Starting phenix.real_space_refine
on Wed Sep 17 10:14:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ukf_26579/09_2025/7ukf_26579.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ukf_26579/09_2025/7ukf_26579.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ukf_26579/09_2025/7ukf_26579.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ukf_26579/09_2025/7ukf_26579.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ukf_26579/09_2025/7ukf_26579.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ukf_26579/09_2025/7ukf_26579.map"
  }
  resolution = 3.02
  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=   0.005 sd=   0.068
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: 6
    Type Number    sf(0)   Gaussians
     Hg      1     10.96       5
     K       4      8.98       5
     S      60      5.16       5
     C    5252      2.51       5
     N    1332      2.21       5
     O    1356      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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8005
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2000
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 2000
          Classifications: {'peptide': 259}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 10, 'TRANS': 248}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {'  K': 4, ' HG': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1842  SG  CYS A 406      56.243  52.488  57.734  1.00 69.40           S

  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 1.63, per 1000 atoms: 0.20
  Number of scatterers: 8005
  At special positions: 0
  Unit cell: (113.162, 112.336, 84.252, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Hg      1     79.96
     K       4     19.00
     S      60     16.00
     O    1356      8.00
     N    1332      7.00
     C    5252      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 506.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1952

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      81.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 177
    Processing helix  chain 'A' and resid 181 through 206
    Processing helix  chain 'A' and resid 220 through 225
    Processing helix  chain 'A' and resid 225 through 250
    Processing helix  chain 'A' and resid 253 through 260
      removed outlier: 3.602A  pdb=" N   SER A 260 " --> pdb=" O   ARG A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 279
      Proline residue:  A 272  - end of helix
    Processing helix  chain 'A' and resid 287 through 293
      removed outlier: 4.020A  pdb=" N   VAL A 290 " --> pdb=" O   GLY A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 304
      removed outlier: 3.972A  pdb=" N   PHE A 298 " --> pdb=" O   VAL A 294 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ARG A 299 " --> pdb=" O   PHE A 295 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ILE A 300 " --> pdb=" O   ARG A 296 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   PHE A 301 " --> pdb=" O   VAL A 297 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LYS A 302 " --> pdb=" O   PHE A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 347
      removed outlier: 5.088A  pdb=" N   SER A 322 " --> pdb=" O   LYS A 318 " (cutoff:3.500A)
      removed outlier: 5.326A  pdb=" N   GLU A 323 " --> pdb=" O   SER A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 368
      removed outlier: 3.818A  pdb=" N   TRP A 362 " --> pdb=" O   PRO A 358 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   TYR A 363 " --> pdb=" O   ALA A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 400
    Processing helix  chain 'A' and resid 400 through 423
      removed outlier: 4.252A  pdb=" N   VAL A 404 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 177
    Processing helix  chain 'B' and resid 181 through 206
    Processing helix  chain 'B' and resid 220 through 225
    Processing helix  chain 'B' and resid 225 through 250
    Processing helix  chain 'B' and resid 253 through 260
      removed outlier: 3.603A  pdb=" N   SER B 260 " --> pdb=" O   ARG B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 279
      Proline residue:  B 272  - end of helix
    Processing helix  chain 'B' and resid 287 through 293
      removed outlier: 4.021A  pdb=" N   VAL B 290 " --> pdb=" O   GLY B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 304
