints excluded: chain K residue  346 THR
Chi-restraints excluded: chain K residue  359 VAL
Chi-restraints excluded: chain K residue  361 LEU
Chi-restraints excluded: chain K residue  364 LEU
Chi-restraints excluded: chain K residue  369 TYR
Chi-restraints excluded: chain K residue  424 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 7 optimal weight:   10.0000
   chunk 10 optimal weight:    0.0980
   chunk 8 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 34 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 2 optimal weight:    8.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
J 164 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4955 r_free = 0.4955 target = 0.177432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4816 r_free = 0.4816 target = 0.167082 restraints weight = 11852.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.4805 rms_B_bonded: 2.91
r_work: 0.4734 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.4734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4745
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4745 r_free = 0.4745    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4745 r_free = 0.4745    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
r_final: 0.4745
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4472
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   3758  Z= 0.201
  Angle     :  1.142  16.034   5198  Z= 0.515
  Chirality :  0.058   0.324    683
  Planarity :  0.009   0.120    653
  Dihedral  : 26.258 126.384    829
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 21.49
  Ramachandran Plot:
    Outliers :  1.16 %
    Allowed  : 26.45 %
    Favored  : 72.39 %
  Rotamer:
    Outliers : 14.14 %
    Allowed  : 21.89 %
    Favored  : 63.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.58 (0.29), residues: 518
  helix: -1.95 (1.18), residues: 18
  sheet: -2.83 (0.42), residues: 96
  loop : -4.44 (0.25), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG J 412 
 TYR   0.016   0.002   TYR K 369 
 PHE   0.018   0.003   PHE J 271 
 TRP   0.011   0.002   TRP J 309 
 HIS   0.011   0.003   HIS J 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 3740)
  covalent geometry    : angle       1.07612 ( 5150)
  SS BOND              : bond        0.00550 (    6)
  SS BOND              : angle       1.37494 (   12)
  hydrogen bonds       : bond        0.04079 (   50)
  hydrogen bonds       : angle       8.21231 (  117)
  link_ALPHA1-3        : bond        0.01126 (    1)
  link_ALPHA1-3        : angle       6.91929 (    3)
  link_ALPHA1-4        : bond        0.01531 (    3)
  link_ALPHA1-4        : angle       3.84246 (    9)
  link_BETA1-2         : bond        0.00647 (    2)
  link_BETA1-2         : angle       3.80036 (    6)
  link_BETA1-4         : bond        0.01554 (    4)
  link_BETA1-4         : angle       4.55176 (   12)
  link_NAG-ASN         : bond        0.00501 (    2)
  link_NAG-ASN         : angle       5.54974 (    6)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 22
  time to evaluate  : 0.167 
Fit side-chains
REVERT: J  377 TRP cc_start: 0.6163 (OUTLIER) cc_final: 0.5128 (p90)
REVERT: K  322 LYS cc_start: 0.3380 (OUTLIER) cc_final: 0.3112 (tmtt)
REVERT: K  328 ILE cc_start: 0.1988 (OUTLIER) cc_final: 0.1737 (mm)
REVERT: K  369 TYR cc_start: 0.4584 (OUTLIER) cc_final: 0.3433 (p90)
  outliers start: 42
  outliers final: 29
  residues processed: 57
  average time/residue: 0.0410
  time to fit residues: 3.3303
Evaluate side-chains
  52 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 19
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  164 HIS
Chi-restraints excluded: chain J residue  181 VAL
Chi-restraints excluded: chain J residue  189 LEU
Chi-restraints excluded: chain J residue  214 LYS
Chi-restraints excluded: chain J residue  219 THR
Chi-restraints excluded: chain J residue  221 THR
Chi-restraints excluded: chain J residue  237 PHE
Chi-restraints excluded: chain J residue  245 ASP
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  265 GLU
Chi-restraints excluded: chain J residue  275 VAL
Chi-restraints excluded: chain J residue  278 VAL
Chi-restraints excluded: chain J residue  281 HIS
Chi-restraints excluded: chain J residue  295 THR
Chi-restraints excluded: chain J residue  319 VAL
Chi-restraints excluded: chain J residue  347 LEU
Chi-restraints excluded: chain J residue  377 TRP
Chi-restraints excluded: chain K residue  164 HIS
Chi-restraints excluded: chain K residue  229 GLU
Chi-restraints excluded: chain K residue  235 SER
Chi-restraints excluded: chain K residue  252 THR
Chi-restraints excluded: chain K residue  260 VAL
Chi-restraints excluded: chain K residue  269 VAL
Chi-restraints excluded: chain K residue  298 VAL
Chi-restraints excluded: chain K residue  302 LEU
Chi-restraints excluded: chain K residue  304 VAL
Chi-restraints excluded: chain K residue  322 LYS
Chi-restraints excluded: chain K residue  328 ILE
Chi-restraints excluded: chain K residue  346 THR
Chi-restraints excluded: chain K residue  359 VAL
Chi-restraints excluded: chain K residue  361 LEU
Chi-restraints excluded: chain K residue  369 TYR
Chi-restraints excluded: chain K residue  424 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 29 optimal weight:   20.0000
   chunk 13 optimal weight:    0.2980
   chunk 16 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 26 optimal weight:   20.0000
   chunk 41 optimal weight:    7.9990
   chunk 52 optimal weight:   20.0000
   chunk 27 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 3 optimal weight:   30.0000
   chunk 21 optimal weight:   10.0000
   overall best weight:    5.4588

