Starting phenix.real_space_refine
on Wed Sep 17 05:51:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9eah_47831/09_2025/9eah_47831.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9eah_47831/09_2025/9eah_47831.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9eah_47831/09_2025/9eah_47831.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9eah_47831/09_2025/9eah_47831.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9eah_47831/09_2025/9eah_47831.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9eah_47831/09_2025/9eah_47831.cif"
  }
  resolution = 3.1
  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=   0.000 sd=   0.011
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      26      5.16       5
     C    3673      2.51       5
     N     902      2.21       5
     O    1005      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s

  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: 5606
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 378, 3024
          Classifications: {'peptide': 378}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 12, 'TRANS': 365}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 935
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 4, 'TRANS': 116}
    Chain: "D"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 815
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 771
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 61
          Unusual residues: {'CLR': 1, 'OLM': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.70, per 1000 atoms: 0.30
  Number of scatterers: 5606
  At special positions: 0
  Unit cell: (68.89, 96.28, 138.61, 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      26     16.00
     O    1005      8.00
     N     902      7.00
     C    3673      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 101 " - pdb=" SG  CYS A 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  25 " - pdb=" SG  CYS C  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  24 " - pdb=" SG  CYS D  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " 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
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 222.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1316

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 8 sheets defined
      50.4% alpha, 21.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 56
      removed outlier: 4.083A  pdb=" N   THR A  33 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 90
      removed outlier: 4.024A  pdb=" N   THR A  80 " --> pdb=" O   CYS A  76 " (cutoff:3.500A)
      Proline residue:  A  82  - end of helix
    Processing helix  chain 'A' and resid 96 through 132
      removed outlier: 4.168A  pdb=" N   LEU A 100 " --> pdb=" O   PHE A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 160
    Processing helix  chain 'A' and resid 160 through 166
    Processing helix  chain 'A' and resid 190 through 204
    Processing helix  chain 'A' and resid 204 through 245
      removed outlier: 3.601A  pdb=" N   VAL A 241 " --> pdb=" O   ASP A 237 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLU A 243 " --> pdb=" O   LEU A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 268
      removed outlier: 3.639A  pdb=" N   LYS A 257 " --> pdb=" O   ASP A 253 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LYS A 267 " --> pdb=" O   LEU A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 305
      removed outlier: 3.644A  pdb=" N   PHE A 290 " --> pdb=" O   PHE A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 317
    Processing helix  chain 'A' and resid 318 through 327
      removed outlier: 3.761A  pdb=" N   THR A 322 " --> pdb=" O   GLN A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 340
      removed outlier: 3.934A  pdb=" N   ARG A 333 " --> pdb=" O   LYS A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1236 through 1269
      Proline residue:  A1255  - end of helix
    Processing helix  chain 'A' and resid 1273 through 1292
      removed outlier: 3.515A  pdb=" N   ILE A1279 " --> pdb=" O   ARG A1275 " (cutoff:3.500A)
      Proline residue:  A1285  - end of helix
      removed outlier: 3.798A  pdb=" N   TYR A1292 " --> pdb=" O   ILE A1288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1293 through 1305
      removed outlier: 3.655A  pdb=" N   LEU A1297 " --> pdb=" O   PHE A1293 " (cutoff:3.500A)
      Proline residue:  A1299  - end of helix
      removed outlier: 3.824A  pdb=" N   TYR A1302 " --> pdb=" O   ASN A1298 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLY A1303 " --> pdb=" O   PRO A1299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1309 through 1315
      removed outlier: 3.532A  pdb=" N   PHE A1313 " --> pdb=" O   PHE A1309 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 33
      No H-bonds generated for 'chain 'C' and resid 31 through 33'
    Processing helix  chain 'C' and resid 107 through 112