      removed outlier: 3.972A  pdb=" N   PHE B 298 " --> pdb=" O   VAL B 294 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ARG B 299 " --> pdb=" O   PHE B 295 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ILE B 300 " --> pdb=" O   ARG B 296 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   PHE B 301 " --> pdb=" O   VAL B 297 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LYS B 302 " --> pdb=" O   PHE B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 347
      removed outlier: 5.087A  pdb=" N   SER B 322 " --> pdb=" O   LYS B 318 " (cutoff:3.500A)
      removed outlier: 5.327A  pdb=" N   GLU B 323 " --> pdb=" O   SER B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 368
      removed outlier: 3.818A  pdb=" N   TRP B 362 " --> pdb=" O   PRO B 358 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   TYR B 363 " --> pdb=" O   ALA B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 400
    Processing helix  chain 'B' and resid 400 through 423
      removed outlier: 4.252A  pdb=" N   VAL B 404 " --> pdb=" O   LEU B 400 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 177
    Processing helix  chain 'C' and resid 181 through 206
    Processing helix  chain 'C' and resid 220 through 225
    Processing helix  chain 'C' and resid 225 through 250
    Processing helix  chain 'C' and resid 253 through 260
      removed outlier: 3.603A  pdb=" N   SER C 260 " --> pdb=" O   ARG C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 279
      Proline residue:  C 272  - end of helix
    Processing helix  chain 'C' and resid 287 through 293
      removed outlier: 4.020A  pdb=" N   VAL C 290 " --> pdb=" O   GLY C 287 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 304
      removed outlier: 3.973A  pdb=" N   PHE C 298 " --> pdb=" O   VAL C 294 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ARG C 299 " --> pdb=" O   PHE C 295 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ILE C 300 " --> pdb=" O   ARG C 296 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   PHE C 301 " --> pdb=" O   VAL C 297 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LYS C 302 " --> pdb=" O   PHE C 298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 309 through 347
      removed outlier: 5.087A  pdb=" N   SER C 322 " --> pdb=" O   LYS C 318 " (cutoff:3.500A)
      removed outlier: 5.326A  pdb=" N   GLU C 323 " --> pdb=" O   SER C 319 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 356 through 368
      removed outlier: 3.818A  pdb=" N   TRP C 362 " --> pdb=" O   PRO C 358 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   TYR C 363 " --> pdb=" O   ALA C 359 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 380 through 400
    Processing helix  chain 'C' and resid 400 through 423
      removed outlier: 4.252A  pdb=" N   VAL C 404 " --> pdb=" O   LEU C 400 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 177
    Processing helix  chain 'D' and resid 181 through 206
    Processing helix  chain 'D' and resid 220 through 225
    Processing helix  chain 'D' and resid 225 through 250
    Processing helix  chain 'D' and resid 253 through 260
      removed outlier: 3.603A  pdb=" N   SER D 260 " --> pdb=" O   ARG D 256 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 260 through 279
      Proline residue:  D 272  - end of helix
    Processing helix  chain 'D' and resid 287 through 293
      removed outlier: 4.020A  pdb=" N   VAL D 290 " --> pdb=" O   GLY D 287 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 294 through 304
      removed outlier: 3.972A  pdb=" N   PHE D 298 " --> pdb=" O   VAL D 294 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ARG D 299 " --> pdb=" O   PHE D 295 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE D 300 " --> pdb=" O   ARG D 296 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   PHE D 301 " --> pdb=" O   VAL D 297 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LYS D 302 " --> pdb=" O   PHE D 298 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 309 through 347
      removed outlier: 5.087A  pdb=" N   SER D 322 " --> pdb=" O   LYS D 318 " (cutoff:3.500A)
      removed outlier: 5.327A  pdb=" N   GLU D 323 " --> pdb=" O   SER D 319 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 356 through 368
      removed outlier: 3.818A  pdb=" N   TRP D 362 " --> pdb=" O   PRO D 358 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   TYR D 363 " --> pdb=" O   ALA D 359 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 380 through 400
    Processing helix  chain 'D' and resid 400 through 423
      removed outlier: 4.252A  pdb=" N   VAL D 404 " --> pdb=" O   LEU D 400 " (cutoff:3.500A)

    601 hydrogen bonds defined for protein.