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

Flipped N/Q/H residues before XYZ refinement:
J 164 HIS
K 311 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4885 r_free = 0.4885 target = 0.169767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4704 r_free = 0.4704 target = 0.156740 restraints weight = 11795.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.4689 rms_B_bonded: 2.94
r_work: 0.4602 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.4602
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4617
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4617 r_free = 0.4617    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4617 r_free = 0.4617    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
r_final: 0.4617
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5060
moved from start:          0.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.086   3758  Z= 0.418
  Angle     :  1.563  15.986   5198  Z= 0.703
  Chirality :  0.065   0.387    683
  Planarity :  0.010   0.125    653
  Dihedral  : 26.460 131.799    823
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 35.36
  Ramachandran Plot:
    Outliers :  0.97 %
    Allowed  : 33.20 %
    Favored  : 65.83 %
  Rotamer:
    Outliers : 17.51 %
    Allowed  : 19.19 %
    Favored  : 63.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.41 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.92 (0.28), residues: 518
  helix: -2.45 (1.36), residues: 11
  sheet: -3.47 (0.40), residues: 106
  loop : -4.53 (0.24), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG J 412 
 TYR   0.015   0.002   TYR K 369 
 PHE   0.034   0.005   PHE J 271 
 TRP   0.019   0.004   TRP J 309 
 HIS   0.033   0.008   HIS J 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00908 ( 3740)
  covalent geometry    : angle       1.45376 ( 5150)
  SS BOND              : bond        0.00590 (    6)
  SS BOND              : angle       0.84761 (   12)
  hydrogen bonds       : bond        0.06178 (   50)
  hydrogen bonds       : angle       9.44999 (  117)
  link_ALPHA1-3        : bond        0.01290 (    1)
  link_ALPHA1-3        : angle       9.35122 (    3)
  link_ALPHA1-4        : bond        0.02265 (    3)
  link_ALPHA1-4        : angle       6.49296 (    9)
  link_BETA1-2         : bond        0.00975 (    2)
  link_BETA1-2         : angle       9.30679 (    6)
  link_BETA1-4         : bond        0.02304 (    4)
  link_BETA1-4         : angle       5.58944 (   12)
  link_NAG-ASN         : bond        0.00373 (    2)
  link_NAG-ASN         : angle       6.72305 (    6)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 22
  time to evaluate  : 0.133 
Fit side-chains
REVERT: J  377 TRP cc_start: 0.7015 (OUTLIER) cc_final: 0.6308 (p90)
REVERT: K  369 TYR cc_start: 0.5033 (OUTLIER) cc_final: 0.3373 (p90)
  outliers start: 52
  outliers final: 39
  residues processed: 67
  average time/residue: 0.0416
  time to fit residues: 3.8589
Evaluate side-chains
  60 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 19
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  164 HIS
Chi-restraints excluded: chain J residue  175 LEU
Chi-restraints excluded: chain J residue  181 VAL
Chi-restraints excluded: chain J residue  189 LEU
Chi-restraints excluded: chain J residue  214 LYS
Chi-restraints excluded: chain J residue  219 THR
Chi-restraints excluded: chain J residue  237 PHE
Chi-restraints excluded: chain J residue  245 ASP
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  265 GLU
Chi-restraints excluded: chain J residue  275 VAL
Chi-restraints excluded: chain J residue  278 VAL
Chi-restraints excluded: chain J residue  281 HIS
Chi-restraints excluded: chain J residue  295 THR
Chi-restraints excluded: chain J residue  319 VAL
Chi-restraints excluded: chain J residue  347 LEU
Chi-restraints excluded: chain J residue  361 LEU
Chi-restraints excluded: chain J residue  377 TRP
Chi-restraints excluded: chain K residue  127 SER
Chi-restraints excluded: chain K residue  131 THR
Chi-restraints excluded: chain K residue  164 HIS
Chi-restraints excluded: chain K residue  184 VAL
Chi-restraints excluded: chain K residue  188 SER
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  229 GLU
Chi-restraints excluded: chain K residue  235 SER
Chi-restraints excluded: chain K residue  237 PHE
Chi-restraints excluded: chain K residue  252 THR
Chi-restraints excluded: chain K residue  260 VAL
Chi-restraints excluded: chain K residue  261 ASP
Chi-restraints excluded: chain K residue  298 VAL
Chi-restraints excluded: chain K residue  302 LEU
Chi-restraints excluded: chain K residue  304 VAL
Chi-restraints excluded: chain K residue  322 LYS
Chi-restraints excluded: chain K residue  328 ILE
Chi-restraints excluded: chain K residue  346 THR
Chi-restraints excluded: chain K residue  359 VAL
Chi-restraints excluded: chain K residue  361 LEU
Chi-restraints excluded: chain K residue  364 LEU
Chi-restraints excluded: chain K residue  369 TYR
Chi-restraints excluded: chain K residue  424 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 53 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 4 optimal weight:   20.0000
   chunk 41 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0370
   overall best weight:    0.9860