      removed outlier: 4.229A  pdb=" N   TRP C 111 " --> pdb=" O   GLY C 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 84
      removed outlier: 4.085A  pdb=" N   PHE D  84 " --> pdb=" O   PRO D  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 64
      removed outlier: 3.601A  pdb=" N   LYS B  64 " --> pdb=" O   ASP B  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 61 through 64'
    Processing helix  chain 'B' and resid 86 through 90
    Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171
      removed outlier: 8.377A  pdb=" N   VAL B 106 " --> pdb=" O   CYS A 180 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   PHE A 182 " --> pdb=" O   VAL B 106 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   VAL B  92 " --> pdb=" O   GLN B  39 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   ARG B  38 " --> pdb=" O   PHE B  47 " (cutoff:3.500A)
      removed outlier: 5.726A  pdb=" N   PHE B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 171
      removed outlier: 8.377A  pdb=" N   VAL B 106 " --> pdb=" O   CYS A 180 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   PHE A 182 " --> pdb=" O   VAL B 106 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 10
      removed outlier: 3.919A  pdb=" N   ALA C  82 " --> pdb=" O   CYS C  25 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 62 through 63
      removed outlier: 6.558A  pdb=" N   TRP C  39 " --> pdb=" O   VAL C  51 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   TYR C  53 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   LEU C  37 " --> pdb=" O   TYR C  53 " (cutoff:3.500A)
      removed outlier: 5.903A  pdb=" N   SER C  55 " --> pdb=" O   PHE C  35 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   PHE C  35 " --> pdb=" O   SER C  55 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 5 through 6
      removed outlier: 3.668A  pdb=" N   VAL D  20 " --> pdb=" O   ILE D  76 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 11 through 13
      removed outlier: 6.870A  pdb=" N   LEU D  12 " --> pdb=" O   GLU D 107 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   VAL D  34 " --> pdb=" O   TYR D  50 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   TYR D  50 " --> pdb=" O   VAL D  34 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   TRP D  36 " --> pdb=" O   LEU D  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 11 through 13
      removed outlier: 6.870A  pdb=" N   LEU D  12 " --> pdb=" O   GLU D 107 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   THR D  99 " --> pdb=" O   GLN D  91 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 19 through 23

    343 hydrogen bonds defined for protein.
    960 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: 0.95

  Time building geometry restraints manager: 0.66 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: 1704
        1.34 -     1.46: 1501
        1.46 -     1.58: 2508
        1.58 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 5751
  Sorted by residual:
  bond pdb=" C3  CLR A1402 "
       pdb=" O1  CLR A1402 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.37e+00
  bond pdb=" C   SER C  57 "
       pdb=" N   SER C  58 "
    ideal  model  delta    sigma   weight residual
    1.332  1.321  0.012 1.40e-02 5.10e+03 6.91e-01
  bond pdb=" CB  VAL A 116 "
       pdb=" CG1 VAL A 116 "
    ideal  model  delta    sigma   weight residual
    1.521  1.497  0.024 3.30e-02 9.18e+02 5.44e-01
  bond pdb=" CG  PRO A 207 "
       pdb=" CD  PRO A 207 "
    ideal  model  delta    sigma   weight residual
    1.503  1.478  0.025 3.40e-02 8.65e+02 5.35e-01
  bond pdb=" C   VAL A 108 "
       pdb=" O   VAL A 108 "
    ideal  model  delta    sigma   weight residual
    1.237  1.244 -0.007 1.12e-02 7.97e+03 4.41e-01
  ... (remaining 5746 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.02: 7588
        1.02 -     2.04: 189
        2.04 -     3.05: 24
        3.05 -     4.07: 13
        4.07 -     5.09: 12
  Bond angle restraints: 7826
  Sorted by residual:
  angle pdb=" C   SER D  51 "
        pdb=" N   ALA D  52 "
        pdb=" CA  ALA D  52 "
      ideal   model   delta    sigma   weight residual
     121.54  125.72   -4.18 1.91e+00 2.74e-01 4.79e+00
  angle pdb=" N   GLU C 108 "
        pdb=" CA  GLU C 108 "
        pdb=" C   GLU C 108 "
      ideal   model   delta    sigma   weight residual
     109.81  114.50   -4.69 2.21e+00 2.05e-01 4.51e+00
  angle pdb=" N   VAL A 131 "
        pdb=" CA  VAL A 131 "
        pdb=" C   VAL A 131 "
      ideal   model   delta    sigma   weight residual
     109.34  112.78   -3.44 2.08e+00 2.31e-01 2.73e+00
  angle pdb=" C   SER D  31 "
        pdb=" N   SER D  32 "
        pdb=" CA  SER D  32 "
      ideal   model   delta    sigma   weight residual
     121.54  118.54    3.00 1.91e+00 2.74e-01 2.47e+00
  angle pdb=" C   GLY C 107 "
        pdb=" N   GLU C 108 "
        pdb=" CA  GLU C 108 "
      ideal   model   delta    sigma   weight residual
     121.80  125.51   -3.71 2.44e+00 1.68e-01 2.32e+00