    1767 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.25

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2440
        1.34 -     1.46: 1907
        1.46 -     1.58: 3757
        1.58 -     1.69: 0
        1.69 -     1.81: 92
  Bond restraints: 8196
  Sorted by residual:
  bond pdb=" C   VAL B 377 "
       pdb=" N   PRO B 378 "
    ideal  model  delta    sigma   weight residual
    1.333  1.320  0.013 1.17e-02 7.31e+03 1.22e+00
  bond pdb=" C   VAL A 377 "
       pdb=" N   PRO A 378 "
    ideal  model  delta    sigma   weight residual
    1.333  1.320  0.012 1.17e-02 7.31e+03 1.12e+00
  bond pdb=" C   VAL C 377 "
       pdb=" N   PRO C 378 "
    ideal  model  delta    sigma   weight residual
    1.333  1.320  0.012 1.17e-02 7.31e+03 1.11e+00
  bond pdb=" C   VAL D 377 "
       pdb=" N   PRO D 378 "
    ideal  model  delta    sigma   weight residual
    1.333  1.320  0.012 1.17e-02 7.31e+03 1.11e+00
  bond pdb=" CB  GLU A 346 "
       pdb=" CG  GLU A 346 "
    ideal  model  delta    sigma   weight residual
    1.520  1.494  0.026 3.00e-02 1.11e+03 7.38e-01
  ... (remaining 8191 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 10563
        1.22 -     2.45: 451
        2.45 -     3.67: 90
        3.67 -     4.89: 20
        4.89 -     6.12: 12
  Bond angle restraints: 11136
  Sorted by residual:
  angle pdb=" N   LEU C 400 "
        pdb=" CA  LEU C 400 "
        pdb=" C   LEU C 400 "
      ideal   model   delta    sigma   weight residual
     109.81  115.30   -5.49 2.21e+00 2.05e-01 6.17e+00
  angle pdb=" N   LEU D 400 "
        pdb=" CA  LEU D 400 "
        pdb=" C   LEU D 400 "
      ideal   model   delta    sigma   weight residual
     109.81  115.27   -5.46 2.21e+00 2.05e-01 6.11e+00
  angle pdb=" N   LEU A 400 "
        pdb=" CA  LEU A 400 "
        pdb=" C   LEU A 400 "
      ideal   model   delta    sigma   weight residual
     109.81  115.26   -5.45 2.21e+00 2.05e-01 6.07e+00
  angle pdb=" N   LEU B 400 "
        pdb=" CA  LEU B 400 "
        pdb=" C   LEU B 400 "
      ideal   model   delta    sigma   weight residual
     109.81  115.24   -5.43 2.21e+00 2.05e-01 6.03e+00
  angle pdb=" CA  LEU C 271 "
        pdb=" C   LEU C 271 "
        pdb=" N   PRO C 272 "
      ideal   model   delta    sigma   weight residual
     118.44  121.56   -3.12 1.59e+00 3.96e-01 3.85e+00
  ... (remaining 11131 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.14: 4010
       10.14 -    20.28: 530
       20.28 -    30.43: 176
       30.43 -    40.57: 76
       40.57 -    50.71: 12
  Dihedral angle restraints: 4804
    sinusoidal: 1772
      harmonic: 3032
  Sorted by residual:
  dihedral pdb=" CB  MET D 333 "
           pdb=" CG  MET D 333 "
           pdb=" SD  MET D 333 "
           pdb=" CE  MET D 333 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  110.71  -50.71     3      1.50e+01 4.44e-03 8.93e+00
  dihedral pdb=" CB  MET A 333 "
           pdb=" CG  MET A 333 "
           pdb=" SD  MET A 333 "
           pdb=" CE  MET A 333 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  110.68  -50.68     3      1.50e+01 4.44e-03 8.93e+00
  dihedral pdb=" CB  MET B 333 "
           pdb=" CG  MET B 333 "
           pdb=" SD  MET B 333 "
           pdb=" CE  MET B 333 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  110.66  -50.66     3      1.50e+01 4.44e-03 8.93e+00
  ... (remaining 4801 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 629
       0.026 -    0.051: 416
       0.051 -    0.077: 183
       0.077 -    0.102: 71
       0.102 -    0.128: 17
  Chirality restraints: 1316
  Sorted by residual:
  chirality pdb=" CA  VAL B 207 "
            pdb=" N   VAL B 207 "
            pdb=" C   VAL B 207 "
            pdb=" CB  VAL B 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.09e-01
  chirality pdb=" CA  VAL C 207 "
            pdb=" N   VAL C 207 "
            pdb=" C   VAL C 207 "
            pdb=" CB  VAL C 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  VAL A 207 "
            pdb=" N   VAL A 207 "
            pdb=" C   VAL A 207 "
            pdb=" CB  VAL A 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.02e-01
  ... (remaining 1313 not shown)

  Planarity restraints: 1364
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 357 "    0.030 5.00e-02 4.00e+02   4.49e-02 3.23e+00
        pdb=" N   PRO C 358 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO C 358 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C 358 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 357 "    0.030 5.00e-02 4.00e+02   4.48e-02 3.20e+00
        pdb=" N   PRO D 358 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO D 358 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO D 358 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 357 "    0.030 5.00e-02 4.00e+02   4.48e-02 3.20e+00