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

Flipped N/Q/H residues before XYZ refinement:
J 164 HIS
K 311 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4946 r_free = 0.4946 target = 0.175641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4812 r_free = 0.4812 target = 0.164690 restraints weight = 11899.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.4838 rms_B_bonded: 2.95
r_work: 0.4768 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.4768
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4748
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4748 r_free = 0.4748    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4748 r_free = 0.4748    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
r_final: 0.4748
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4509
moved from start:          0.3118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   3758  Z= 0.191
  Angle     :  1.129  11.533   5198  Z= 0.513
  Chirality :  0.058   0.398    683
  Planarity :  0.009   0.121    653
  Dihedral  : 23.411 123.512    823
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 18.74
  Ramachandran Plot:
    Outliers :  0.97 %
    Allowed  : 24.13 %
    Favored  : 74.90 %
  Rotamer:
    Outliers : 13.13 %
    Allowed  : 23.57 %
    Favored  : 63.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.73 (0.29), residues: 518
  helix: -1.93 (1.19), residues: 18
  sheet: -3.23 (0.38), residues: 110
  loop : -4.47 (0.25), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 288 
 TYR   0.017   0.001   TYR K 369 
 PHE   0.020   0.002   PHE J 271 
 TRP   0.015   0.002   TRP J 273 
 HIS   0.009   0.003   HIS J 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 3740)
  covalent geometry    : angle       1.05590 ( 5150)
  SS BOND              : bond        0.00430 (    6)
  SS BOND              : angle       1.19460 (   12)
  hydrogen bonds       : bond        0.03849 (   50)
  hydrogen bonds       : angle       8.41281 (  117)
  link_ALPHA1-3        : bond        0.01718 (    1)
  link_ALPHA1-3        : angle       7.01363 (    3)
  link_ALPHA1-4        : bond        0.02633 (    3)
  link_ALPHA1-4        : angle       5.01368 (    9)
  link_BETA1-2         : bond        0.00400 (    2)
  link_BETA1-2         : angle       4.24990 (    6)
  link_BETA1-4         : bond        0.01565 (    4)
  link_BETA1-4         : angle       3.80838 (   12)
  link_NAG-ASN         : bond        0.00445 (    2)
  link_NAG-ASN         : angle       5.97399 (    6)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 17
  time to evaluate  : 0.133 
Fit side-chains
REVERT: J  164 HIS cc_start: 0.1601 (OUTLIER) cc_final: 0.0584 (t-90)
REVERT: J  377 TRP cc_start: 0.5824 (OUTLIER) cc_final: 0.4793 (p90)
REVERT: K  328 ILE cc_start: 0.1697 (OUTLIER) cc_final: 0.1476 (mm)
REVERT: K  369 TYR cc_start: 0.4400 (OUTLIER) cc_final: 0.3147 (p90)
REVERT: K  424 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.5170 (pp-130)
  outliers start: 39
  outliers final: 25
  residues processed: 50
  average time/residue: 0.0408
  time to fit residues: 2.9413
Evaluate side-chains
  46 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 16
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  164 HIS
Chi-restraints excluded: chain J residue  175 LEU
Chi-restraints excluded: chain J residue  181 VAL
Chi-restraints excluded: chain J residue  189 LEU
Chi-restraints excluded: chain J residue  214 LYS
Chi-restraints excluded: chain J residue  219 THR
Chi-restraints excluded: chain J residue  237 PHE
Chi-restraints excluded: chain J residue  245 ASP
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  275 VAL
Chi-restraints excluded: chain J residue  278 VAL
Chi-restraints excluded: chain J residue  281 HIS
Chi-restraints excluded: chain J residue  319 VAL
Chi-restraints excluded: chain J residue  347 LEU
Chi-restraints excluded: chain J residue  377 TRP
Chi-restraints excluded: chain K residue  127 SER
Chi-restraints excluded: chain K residue  164 HIS
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  229 GLU
Chi-restraints excluded: chain K residue  235 SER
Chi-restraints excluded: chain K residue  252 THR
Chi-restraints excluded: chain K residue  260 VAL
Chi-restraints excluded: chain K residue  302 LEU
Chi-restraints excluded: chain K residue  304 VAL
Chi-restraints excluded: chain K residue  328 ILE
Chi-restraints excluded: chain K residue  346 THR
Chi-restraints excluded: chain K residue  359 VAL
Chi-restraints excluded: chain K residue  361 LEU
Chi-restraints excluded: chain K residue  369 TYR
Chi-restraints excluded: chain K residue  424 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 30 optimal weight:   20.0000
   chunk 15 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 14 optimal weight:    0.3980
   chunk 20 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
J 164 HIS
K 311 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4945 r_free = 0.4945 target = 0.175454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4813 r_free = 0.4813 target = 0.164576 restraints weight = 11982.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.4807 rms_B_bonded: 2.97