  ... (remaining 7821 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.20: 3174
       16.20 -    32.39: 168
       32.39 -    48.59: 38
       48.59 -    64.78: 3
       64.78 -    80.98: 6
  Dihedral angle restraints: 3389
    sinusoidal: 1336
      harmonic: 2053
  Sorted by residual:
  dihedral pdb=" CA  TYR C 104 "
           pdb=" C   TYR C 104 "
           pdb=" N   TRP C 105 "
           pdb=" CA  TRP C 105 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.50  -19.50     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  ASN B  76 "
           pdb=" CB  ASN B  76 "
           pdb=" CG  ASN B  76 "
           pdb=" OD1 ASN B  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -157.49   67.49     2      2.00e+01 2.50e-03 1.02e+01
  dihedral pdb=" CA  TYR A 326 "
           pdb=" C   TYR A 326 "
           pdb=" N   ILE A 327 "
           pdb=" CA  ILE A 327 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.09  -14.91     0      5.00e+00 4.00e-02 8.89e+00
  ... (remaining 3386 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 494
       0.026 -    0.052: 248
       0.052 -    0.079: 83
       0.079 -    0.105: 43
       0.105 -    0.131: 13
  Chirality restraints: 881
  Sorted by residual:
  chirality pdb=" CA  TRP C 105 "
            pdb=" N   TRP C 105 "
            pdb=" C   TRP C 105 "
            pdb=" CB  TRP C 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.30e-01
  chirality pdb=" CA  ILE D  49 "
            pdb=" N   ILE D  49 "
            pdb=" C   ILE D  49 "
            pdb=" CB  ILE D  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  chirality pdb=" CA  ILE D  22 "
            pdb=" N   ILE D  22 "
            pdb=" C   ILE D  22 "
            pdb=" CB  ILE D  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.55e-01
  ... (remaining 878 not shown)

  Planarity restraints: 959
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 108 "    0.029 5.00e-02 4.00e+02   4.42e-02 3.13e+00
        pdb=" N   PRO C 109 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO C 109 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C 109 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B  29 "    0.007 2.00e-02 2.50e+03   1.40e-02 1.97e+00
        pdb=" C   PHE B  29 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   PHE B  29 "    0.009 2.00e-02 2.50e+03
        pdb=" N   TYR B  30 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A  94 "    0.022 5.00e-02 4.00e+02   3.28e-02 1.72e+00
        pdb=" N   PRO A  95 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "    0.018 5.00e-02 4.00e+02
  ... (remaining 956 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1276
        2.78 -     3.31: 5250
        3.31 -     3.84: 9265
        3.84 -     4.37: 11426
        4.37 -     4.90: 20022
  Nonbonded interactions: 47239
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN D  91 "
            pdb=" O   LEU D  97 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" O   GLY C 103 "
            pdb=" OH  TYR D  95 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OG  SER B  52 "
            pdb=" OG1 THR B  56 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   THR A 234 "
            pdb=" ND2 ASN A 238 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" OG  SER B  17 "
            pdb=" O   MET B  82 "
     model   vdw
     2.281 3.040
  ... (remaining 47234 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             3.690
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     7.800
  Find NCS groups from input model:        0.030
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
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      :  0.002   0.031   5755  Z= 0.112
  Angle     :  0.447   5.089   7834  Z= 0.232
  Chirality :  0.039   0.131    881
  Planarity :  0.003   0.044    959
  Dihedral  : 10.948  80.980   2061
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  5.42 %
    Favored  : 93.90 %
  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: -0.11 (0.34), residues: 688
  helix:  0.07 (0.30), residues: 309
  sheet:  0.56 (0.47), residues: 141
  loop : -0.43 (0.44), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  38 
 TYR   0.012   0.001   TYR D  92 
 PHE   0.012   0.001   PHE A  44 
 TRP   0.010   0.001   TRP A 232 
 HIS   0.001   0.000   HIS A1256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 5751)
  covalent geometry    : angle       0.44590 ( 7826)
  SS BOND              : bond        0.00166 (    4)
  SS BOND              : angle       1.20457 (    8)
  hydrogen bonds       : bond        0.21892 (  333)
  hydrogen bonds       : angle       8.00176 (  960)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A   57 MET cc_start: 0.7808 (mmt) cc_final: 0.7037 (mtp)
REVERT: A  237 ASP cc_start: 0.7078 (m-30) cc_final: 0.6789 (m-30)
REVERT: A 1288 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7993 (tt)
REVERT: C   39 TRP cc_start: 0.8293 (m100) cc_final: 0.7994 (m100)