        pdb=" N   PRO B 358 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 358 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 358 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1361 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.86: 2973
        2.86 -     3.43: 9594
        3.43 -     4.00: 14762
        4.00 -     4.57: 21588
        4.57 -     5.14: 30209
  Nonbonded interactions: 79126
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 166 "
            pdb=" OE1 GLN B 169 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG1 THR D 166 "
            pdb=" OE1 GLN D 169 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OG1 THR A 166 "
            pdb=" OE1 GLN A 169 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OG1 THR C 166 "
            pdb=" OE1 GLN C 169 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OH  TYR D 188 "
            pdb=" O   PHE D 303 "
     model   vdw
     2.339 3.040
  ... (remaining 79121 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 166 through 424)
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.770
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
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      :  0.004   0.031   8196  Z= 0.183
  Angle     :  0.611   6.115  11136  Z= 0.349
  Chirality :  0.041   0.128   1316
  Planarity :  0.005   0.045   1364
  Dihedral  : 11.495  50.711   2852
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.27), residues: 1028
  helix:  0.91 (0.18), residues: 796
  sheet:  None (None), residues: 0
  loop :  0.83 (0.47), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 299 
 TYR   0.017   0.002   TYR C 188 
 PHE   0.010   0.001   PHE C 326 
 TRP   0.007   0.001   TRP B 172 
 HIS   0.001   0.000   HIS C 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8196)
  covalent geometry    : angle       0.61085 (11136)
  hydrogen bonds       : bond        0.09225 (  601)
  hydrogen bonds       : angle       5.31653 ( 1767)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.313 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1133
  time to fit residues: 18.5446
Evaluate side-chains
  111 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 408 ASN
B 408 ASN
C 408 ASN
D 408 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.215178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.151255 restraints weight = 5703.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.59
r_work: 0.3312 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.0931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   8196  Z= 0.196
  Angle     :  0.576   6.223  11136  Z= 0.301
  Chirality :  0.041   0.130   1316
  Planarity :  0.005   0.046   1364
  Dihedral  :  3.827  13.264   1148
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  6.01 %
    Favored  : 93.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.26), residues: 1028
  helix:  0.83 (0.18), residues: 840
  sheet:  None (None), residues: 0
  loop : -0.13 (0.47), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 305 
 TYR   0.018   0.002   TYR A 225 
 PHE   0.011   0.001   PHE D 326 
 TRP   0.007   0.002   TRP C 172 
 HIS   0.002   0.000   HIS A 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 8196)
  covalent geometry    : angle       0.57640 (11136)
  hydrogen bonds       : bond        0.05101 (  601)
  hydrogen bonds       : angle       4.38066 ( 1767)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 107
  time to evaluate  : 0.283 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 108
  average time/residue: 0.0928
  time to fit residues: 13.6990
Evaluate side-chains
  104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain C residue  239 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 95 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 76 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.215029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.151087 restraints weight = 5849.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 1.63
r_work: 0.3340 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8196  Z= 0.150
  Angle     :  0.524   5.970  11136  Z= 0.274
  Chirality :  0.039   0.133   1316
  Planarity :  0.005   0.045   1364
  Dihedral  :  3.632  12.761   1148
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.26), residues: 1028
  helix:  1.11 (0.18), residues: 840
  sheet:  None (None), residues: 0
  loop : -0.06 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 305 
 TYR   0.017   0.001   TYR A 188 
 PHE   0.011   0.001   PHE D 326 
 TRP   0.007   0.001   TRP D 172 
 HIS   0.002   0.000   HIS B 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 8196)
  covalent geometry    : angle       0.52447 (11136)
  hydrogen bonds       : bond        0.04629 (  601)
  hydrogen bonds       : angle       4.13083 ( 1767)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  257 PHE cc_start: 0.6548 (t80) cc_final: 0.6291 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0858
  time to fit residues: 13.8277