r_work: 0.4737 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.4737
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4751
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4751 r_free = 0.4751    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4750 r_free = 0.4750    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       91 |
|-----------------------------------------------------------------------------|
r_final: 0.4750
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4490
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   3758  Z= 0.191
  Angle     :  1.088  11.457   5198  Z= 0.494
  Chirality :  0.056   0.410    683
  Planarity :  0.009   0.119    653
  Dihedral  : 22.479 121.812    819
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 19.66
  Ramachandran Plot:
    Outliers :  0.97 %
    Allowed  : 27.99 %
    Favored  : 71.04 %
  Rotamer:
    Outliers : 12.12 %
    Allowed  : 23.23 %
    Favored  : 64.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.64 (0.29), residues: 518
  helix: -1.83 (1.23), residues: 18
  sheet: -3.10 (0.40), residues: 110
  loop : -4.43 (0.25), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 412 
 TYR   0.016   0.001   TYR K 369 
 PHE   0.017   0.003   PHE J 271 
 TRP   0.010   0.002   TRP J 309 
 HIS   0.005   0.002   HIS K 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 3740)
  covalent geometry    : angle       1.01732 ( 5150)
  SS BOND              : bond        0.00198 (    6)
  SS BOND              : angle       0.97283 (   12)
  hydrogen bonds       : bond        0.03704 (   50)
  hydrogen bonds       : angle       8.19032 (  117)
  link_ALPHA1-3        : bond        0.01370 (    1)
  link_ALPHA1-3        : angle       6.14974 (    3)
  link_ALPHA1-4        : bond        0.02654 (    3)
  link_ALPHA1-4        : angle       4.98811 (    9)
  link_BETA1-2         : bond        0.00427 (    2)
  link_BETA1-2         : angle       4.21208 (    6)
  link_BETA1-4         : bond        0.01458 (    4)
  link_BETA1-4         : angle       3.73496 (   12)
  link_NAG-ASN         : bond        0.00553 (    2)
  link_NAG-ASN         : angle       5.72685 (    6)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 19
  time to evaluate  : 0.138 
Fit side-chains
REVERT: J  164 HIS cc_start: 0.2416 (OUTLIER) cc_final: 0.1576 (t-90)
REVERT: J  265 GLU cc_start: 0.3593 (OUTLIER) cc_final: 0.3364 (tt0)
REVERT: J  377 TRP cc_start: 0.6018 (OUTLIER) cc_final: 0.4983 (p90)
REVERT: J  397 ASP cc_start: 0.6038 (m-30) cc_final: 0.5823 (m-30)
REVERT: K  316 LYS cc_start: 0.6500 (tttt) cc_final: 0.6273 (tptt)
REVERT: K  328 ILE cc_start: 0.1835 (OUTLIER) cc_final: 0.1556 (mm)
REVERT: K  369 TYR cc_start: 0.4503 (OUTLIER) cc_final: 0.3235 (p90)
REVERT: K  424 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.5194 (pp-130)
  outliers start: 36
  outliers final: 27
  residues processed: 49
  average time/residue: 0.0395
  time to fit residues: 2.8610
Evaluate side-chains
  52 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 19
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  164 HIS
Chi-restraints excluded: chain J residue  175 LEU
Chi-restraints excluded: chain J residue  181 VAL
Chi-restraints excluded: chain J residue  189 LEU
Chi-restraints excluded: chain J residue  214 LYS
Chi-restraints excluded: chain J residue  219 THR
Chi-restraints excluded: chain J residue  237 PHE
Chi-restraints excluded: chain J residue  245 ASP
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  265 GLU
Chi-restraints excluded: chain J residue  275 VAL
Chi-restraints excluded: chain J residue  278 VAL
Chi-restraints excluded: chain J residue  281 HIS
Chi-restraints excluded: chain J residue  319 VAL
Chi-restraints excluded: chain J residue  347 LEU
Chi-restraints excluded: chain J residue  377 TRP
Chi-restraints excluded: chain K residue  127 SER
Chi-restraints excluded: chain K residue  164 HIS
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  229 GLU
Chi-restraints excluded: chain K residue  235 SER
Chi-restraints excluded: chain K residue  237 PHE
Chi-restraints excluded: chain K residue  252 THR
Chi-restraints excluded: chain K residue  260 VAL
Chi-restraints excluded: chain K residue  302 LEU
Chi-restraints excluded: chain K residue  304 VAL
Chi-restraints excluded: chain K residue  311 ASN
Chi-restraints excluded: chain K residue  328 ILE
Chi-restraints excluded: chain K residue  346 THR
Chi-restraints excluded: chain K residue  359 VAL
Chi-restraints excluded: chain K residue  361 LEU
Chi-restraints excluded: chain K residue  369 TYR
Chi-restraints excluded: chain K residue  424 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 19 optimal weight:    0.0980
   chunk 4 optimal weight:   20.0000
   chunk 16 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
J 164 HIS