REVERT: C   68 LYS cc_start: 0.7521 (ttmm) cc_final: 0.7241 (ttpt)
REVERT: B   72 ASP cc_start: 0.6796 (t0) cc_final: 0.5784 (m-30)
REVERT: B   77 THR cc_start: 0.7140 (m) cc_final: 0.6882 (m)
REVERT: B   95 CYS cc_start: 0.8463 (p) cc_final: 0.8084 (p)
  outliers start: 4
  outliers final: 2
  residues processed: 77
  average time/residue: 0.0750
  time to fit residues: 7.8351
Evaluate side-chains
  70 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1288 ILE
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain B residue   92 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    0.0050
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    9.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.7796

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
A 296 GLN
D   4 GLN
B  76 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.195568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.149445 restraints weight = 5830.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 3.29
r_work: 0.3265 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.0942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5755  Z= 0.170
  Angle     :  0.527   5.125   7834  Z= 0.284
  Chirality :  0.041   0.135    881
  Planarity :  0.004   0.053    959
  Dihedral  :  6.451  70.987    846
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  :  6.27 %
    Favored  : 91.36 %
  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:  0.48 (0.33), residues: 688
  helix:  1.00 (0.29), residues: 314
  sheet:  0.14 (0.44), residues: 152
  loop : -0.36 (0.46), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  19 
 TYR   0.013   0.001   TYR A  87 
 PHE   0.020   0.001   PHE A  44 
 TRP   0.015   0.001   TRP A 232 
 HIS   0.002   0.001   HIS A1256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 5751)
  covalent geometry    : angle       0.52474 ( 7826)
  SS BOND              : bond        0.00258 (    4)
  SS BOND              : angle       1.45424 (    8)
  hydrogen bonds       : bond        0.05347 (  333)
  hydrogen bonds       : angle       5.24982 (  960)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A  237 ASP cc_start: 0.7041 (m-30) cc_final: 0.6710 (m-30)
REVERT: A  253 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7807 (m-30)
REVERT: A 1288 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7891 (tt)
REVERT: C   39 TRP cc_start: 0.8383 (m100) cc_final: 0.8172 (m100)
REVERT: C   70 ARG cc_start: 0.8168 (mtm-85) cc_final: 0.7908 (mtm-85)
REVERT: B   22 CYS cc_start: 0.7322 (t) cc_final: 0.6670 (t)
REVERT: B   31 ARG cc_start: 0.7880 (ptm160) cc_final: 0.7671 (ptm160)
REVERT: B   56 THR cc_start: 0.8194 (p) cc_final: 0.7960 (t)
REVERT: B   72 ASP cc_start: 0.6788 (t0) cc_final: 0.5770 (m-30)
REVERT: B   77 THR cc_start: 0.7188 (m) cc_final: 0.6897 (m)
  outliers start: 14
  outliers final: 7
  residues processed: 84
  average time/residue: 0.0770
  time to fit residues: 8.7169
Evaluate side-chains
  76 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue 1288 ILE
Chi-restraints excluded: chain A residue 1297 LEU
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain B residue   92 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0980
   chunk 34 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0020
   chunk 41 optimal weight:    0.1980
   chunk 9 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.4188

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

Flipped N/Q/H residues before XYZ refinement:
B  76 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.198408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.150639 restraints weight = 5763.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 3.29
r_work: 0.3310 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.1280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5755  Z= 0.121
  Angle     :  0.468   5.125   7834  Z= 0.249
  Chirality :  0.040   0.125    881
  Planarity :  0.004   0.049    959
  Dihedral  :  6.362  71.319    846
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  7.80 %
    Favored  : 90.17 %
  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:  0.83 (0.33), residues: 688
  helix:  1.49 (0.29), residues: 314
  sheet:  0.16 (0.43), residues: 152
  loop : -0.39 (0.46), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  19 
 TYR   0.010   0.001   TYR D  92 
 PHE   0.018   0.001   PHE A  44 
 TRP   0.014   0.001   TRP A 232 
 HIS   0.002   0.001   HIS A1256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 5751)
  covalent geometry    : angle       0.46654 ( 7826)
  SS BOND              : bond        0.00202 (    4)
  SS BOND              : angle       1.19048 (    8)
  hydrogen bonds       : bond        0.04259 (  333)
  hydrogen bonds       : angle       4.76055 (  960)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A  237 ASP cc_start: 0.6986 (m-30) cc_final: 0.6651 (m-30)
REVERT: A  306 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8047 (mt-10)