Evaluate side-chains
  103 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0000
   chunk 23 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.5984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.215557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.154193 restraints weight = 6259.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 2.00
r_work: 0.3338 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8196  Z= 0.135
  Angle     :  0.508   5.702  11136  Z= 0.265
  Chirality :  0.038   0.132   1316
  Planarity :  0.004   0.045   1364
  Dihedral  :  3.521  12.434   1148
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.08 %
    Favored  : 88.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.11 (0.26), residues: 1028
  helix:  1.66 (0.18), residues: 792
  sheet:  None (None), residues: 0
  loop :  0.74 (0.45), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 305 
 TYR   0.017   0.001   TYR A 188 
 PHE   0.011   0.001   PHE D 326 
 TRP   0.006   0.001   TRP D 172 
 HIS   0.001   0.000   HIS D 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8196)
  covalent geometry    : angle       0.50765 (11136)
  hydrogen bonds       : bond        0.04475 (  601)
  hydrogen bonds       : angle       4.01398 ( 1767)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.318 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0788
  time to fit residues: 13.0608
Evaluate side-chains
  108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 96 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 93 optimal weight:    0.5980
   chunk 50 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.214411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.154581 restraints weight = 6554.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 1.94
r_work: 0.3453 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3327 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8196  Z= 0.154
  Angle     :  0.519   5.551  11136  Z= 0.271
  Chirality :  0.039   0.132   1316
  Planarity :  0.004   0.045   1364
  Dihedral  :  3.534  12.137   1148
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 11.56 %
    Favored  : 88.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.17 (0.26), residues: 1028
  helix:  1.75 (0.18), residues: 792
  sheet:  None (None), residues: 0
  loop :  0.59 (0.44), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 305 
 TYR   0.016   0.001   TYR A 188 
 PHE   0.011   0.001   PHE C 257 
 TRP   0.006   0.001   TRP A 362 
 HIS   0.002   0.000   HIS B 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 8196)
  covalent geometry    : angle       0.51904 (11136)
  hydrogen bonds       : bond        0.04588 (  601)
  hydrogen bonds       : angle       3.99675 ( 1767)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 114
  time to evaluate  : 0.309 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 114
  average time/residue: 0.0800
  time to fit residues: 13.3276
Evaluate side-chains
  115 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 112
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain C residue  279 MET
Chi-restraints excluded: chain D residue  279 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 25 optimal weight:    5.9990
   chunk 1 optimal weight:    0.2980
   chunk 47 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    0.9782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.213801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.154041 restraints weight = 6717.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 1.96
r_work: 0.3296 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8196  Z= 0.173
  Angle     :  0.541   5.319  11136  Z= 0.281
  Chirality :  0.040   0.131   1316
  Planarity :  0.004   0.045   1364
  Dihedral  :  3.541  12.363   1148
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 11.79 %
    Favored  : 87.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.26), residues: 1028
  helix:  1.40 (0.18), residues: 840
  sheet:  None (None), residues: 0
  loop :  0.03 (0.49), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 305 
 TYR   0.015   0.001   TYR A 188 
 PHE   0.011   0.001   PHE B 257 
 TRP   0.006   0.002   TRP B 172 
 HIS   0.002   0.001   HIS B 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 8196)
  covalent geometry    : angle       0.54097 (11136)
  hydrogen bonds       : bond        0.04752 (  601)
  hydrogen bonds       : angle       4.02721 ( 1767)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.374 
Fit side-chains
REVERT: C  411 ARG cc_start: 0.8319 (tmm-80) cc_final: 0.8040 (tmm-80)
REVERT: D  411 ARG cc_start: 0.8325 (tmm-80) cc_final: 0.8116 (tmm-80)
  outliers start: 8
  outliers final: 8
  residues processed: 122
  average time/residue: 0.0869
  time to fit residues: 14.9352
Evaluate side-chains
  120 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain C residue  227 VAL
Chi-restraints excluded: chain C residue  239 ILE