K 311 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4918 r_free = 0.4918 target = 0.172460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4763 r_free = 0.4763 target = 0.160155 restraints weight = 12155.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.4789 rms_B_bonded: 3.05
r_work: 0.4714 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.4714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4692
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4692 r_free = 0.4692    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       91 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4691 r_free = 0.4691    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
r_final: 0.4691
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4720
moved from start:          0.3357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   3758  Z= 0.252
  Angle     :  1.210  12.579   5198  Z= 0.545
  Chirality :  0.058   0.414    683
  Planarity :  0.010   0.121    653
  Dihedral  : 22.764 124.100    819
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 24.99
  Ramachandran Plot:
    Outliers :  0.97 %
    Allowed  : 29.15 %
    Favored  : 69.88 %
  Rotamer:
    Outliers : 12.46 %
    Allowed  : 22.56 %
    Favored  : 64.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.57 (0.30), residues: 518
  helix: -1.91 (1.60), residues: 11
  sheet: -3.06 (0.43), residues: 104
  loop : -4.34 (0.25), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 288 
 TYR   0.016   0.002   TYR K 369 
 PHE   0.022   0.003   PHE J 271 
 TRP   0.012   0.002   TRP J 309 
 HIS   0.009   0.003   HIS J 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 ( 3740)
  covalent geometry    : angle       1.12299 ( 5150)
  SS BOND              : bond        0.00222 (    6)
  SS BOND              : angle       1.10735 (   12)
  hydrogen bonds       : bond        0.04393 (   50)
  hydrogen bonds       : angle       8.27205 (  117)
  link_ALPHA1-3        : bond        0.01570 (    1)
  link_ALPHA1-3        : angle       7.50716 (    3)
  link_ALPHA1-4        : bond        0.02427 (    3)
  link_ALPHA1-4        : angle       5.72111 (    9)
  link_BETA1-2         : bond        0.00396 (    2)
  link_BETA1-2         : angle       5.71532 (    6)
  link_BETA1-4         : bond        0.01919 (    4)
  link_BETA1-4         : angle       4.30067 (   12)
  link_NAG-ASN         : bond        0.00496 (    2)
  link_NAG-ASN         : angle       6.05265 (    6)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 21
  time to evaluate  : 0.140 
Fit side-chains
REVERT: J  164 HIS cc_start: 0.2413 (OUTLIER) cc_final: 0.1625 (t-90)
REVERT: J  377 TRP cc_start: 0.6217 (OUTLIER) cc_final: 0.5212 (p90)
REVERT: K  316 LYS cc_start: 0.6758 (tttt) cc_final: 0.6505 (tptt)
REVERT: K  328 ILE cc_start: 0.2020 (OUTLIER) cc_final: 0.1663 (mm)
REVERT: K  369 TYR cc_start: 0.4458 (OUTLIER) cc_final: 0.3121 (p90)
REVERT: K  424 MET cc_start: 0.6381 (OUTLIER) cc_final: 0.5169 (pp-130)
  outliers start: 37
  outliers final: 29
  residues processed: 51
  average time/residue: 0.0401
  time to fit residues: 3.0026
Evaluate side-chains
  54 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 20
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  164 HIS
Chi-restraints excluded: chain J residue  175 LEU
Chi-restraints excluded: chain J residue  181 VAL
Chi-restraints excluded: chain J residue  189 LEU
Chi-restraints excluded: chain J residue  214 LYS
Chi-restraints excluded: chain J residue  219 THR
Chi-restraints excluded: chain J residue  237 PHE
Chi-restraints excluded: chain J residue  245 ASP
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  275 VAL
Chi-restraints excluded: chain J residue  278 VAL
Chi-restraints excluded: chain J residue  281 HIS
Chi-restraints excluded: chain J residue  319 VAL
Chi-restraints excluded: chain J residue  347 LEU
Chi-restraints excluded: chain J residue  361 LEU
Chi-restraints excluded: chain J residue  377 TRP
Chi-restraints excluded: chain K residue  127 SER
Chi-restraints excluded: chain K residue  164 HIS
Chi-restraints excluded: chain K residue  181 VAL
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  229 GLU
Chi-restraints excluded: chain K residue  235 SER
Chi-restraints excluded: chain K residue  237 PHE
Chi-restraints excluded: chain K residue  252 THR
Chi-restraints excluded: chain K residue  260 VAL
Chi-restraints excluded: chain K residue  261 ASP
Chi-restraints excluded: chain K residue  302 LEU
Chi-restraints excluded: chain K residue  304 VAL
Chi-restraints excluded: chain K residue  328 ILE
Chi-restraints excluded: chain K residue  346 THR
Chi-restraints excluded: chain K residue  359 VAL
Chi-restraints excluded: chain K residue  361 LEU
Chi-restraints excluded: chain K residue  369 TYR
Chi-restraints excluded: chain K residue  424 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 54 optimal weight:   20.0000
   chunk 24 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0270
   chunk 40 optimal weight:    0.8980
   chunk 15 optimal weight:    7.9990
   overall best weight:    0.9240