REVERT: A 1288 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7887 (tt)
REVERT: C   70 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7764 (mtm-85)
REVERT: B   56 THR cc_start: 0.8124 (p) cc_final: 0.7900 (t)
REVERT: B   72 ASP cc_start: 0.6835 (t0) cc_final: 0.5785 (m-30)
REVERT: B   77 THR cc_start: 0.7175 (m) cc_final: 0.6905 (m)
  outliers start: 12
  outliers final: 6
  residues processed: 82
  average time/residue: 0.0753
  time to fit residues: 8.2986
Evaluate side-chains
  76 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue 1288 ILE
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain D residue   66 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  103 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 50 optimal weight:    0.0980
   chunk 16 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 5 optimal weight:    0.3980
   chunk 53 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A1315 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.197493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.149376 restraints weight = 5788.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 3.32
r_work: 0.3303 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5755  Z= 0.138
  Angle     :  0.476   5.084   7834  Z= 0.253
  Chirality :  0.040   0.127    881
  Planarity :  0.004   0.053    959
  Dihedral  :  6.316  70.872    846
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  :  8.47 %
    Favored  : 88.81 %
  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 (0.33), residues: 688
  helix:  1.59 (0.29), residues: 314
  sheet:  0.10 (0.43), residues: 153
  loop : -0.44 (0.46), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  19 
 TYR   0.012   0.001   TYR B  93 
 PHE   0.016   0.001   PHE A  44 
 TRP   0.014   0.001   TRP A 232 
 HIS   0.002   0.001   HIS A1256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 5751)
  covalent geometry    : angle       0.47469 ( 7826)
  SS BOND              : bond        0.00259 (    4)
  SS BOND              : angle       1.12005 (    8)
  hydrogen bonds       : bond        0.04174 (  333)
  hydrogen bonds       : angle       4.64941 (  960)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A  237 ASP cc_start: 0.6914 (m-30) cc_final: 0.6581 (m-30)
REVERT: A  253 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7785 (m-30)
REVERT: A 1288 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7829 (tt)
REVERT: C   70 ARG cc_start: 0.8236 (mtm-85) cc_final: 0.7781 (mtm-85)
REVERT: B   56 THR cc_start: 0.8167 (p) cc_final: 0.7935 (t)
REVERT: B   72 ASP cc_start: 0.6818 (t0) cc_final: 0.5787 (m-30)
REVERT: B   77 THR cc_start: 0.7254 (m) cc_final: 0.6974 (m)
  outliers start: 16
  outliers final: 6
  residues processed: 91
  average time/residue: 0.0744
  time to fit residues: 9.0850
Evaluate side-chains
  82 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue 1288 ILE
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain D residue   66 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  103 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 58 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 64 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 47 optimal weight:    0.2980
   chunk 10 optimal weight:    0.0470
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.4478

-------------------------------------------------------------------------------
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 = 0.4214 r_free = 0.4214 target = 0.199129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.151459 restraints weight = 5858.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 3.28
r_work: 0.3282 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5755  Z= 0.121
  Angle     :  0.462   5.010   7834  Z= 0.245
  Chirality :  0.040   0.125    881
  Planarity :  0.004   0.051    959
  Dihedral  :  6.279  71.080    846
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  9.66 %
    Favored  : 88.31 %
  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:  0.95 (0.33), residues: 688
  helix:  1.74 (0.29), residues: 314
  sheet:  0.08 (0.43), residues: 153
  loop : -0.47 (0.45), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  19 
 TYR   0.011   0.001   TYR B  93 
 PHE   0.015   0.001   PHE A  44 
 TRP   0.014   0.001   TRP A 232 
 HIS   0.002   0.001   HIS A1256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 5751)
  covalent geometry    : angle       0.46139 ( 7826)
  SS BOND              : bond        0.00278 (    4)
  SS BOND              : angle       1.07776 (    8)
  hydrogen bonds       : bond        0.03938 (  333)
  hydrogen bonds       : angle       4.51152 (  960)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  198 THR cc_start: 0.8441 (m) cc_final: 0.8095 (m)
REVERT: A  237 ASP cc_start: 0.6845 (m-30) cc_final: 0.6499 (m-30)
REVERT: A  253 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7774 (m-30)