Chi-restraints excluded: chain C residue  279 MET
Chi-restraints excluded: chain D residue  227 VAL
Chi-restraints excluded: chain D residue  279 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 96 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 97 optimal weight:    0.5980
   chunk 50 optimal weight:    5.9990
   chunk 6 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0770
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.5938

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.215588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.153478 restraints weight = 6840.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 2.05
r_work: 0.3341 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8196  Z= 0.135
  Angle     :  0.513   5.169  11136  Z= 0.266
  Chirality :  0.038   0.133   1316
  Planarity :  0.004   0.044   1364
  Dihedral  :  3.478  11.980   1148
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 14.03 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.26), residues: 1028
  helix:  1.53 (0.18), residues: 840
  sheet:  None (None), residues: 0
  loop :  0.08 (0.50), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 256 
 TYR   0.016   0.001   TYR A 188 
 PHE   0.014   0.001   PHE A 257 
 TRP   0.007   0.001   TRP C 172 
 HIS   0.001   0.000   HIS B 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8196)
  covalent geometry    : angle       0.51263 (11136)
  hydrogen bonds       : bond        0.04402 (  601)
  hydrogen bonds       : angle       3.91275 ( 1767)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 0.340 
Fit side-chains
REVERT: C  411 ARG cc_start: 0.8253 (tmm-80) cc_final: 0.7973 (tmm-80)
REVERT: D  411 ARG cc_start: 0.8262 (tmm-80) cc_final: 0.8055 (tmm-80)
  outliers start: 7
  outliers final: 7
  residues processed: 121
  average time/residue: 0.0898
  time to fit residues: 15.2977
Evaluate side-chains
  122 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 115
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain C residue  227 VAL
Chi-restraints excluded: chain C residue  279 MET
Chi-restraints excluded: chain D residue  227 VAL
Chi-restraints excluded: chain D residue  279 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 94 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0050
   chunk 64 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 89 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   chunk 76 optimal weight:   10.0000
   chunk 78 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.6394

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.215523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.151648 restraints weight = 6880.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 1.73
r_work: 0.3353 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8196  Z= 0.140
  Angle     :  0.510   5.192  11136  Z= 0.266
  Chirality :  0.038   0.133   1316
  Planarity :  0.004   0.044   1364
  Dihedral  :  3.448  12.190   1148
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 14.15 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.40 (0.26), residues: 1028
  helix:  1.95 (0.18), residues: 792
  sheet:  None (None), residues: 0
  loop :  0.51 (0.45), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 305 
 TYR   0.016   0.001   TYR A 188 
 PHE   0.015   0.001   PHE B 257 
 TRP   0.006   0.001   TRP A 172 
 HIS   0.001   0.000   HIS A 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8196)
  covalent geometry    : angle       0.50967 (11136)
  hydrogen bonds       : bond        0.04398 (  601)
  hydrogen bonds       : angle       3.87414 ( 1767)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  411 ARG cc_start: 0.8278 (tmm-80) cc_final: 0.8061 (tmm-80)
REVERT: C  411 ARG cc_start: 0.8260 (tmm-80) cc_final: 0.7990 (tmm-80)
REVERT: D  411 ARG cc_start: 0.8273 (tmm-80) cc_final: 0.8069 (tmm-80)
  outliers start: 8
  outliers final: 7
  residues processed: 123
  average time/residue: 0.0909
  time to fit residues: 15.6293
Evaluate side-chains
  124 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain C residue  227 VAL
Chi-restraints excluded: chain C residue  279 MET
Chi-restraints excluded: chain D residue  227 VAL
Chi-restraints excluded: chain D residue  279 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 51 optimal weight:    0.2980
   chunk 34 optimal weight:    2.9990
   chunk 98 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.7382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.215180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.166544 restraints weight = 6844.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 1.99
r_work: 0.3328 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8196  Z= 0.149
  Angle     :  0.519   5.698  11136  Z= 0.270
  Chirality :  0.039   0.133   1316
  Planarity :  0.004   0.044   1364
  Dihedral  :  3.456  12.165   1148