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

Flipped N/Q/H residues before XYZ refinement:
J 164 HIS
K 311 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4939 r_free = 0.4939 target = 0.173571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4800 r_free = 0.4800 target = 0.162090 restraints weight = 11957.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.4801 rms_B_bonded: 3.07
r_work: 0.4730 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.4730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4743
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4743 r_free = 0.4743    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4743 r_free = 0.4743    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
r_final: 0.4743
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4473
moved from start:          0.3683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   3758  Z= 0.174
  Angle     :  1.037  12.215   5198  Z= 0.473
  Chirality :  0.055   0.415    683
  Planarity :  0.009   0.118    653
  Dihedral  : 21.467 120.440    819
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 19.96
  Ramachandran Plot:
    Outliers :  0.97 %
    Allowed  : 27.03 %
    Favored  : 72.01 %
  Rotamer:
    Outliers : 11.45 %
    Allowed  : 24.24 %
    Favored  : 64.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.47 (0.31), residues: 518
  helix: -1.77 (1.24), residues: 18
  sheet: -3.01 (0.42), residues: 115
  loop : -4.30 (0.26), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG J 288 
 TYR   0.017   0.001   TYR K 369 
 PHE   0.013   0.002   PHE J 271 
 TRP   0.009   0.001   TRP J 309 
 HIS   0.012   0.003   HIS J 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 3740)
  covalent geometry    : angle       0.96301 ( 5150)
  SS BOND              : bond        0.00211 (    6)
  SS BOND              : angle       1.00062 (   12)
  hydrogen bonds       : bond        0.03567 (   50)
  hydrogen bonds       : angle       7.92632 (  117)
  link_ALPHA1-3        : bond        0.01419 (    1)
  link_ALPHA1-3        : angle       6.07053 (    3)
  link_ALPHA1-4        : bond        0.02453 (    3)
  link_ALPHA1-4        : angle       5.30010 (    9)
  link_BETA1-2         : bond        0.00395 (    2)
  link_BETA1-2         : angle       3.84616 (    6)
  link_BETA1-4         : bond        0.01396 (    4)
  link_BETA1-4         : angle       3.59835 (   12)
  link_NAG-ASN         : bond        0.00556 (    2)
  link_NAG-ASN         : angle       5.70766 (    6)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 19
  time to evaluate  : 0.166 
Fit side-chains
REVERT: J  164 HIS cc_start: 0.2217 (OUTLIER) cc_final: 0.1863 (t-90)
REVERT: J  377 TRP cc_start: 0.6007 (OUTLIER) cc_final: 0.4973 (p90)
REVERT: K  328 ILE cc_start: 0.2064 (OUTLIER) cc_final: 0.1535 (mm)
REVERT: K  369 TYR cc_start: 0.4399 (OUTLIER) cc_final: 0.3148 (p90)
REVERT: K  424 MET cc_start: 0.6369 (OUTLIER) cc_final: 0.5343 (pp-130)
  outliers start: 34
  outliers final: 27
  residues processed: 48
  average time/residue: 0.0309
  time to fit residues: 2.3217
Evaluate side-chains
  50 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 18
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  164 HIS
Chi-restraints excluded: chain J residue  175 LEU
Chi-restraints excluded: chain J residue  181 VAL
Chi-restraints excluded: chain J residue  189 LEU
Chi-restraints excluded: chain J residue  214 LYS
Chi-restraints excluded: chain J residue  219 THR
Chi-restraints excluded: chain J residue  237 PHE
Chi-restraints excluded: chain J residue  245 ASP
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  275 VAL
Chi-restraints excluded: chain J residue  278 VAL
Chi-restraints excluded: chain J residue  281 HIS
Chi-restraints excluded: chain J residue  319 VAL
Chi-restraints excluded: chain J residue  347 LEU
Chi-restraints excluded: chain J residue  377 TRP
Chi-restraints excluded: chain K residue  127 SER
Chi-restraints excluded: chain K residue  164 HIS
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  229 GLU
Chi-restraints excluded: chain K residue  235 SER
Chi-restraints excluded: chain K residue  252 THR
Chi-restraints excluded: chain K residue  260 VAL
Chi-restraints excluded: chain K residue  261 ASP
Chi-restraints excluded: chain K residue  302 LEU
Chi-restraints excluded: chain K residue  304 VAL
Chi-restraints excluded: chain K residue  311 ASN
Chi-restraints excluded: chain K residue  328 ILE
Chi-restraints excluded: chain K residue  346 THR
Chi-restraints excluded: chain K residue  359 VAL
Chi-restraints excluded: chain K residue  361 LEU
Chi-restraints excluded: chain K residue  369 TYR
Chi-restraints excluded: chain K residue  424 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 8 optimal weight:    9.9990
   chunk 26 optimal weight:   20.0000
   chunk 22 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 6 optimal weight:   20.0000
   chunk 1 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0570
   chunk 52 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   overall best weight:    2.7304