REVERT: A 1288 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7789 (tt)
REVERT: C   70 ARG cc_start: 0.8246 (mtm-85) cc_final: 0.7837 (mtm-85)
REVERT: B   56 THR cc_start: 0.8136 (p) cc_final: 0.7906 (t)
REVERT: B   72 ASP cc_start: 0.6840 (t0) cc_final: 0.5780 (m-30)
REVERT: B   77 THR cc_start: 0.7221 (m) cc_final: 0.6914 (m)
  outliers start: 12
  outliers final: 6
  residues processed: 87
  average time/residue: 0.0770
  time to fit residues: 8.9409
Evaluate side-chains
  86 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue 1288 ILE
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain D residue   66 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  103 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 52 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 7 optimal weight:    0.2980
   chunk 40 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  76 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.197088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.150980 restraints weight = 5865.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 3.41
r_work: 0.3250 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5755  Z= 0.158
  Angle     :  0.489   5.248   7834  Z= 0.259
  Chirality :  0.041   0.131    881
  Planarity :  0.004   0.054    959
  Dihedral  :  6.315  70.421    846
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 10.00 %
    Favored  : 87.63 %
  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:  0.90 (0.33), residues: 688
  helix:  1.70 (0.29), residues: 314
  sheet:  0.06 (0.43), residues: 153
  loop : -0.51 (0.45), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  19 
 TYR   0.013   0.002   TYR A  87 
 PHE   0.015   0.001   PHE A  44 
 TRP   0.014   0.001   TRP A 232 
 HIS   0.003   0.001   HIS A1256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 5751)
  covalent geometry    : angle       0.48801 ( 7826)
  SS BOND              : bond        0.00254 (    4)
  SS BOND              : angle       1.22233 (    8)
  hydrogen bonds       : bond        0.04196 (  333)
  hydrogen bonds       : angle       4.56142 (  960)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  173 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7555 (mt-10)
REVERT: A  198 THR cc_start: 0.8429 (m) cc_final: 0.8093 (m)
REVERT: A  237 ASP cc_start: 0.6870 (m-30) cc_final: 0.6500 (m-30)
REVERT: A  253 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7813 (m-30)
REVERT: A 1288 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7810 (tt)
REVERT: C   70 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.7830 (mtm-85)
REVERT: B   56 THR cc_start: 0.8186 (p) cc_final: 0.7932 (t)
REVERT: B   72 ASP cc_start: 0.6832 (t0) cc_final: 0.5782 (m-30)
REVERT: B   77 THR cc_start: 0.7382 (m) cc_final: 0.7075 (m)
  outliers start: 14
  outliers final: 9
  residues processed: 91
  average time/residue: 0.0786
  time to fit residues: 9.5836
Evaluate side-chains
  88 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue 1288 ILE
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain D residue   66 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  103 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0970
   chunk 41 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   chunk 65 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
B  76 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.197849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.148932 restraints weight = 5858.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 3.37
r_work: 0.3226 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5755  Z= 0.136
  Angle     :  0.475   5.176   7834  Z= 0.251
  Chirality :  0.040   0.127    881
  Planarity :  0.004   0.054    959
  Dihedral  :  6.324  70.440    846
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 10.00 %
    Favored  : 87.29 %
  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:  0.97 (0.33), residues: 688
  helix:  1.79 (0.28), residues: 314
  sheet:  0.08 (0.43), residues: 153
  loop : -0.53 (0.45), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  19 
 TYR   0.012   0.001   TYR C  53 
 PHE   0.014   0.001   PHE A  44 
 TRP   0.015   0.001   TRP A 232 
 HIS   0.002   0.001   HIS A1256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 5751)
  covalent geometry    : angle       0.47342 ( 7826)
  SS BOND              : bond        0.00238 (    4)
  SS BOND              : angle       1.15891 (    8)
  hydrogen bonds       : bond        0.04046 (  333)
  hydrogen bonds       : angle       4.49205 (  960)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.206 
Fit side-chains
REVERT: A  173 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7524 (mt-10)
REVERT: A  198 THR cc_start: 0.8407 (m) cc_final: 0.8069 (m)
REVERT: A  237 ASP cc_start: 0.6813 (m-30) cc_final: 0.6463 (m-30)
REVERT: A  253 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7743 (m-30)
REVERT: A 1288 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7727 (tt)