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 14.62 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.26), residues: 1028
  helix:  1.94 (0.18), residues: 792
  sheet:  None (None), residues: 0
  loop :  0.48 (0.44), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 256 
 TYR   0.015   0.001   TYR A 188 
 PHE   0.016   0.001   PHE A 257 
 TRP   0.006   0.001   TRP A 172 
 HIS   0.002   0.000   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 8196)
  covalent geometry    : angle       0.51934 (11136)
  hydrogen bonds       : bond        0.04460 (  601)
  hydrogen bonds       : angle       3.89112 ( 1767)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 125
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A  301 PHE cc_start: 0.7873 (m-80) cc_final: 0.7522 (m-10)
REVERT: C  411 ARG cc_start: 0.8417 (tmm-80) cc_final: 0.8188 (tmm-80)
REVERT: D  411 ARG cc_start: 0.8425 (tmm-80) cc_final: 0.8194 (tmm-80)
  outliers start: 7
  outliers final: 7
  residues processed: 129
  average time/residue: 0.1006
  time to fit residues: 17.6214
Evaluate side-chains
  126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain C residue  227 VAL
Chi-restraints excluded: chain C residue  279 MET
Chi-restraints excluded: chain D residue  227 VAL
Chi-restraints excluded: chain D residue  279 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0980
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 81 optimal weight:    0.1980
   chunk 62 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 82 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.4580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.216816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.171265 restraints weight = 6962.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 1.84
r_work: 0.3352 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8196  Z= 0.124
  Angle     :  0.500   5.186  11136  Z= 0.260
  Chirality :  0.038   0.134   1316
  Planarity :  0.004   0.044   1364
  Dihedral  :  3.385  12.014   1148
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 14.50 %
    Favored  : 84.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.52 (0.26), residues: 1028
  helix:  2.05 (0.18), residues: 792
  sheet:  None (None), residues: 0
  loop :  0.48 (0.45), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 256 
 TYR   0.016   0.001   TYR A 188 
 PHE   0.017   0.001   PHE B 257 
 TRP   0.006   0.001   TRP B 172 
 HIS   0.001   0.000   HIS B 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8196)
  covalent geometry    : angle       0.50025 (11136)
  hydrogen bonds       : bond        0.04199 (  601)
  hydrogen bonds       : angle       3.78844 ( 1767)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 0.309 
Fit side-chains
REVERT: B  301 PHE cc_start: 0.7895 (m-80) cc_final: 0.7475 (m-10)
REVERT: C  301 PHE cc_start: 0.7848 (m-80) cc_final: 0.7423 (m-10)
REVERT: C  411 ARG cc_start: 0.8427 (tmm-80) cc_final: 0.8203 (tmm-80)
REVERT: D  301 PHE cc_start: 0.7881 (m-80) cc_final: 0.7445 (m-10)
REVERT: D  411 ARG cc_start: 0.8435 (tmm-80) cc_final: 0.8216 (tmm-80)
  outliers start: 7
  outliers final: 6
  residues processed: 135
  average time/residue: 0.0849
  time to fit residues: 16.1088
Evaluate side-chains
  134 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 128
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain C residue  227 VAL
Chi-restraints excluded: chain D residue  227 VAL
Chi-restraints excluded: chain D residue  279 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0060
   chunk 64 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 66 optimal weight:    0.3980
   chunk 81 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.5796

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.216070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.154241 restraints weight = 6870.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 1.98
r_work: 0.3356 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8196  Z= 0.134
  Angle     :  0.508   5.854  11136  Z= 0.264
  Chirality :  0.038   0.133   1316
  Planarity :  0.004   0.043   1364
  Dihedral  :  3.376  12.003   1148
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 14.39 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.50 (0.26), residues: 1028
  helix:  2.05 (0.18), residues: 792
  sheet:  None (None), residues: 0
  loop :  0.42 (0.44), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 256 
 TYR   0.016   0.001   TYR A 188 
 PHE   0.017   0.001   PHE B 257 
 TRP   0.006   0.001   TRP A 172 
 HIS   0.001   0.000   HIS B 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8196)
  covalent geometry    : angle       0.50848 (11136)
  hydrogen bonds       : bond        0.04284 (  601)
  hydrogen bonds       : angle       3.79242 ( 1767)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2789.51 seconds
wall clock time: 48 minutes 28.57 seconds (2908.57 seconds total)