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

Flipped N/Q/H residues before XYZ refinement:
J 164 HIS
K 311 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4923 r_free = 0.4923 target = 0.172704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4766 r_free = 0.4766 target = 0.160313 restraints weight = 11749.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.4791 rms_B_bonded: 2.96
r_work: 0.4715 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.4715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4729
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4729 r_free = 0.4729    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4729 r_free = 0.4729    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       96 |
|-----------------------------------------------------------------------------|
r_final: 0.4729
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4712
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   3758  Z= 0.249
  Angle     :  1.187  12.733   5198  Z= 0.537
  Chirality :  0.057   0.425    683
  Planarity :  0.010   0.120    653
  Dihedral  : 22.494 124.004    819
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 24.60
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 28.96 %
    Favored  : 70.27 %
  Rotamer:
    Outliers : 11.78 %
    Allowed  : 23.23 %
    Favored  : 64.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.42 (0.31), residues: 518
  helix: -1.78 (1.63), residues: 11
  sheet: -2.84 (0.46), residues: 98
  loop : -4.26 (0.26), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 288 
 TYR   0.016   0.002   TYR K 369 
 PHE   0.023   0.003   PHE K 237 
 TRP   0.011   0.002   TRP J 309 
 HIS   0.008   0.003   HIS J 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 ( 3740)
  covalent geometry    : angle       1.10073 ( 5150)
  SS BOND              : bond        0.00255 (    6)
  SS BOND              : angle       1.15328 (   12)
  hydrogen bonds       : bond        0.04356 (   50)
  hydrogen bonds       : angle       8.08735 (  117)
  link_ALPHA1-3        : bond        0.01947 (    1)
  link_ALPHA1-3        : angle       7.60694 (    3)
  link_ALPHA1-4        : bond        0.02063 (    3)
  link_ALPHA1-4        : angle       5.55116 (    9)
  link_BETA1-2         : bond        0.00459 (    2)
  link_BETA1-2         : angle       5.62600 (    6)
  link_BETA1-4         : bond        0.02057 (    4)
  link_BETA1-4         : angle       4.24949 (   12)
  link_NAG-ASN         : bond        0.00529 (    2)
  link_NAG-ASN         : angle       5.93430 (    6)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 21
  time to evaluate  : 0.129 
Fit side-chains
REVERT: J  164 HIS cc_start: 0.2032 (OUTLIER) cc_final: 0.1466 (t-90)
REVERT: J  377 TRP cc_start: 0.6286 (OUTLIER) cc_final: 0.5265 (p90)
REVERT: K  316 LYS cc_start: 0.6731 (tttt) cc_final: 0.6465 (tptt)
REVERT: K  328 ILE cc_start: 0.2343 (OUTLIER) cc_final: 0.1748 (mm)
REVERT: K  369 TYR cc_start: 0.4513 (OUTLIER) cc_final: 0.3193 (p90)
REVERT: K  424 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.5267 (pp-130)
  outliers start: 35
  outliers final: 27
  residues processed: 50
  average time/residue: 0.0413
  time to fit residues: 2.9850
Evaluate side-chains
  53 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 21
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  164 HIS
Chi-restraints excluded: chain J residue  175 LEU
Chi-restraints excluded: chain J residue  181 VAL
Chi-restraints excluded: chain J residue  189 LEU
Chi-restraints excluded: chain J residue  214 LYS
Chi-restraints excluded: chain J residue  219 THR
Chi-restraints excluded: chain J residue  237 PHE
Chi-restraints excluded: chain J residue  245 ASP
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  275 VAL
Chi-restraints excluded: chain J residue  278 VAL
Chi-restraints excluded: chain J residue  281 HIS
Chi-restraints excluded: chain J residue  319 VAL
Chi-restraints excluded: chain J residue  347 LEU
Chi-restraints excluded: chain J residue  377 TRP
Chi-restraints excluded: chain K residue  127 SER
Chi-restraints excluded: chain K residue  164 HIS
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  229 GLU
Chi-restraints excluded: chain K residue  235 SER
Chi-restraints excluded: chain K residue  252 THR
Chi-restraints excluded: chain K residue  260 VAL
Chi-restraints excluded: chain K residue  261 ASP
Chi-restraints excluded: chain K residue  302 LEU
Chi-restraints excluded: chain K residue  304 VAL
Chi-restraints excluded: chain K residue  311 ASN
Chi-restraints excluded: chain K residue  328 ILE
Chi-restraints excluded: chain K residue  346 THR
Chi-restraints excluded: chain K residue  359 VAL
Chi-restraints excluded: chain K residue  361 LEU
Chi-restraints excluded: chain K residue  369 TYR
Chi-restraints excluded: chain K residue  424 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 2 optimal weight:    0.3980
   chunk 26 optimal weight:   20.0000
   chunk 36 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 52 optimal weight:    0.0070
   chunk 30 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 49 optimal weight:    9.9990
   chunk 3 optimal weight:    7.9990
   overall best weight:    0.8000

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

Flipped N/Q/H residues before XYZ refinement:
J 164 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4969 r_free = 0.4969 target = 0.180655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4840 r_free = 0.4840 target = 0.169100 restraints weight = 12111.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.4825 rms_B_bonded: 3.15
r_work: 0.4751 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.4751
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4765
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4765 r_free = 0.4765    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       96 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4766 r_free = 0.4766    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       96 |
|-----------------------------------------------------------------------------|
r_final: 0.4766
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4499
moved from start:          0.3934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   3758  Z= 0.177
  Angle     :  1.035  11.176   5198  Z= 0.476
  Chirality :  0.055   0.420    683
  Planarity :  0.009   0.117    653
  Dihedral  : 21.168 120.268    819
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 19.25
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 25.87 %
    Favored  : 73.36 %
  Rotamer:
    Outliers : 10.77 %
    Allowed  : 24.24 %
    Favored  : 64.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.38 (0.31), residues: 518
  helix: -1.76 (1.23), residues: 18
  sheet: -2.84 (0.47), residues: 100
  loop : -4.26 (0.26), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG J 412 
 TYR   0.017   0.001   TYR K 369 
 PHE   0.013   0.002   PHE J 271 
 TRP   0.009   0.001   TRP J 309 
 HIS   0.004   0.001   HIS K 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 3740)
  covalent geometry    : angle       0.96383 ( 5150)
  SS BOND              : bond        0.00192 (    6)
  SS BOND              : angle       0.95016 (   12)
  hydrogen bonds       : bond        0.03568 (   50)
  hydrogen bonds       : angle       7.77893 (  117)
  link_ALPHA1-3        : bond        0.01376 (    1)
  link_ALPHA1-3        : angle       6.07579 (    3)
  link_ALPHA1-4        : bond        0.02091 (    3)
  link_ALPHA1-4        : angle       4.96361 (    9)
  link_BETA1-2         : bond        0.00344 (    2)
  link_BETA1-2         : angle       4.11914 (    6)
  link_BETA1-4         : bond        0.01326 (    4)
  link_BETA1-4         : angle       3.52904 (   12)
  link_NAG-ASN         : bond        0.00559 (    2)
  link_NAG-ASN         : angle       5.68766 (    6)