REVERT: C   70 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7948 (mtm-85)
REVERT: B   38 ARG cc_start: 0.8475 (ptp-170) cc_final: 0.8214 (ptp-170)
REVERT: B   56 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7890 (t)
REVERT: B   72 ASP cc_start: 0.6818 (t0) cc_final: 0.5748 (m-30)
REVERT: B   77 THR cc_start: 0.7206 (m) cc_final: 0.6863 (m)
  outliers start: 16
  outliers final: 9
  residues processed: 92
  average time/residue: 0.0838
  time to fit residues: 10.2011
Evaluate side-chains
  90 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue 1288 ILE
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain D residue   66 SER
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  103 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 65 optimal weight:    0.0170
   chunk 28 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 56 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.5820

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

Flipped N/Q/H residues before XYZ refinement:
B  76 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.198095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.150565 restraints weight = 5775.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 3.25
r_work: 0.3293 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5755  Z= 0.136
  Angle     :  0.477   5.089   7834  Z= 0.253
  Chirality :  0.040   0.128    881
  Planarity :  0.004   0.055    959
  Dihedral  :  6.312  70.428    846
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 10.17 %
    Favored  : 87.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.00 (0.33), residues: 688
  helix:  1.84 (0.28), residues: 314
  sheet:  0.08 (0.43), residues: 153
  loop : -0.54 (0.45), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  19 
 TYR   0.011   0.001   TYR A  87 
 PHE   0.015   0.001   PHE A  44 
 TRP   0.015   0.001   TRP A 232 
 HIS   0.002   0.001   HIS A1256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 5751)
  covalent geometry    : angle       0.47495 ( 7826)
  SS BOND              : bond        0.00221 (    4)
  SS BOND              : angle       1.35542 (    8)
  hydrogen bonds       : bond        0.03997 (  333)
  hydrogen bonds       : angle       4.46371 (  960)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A  198 THR cc_start: 0.8490 (m) cc_final: 0.8150 (m)
REVERT: A  237 ASP cc_start: 0.6874 (m-30) cc_final: 0.6522 (m-30)
REVERT: A  253 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7855 (m-30)
REVERT: A  310 LYS cc_start: 0.7832 (mmmm) cc_final: 0.7580 (mmtm)
REVERT: A 1288 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7863 (tt)
REVERT: C   70 ARG cc_start: 0.8307 (mtm-85) cc_final: 0.8085 (mtm-85)
REVERT: B   56 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7934 (t)
REVERT: B   72 ASP cc_start: 0.6815 (t0) cc_final: 0.5816 (m-30)
REVERT: B   77 THR cc_start: 0.7213 (m) cc_final: 0.6930 (m)
  outliers start: 16
  outliers final: 9
  residues processed: 89
  average time/residue: 0.0824
  time to fit residues: 9.7238
Evaluate side-chains
  88 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue 1288 ILE
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain D residue   66 SER
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  103 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 39 optimal weight:    8.9990
   chunk 17 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 37 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 324 ASN
B  76 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.196444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.152579 restraints weight = 5858.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 3.70
r_work: 0.3276 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5755  Z= 0.178
  Angle     :  0.512   5.209   7834  Z= 0.272
  Chirality :  0.042   0.134    881
  Planarity :  0.004   0.056    959
  Dihedral  :  6.420  70.200    846
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 11.19 %
    Favored  : 86.44 %
  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 (0.33), residues: 688
  helix:  1.69 (0.28), residues: 314
  sheet:  0.07 (0.43), residues: 152
  loop : -0.58 (0.44), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  19 
 TYR   0.013   0.002   TYR A  87 
 PHE   0.016   0.001   PHE B  47 
 TRP   0.014   0.001   TRP A 232 
 HIS   0.003   0.001   HIS A1256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 5751)
  covalent geometry    : angle       0.50989 ( 7826)
  SS BOND              : bond        0.00318 (    4)
  SS BOND              : angle       1.67903 (    8)
  hydrogen bonds       : bond        0.04287 (  333)
  hydrogen bonds       : angle       4.58488 (  960)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A  237 ASP cc_start: 0.6823 (m-30) cc_final: 0.6485 (m-30)
REVERT: A  253 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7836 (m-30)
REVERT: A  310 LYS cc_start: 0.7824 (mmmm) cc_final: 0.7560 (mmtm)