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

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

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1036 Ramachandran restraints generated.
    518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 17
  time to evaluate  : 0.151 
Fit side-chains
REVERT: J  164 HIS cc_start: 0.1432 (OUTLIER) cc_final: 0.1115 (t-90)
REVERT: J  377 TRP cc_start: 0.6234 (OUTLIER) cc_final: 0.5066 (p90)
REVERT: K  328 ILE cc_start: 0.2235 (OUTLIER) cc_final: 0.1679 (mm)
REVERT: K  369 TYR cc_start: 0.4433 (OUTLIER) cc_final: 0.3194 (p90)
REVERT: K  424 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.5482 (pp-130)
  outliers start: 32
  outliers final: 26
  residues processed: 44
  average time/residue: 0.0359
  time to fit residues: 2.4185
Evaluate side-chains
  48 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 17
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  164 HIS
Chi-restraints excluded: chain J residue  175 LEU
Chi-restraints excluded: chain J residue  181 VAL
Chi-restraints excluded: chain J residue  189 LEU
Chi-restraints excluded: chain J residue  214 LYS
Chi-restraints excluded: chain J residue  219 THR
Chi-restraints excluded: chain J residue  237 PHE
Chi-restraints excluded: chain J residue  245 ASP
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  275 VAL
Chi-restraints excluded: chain J residue  278 VAL
Chi-restraints excluded: chain J residue  281 HIS
Chi-restraints excluded: chain J residue  319 VAL
Chi-restraints excluded: chain J residue  347 LEU
Chi-restraints excluded: chain J residue  377 TRP
Chi-restraints excluded: chain K residue  127 SER
Chi-restraints excluded: chain K residue  164 HIS
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  229 GLU
Chi-restraints excluded: chain K residue  235 SER
Chi-restraints excluded: chain K residue  252 THR
Chi-restraints excluded: chain K residue  260 VAL
Chi-restraints excluded: chain K residue  261 ASP
Chi-restraints excluded: chain K residue  302 LEU
Chi-restraints excluded: chain K residue  304 VAL
Chi-restraints excluded: chain K residue  328 ILE
Chi-restraints excluded: chain K residue  346 THR
Chi-restraints excluded: chain K residue  359 VAL
Chi-restraints excluded: chain K residue  361 LEU
Chi-restraints excluded: chain K residue  369 TYR
Chi-restraints excluded: chain K residue  424 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0770
   chunk 4 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   chunk 49 optimal weight:   20.0000
   chunk 28 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0000
   chunk 29 optimal weight:   10.0000
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.7544

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

Flipped N/Q/H residues before XYZ refinement:
J 164 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4944 r_free = 0.4944 target = 0.175801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4817 r_free = 0.4817 target = 0.164720 restraints weight = 11887.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.4806 rms_B_bonded: 3.03
r_work: 0.4734 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.4734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4747
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4747 r_free = 0.4747    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       96 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4746 r_free = 0.4746    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      103 |
|-----------------------------------------------------------------------------|
r_final: 0.4746
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4458
moved from start:          0.4068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   3758  Z= 0.164
  Angle     :  1.002  10.802   5198  Z= 0.457
  Chirality :  0.054   0.423    683
  Planarity :  0.009   0.115    653
  Dihedral  : 20.487 119.308    819
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 18.33
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 27.41 %
    Favored  : 71.81 %
  Rotamer:
    Outliers : 10.10 %
    Allowed  : 24.58 %
    Favored  : 65.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.25 (0.32), residues: 518
  helix: -1.70 (1.25), residues: 18
  sheet: -2.46 (0.50), residues: 100
  loop : -4.26 (0.26), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG K 288 
 TYR   0.016   0.001   TYR K 369 
 PHE   0.019   0.002   PHE J 401 
 TRP   0.008   0.001   TRP J 309 
 HIS   0.004   0.002   HIS J 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3740)
  covalent geometry    : angle       0.93310 ( 5150)
  SS BOND              : bond        0.00169 (    6)
  SS BOND              : angle       0.90869 (   12)
  hydrogen bonds       : bond        0.03441 (   50)
  hydrogen bonds       : angle       7.59560 (  117)
  link_ALPHA1-3        : bond        0.01352 (    1)
  link_ALPHA1-3        : angle       5.82709 (    3)
  link_ALPHA1-4        : bond        0.02103 (    3)
  link_ALPHA1-4        : angle       4.82513 (    9)
  link_BETA1-2         : bond        0.00351 (    2)
  link_BETA1-2         : angle       3.61256 (    6)
  link_BETA1-4         : bond        0.01316 (    4)
  link_BETA1-4         : angle       3.51900 (   12)
  link_NAG-ASN         : bond        0.00607 (    2)
  link_NAG-ASN         : angle       5.60051 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1069.35 seconds
wall clock time: 19 minutes 1.71 seconds (1141.71 seconds total)