REVERT: A 1288 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7797 (tt)
REVERT: C   70 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.8054 (mtm-85)
REVERT: B   56 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7898 (t)
REVERT: B   72 ASP cc_start: 0.6845 (t0) cc_final: 0.5823 (m-30)
REVERT: B   77 THR cc_start: 0.7178 (m) cc_final: 0.6901 (m)
  outliers start: 14
  outliers final: 9
  residues processed: 85
  average time/residue: 0.0779
  time to fit residues: 8.8965
Evaluate side-chains
  84 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue 1288 ILE
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain D residue   66 SER
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  103 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 23 optimal weight:    0.0670
   chunk 21 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0970
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.4116

-------------------------------------------------------------------------------
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 = 0.4232 r_free = 0.4232 target = 0.200934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.152418 restraints weight = 5895.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 3.64
r_work: 0.3312 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5755  Z= 0.117
  Angle     :  0.469   5.112   7834  Z= 0.249
  Chirality :  0.040   0.129    881
  Planarity :  0.004   0.054    959
  Dihedral  :  6.364  70.432    846
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 11.53 %
    Favored  : 86.44 %
  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:  1.05 (0.33), residues: 688
  helix:  1.94 (0.28), residues: 313
  sheet:  0.08 (0.43), residues: 152
  loop : -0.58 (0.44), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  19 
 TYR   0.014   0.001   TYR B  32 
 PHE   0.014   0.001   PHE A  44 
 TRP   0.015   0.001   TRP A 232 
 HIS   0.002   0.001   HIS A1256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5751)
  covalent geometry    : angle       0.46748 ( 7826)
  SS BOND              : bond        0.00254 (    4)
  SS BOND              : angle       1.39057 (    8)
  hydrogen bonds       : bond        0.03862 (  333)
  hydrogen bonds       : angle       4.43007 (  960)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  198 THR cc_start: 0.8477 (m) cc_final: 0.8132 (m)
REVERT: A  237 ASP cc_start: 0.6877 (m-30) cc_final: 0.6529 (m-30)
REVERT: A  253 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7790 (m-30)
REVERT: A  310 LYS cc_start: 0.7817 (mmmm) cc_final: 0.7553 (mmtm)
REVERT: A 1288 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7756 (tt)
REVERT: C   70 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.8077 (mtm-85)
REVERT: B   32 TYR cc_start: 0.8772 (m-10) cc_final: 0.8557 (m-10)
REVERT: B   56 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7878 (t)
REVERT: B   72 ASP cc_start: 0.6816 (t0) cc_final: 0.5835 (m-30)
REVERT: B   77 THR cc_start: 0.7139 (m) cc_final: 0.6858 (m)
  outliers start: 12
  outliers final: 7
  residues processed: 84
  average time/residue: 0.0846
  time to fit residues: 9.3650
Evaluate side-chains
  83 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue 1288 ILE
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  103 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 41 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 56 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 58 optimal weight:    0.1980
   chunk 28 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 22 optimal weight:    0.2980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.4209 r_free = 0.4209 target = 0.198757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.150841 restraints weight = 5794.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 3.27
r_work: 0.3312 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5755  Z= 0.129
  Angle     :  0.476   5.119   7834  Z= 0.253
  Chirality :  0.040   0.131    881
  Planarity :  0.005   0.084    959
  Dihedral  :  6.346  70.269    846
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 12.03 %
    Favored  : 86.27 %
  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:  1.01 (0.33), residues: 688
  helix:  1.87 (0.28), residues: 314
  sheet:  0.12 (0.43), residues: 151
  loop : -0.60 (0.44), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  19 
 TYR   0.014   0.001   TYR B  32 
 PHE   0.014   0.001   PHE A  44 
 TRP   0.015   0.001   TRP A 232 
 HIS   0.002   0.001   HIS A1256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5751)
  covalent geometry    : angle       0.47384 ( 7826)
  SS BOND              : bond        0.00236 (    4)
  SS BOND              : angle       1.44116 (    8)
  hydrogen bonds       : bond        0.03922 (  333)
  hydrogen bonds       : angle       4.42898 (  960)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1770.73 seconds
wall clock time: 31 minutes 7.47 seconds (1867.47 seconds total)