Starting phenix.real_space_refine
on Fri Aug 22 17:05:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sv1_40781/08_2025/8sv1_40781.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sv1_40781/08_2025/8sv1_40781.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sv1_40781/08_2025/8sv1_40781.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sv1_40781/08_2025/8sv1_40781.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sv1_40781/08_2025/8sv1_40781.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sv1_40781/08_2025/8sv1_40781.map"
  }
  resolution = 3.5
  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=   0.068
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: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    4004      2.51       5
     N    1062      2.21       5
     O    1210      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6330
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1158
          Classifications: {'peptide': 148}
          Link IDs: {'PTRANS': 7, 'TRANS': 140}
    Chain: "B"
      Number of atoms: 718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 718
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 5, 'TRANS': 82}
    Chain: "a"
      Number of atoms: 1158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1158
          Classifications: {'peptide': 148}
          Link IDs: {'PTRANS': 7, 'TRANS': 140}
    Chain: "b"
      Number of atoms: 718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 718
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 5, 'TRANS': 82}
    Chain: "C"
      Number of atoms: 1289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 1289
          Classifications: {'peptide': 160}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 155}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "c"
      Number of atoms: 1289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 1289
          Classifications: {'peptide': 160}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 155}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 1.79, per 1000 atoms: 0.28
  Number of scatterers: 6330
  At special positions: 0
  Unit cell: (72.21, 135.29, 65.57, 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      54     16.00
     O    1210      8.00
     N    1062      7.00
     C    4004      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: 0.43
  Conformation dependent library (CDL) restraints added in 349.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1516

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 12 sheets defined
      19.7% alpha, 21.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 181 through 197
    Processing helix  chain 'A' and resid 207 through 221
    Processing helix  chain 'A' and resid 222 through 227
    Processing helix  chain 'A' and resid 257 through 265
      removed outlier: 3.517A  pdb=" N   LEU A 265 " --> pdb=" O   ILE A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 274
      removed outlier: 3.751A  pdb=" N   LYS A 274 " --> pdb=" O   PRO A 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 361
    Processing helix  chain 'B' and resid 365 through 376
    Processing helix  chain 'a' and resid 181 through 197
    Processing helix  chain 'a' and resid 207 through 221
    Processing helix  chain 'a' and resid 223 through 227
    Processing helix  chain 'a' and resid 257 through 264
    Processing helix  chain 'a' and resid 270 through 274
      removed outlier: 3.558A  pdb=" N   LYS a 274 " --> pdb=" O   PRO a 271 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 347 through 361
      removed outlier: 3.573A  pdb=" N   ALA b 361 " --> pdb=" O   MET b 357 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 365 through 376
    Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 204
      removed outlier: 3.554A  pdb=" N   LEU A 232 " --> pdb=" O   VAL A 279 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   LYS A 278 " --> pdb=" O   ILE B 328 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 238 through 239
    Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 296
      removed outlier: 3.863A  pdb=" N   PHE A 295 " --> pdb=" O   LYS b 319 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LYS b 319 " --> pdb=" O   PHE A 295 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 320 through 322
    Processing sheet with id=AA5, first strand: chain 'B' and resid 340 through 341
    Processing sheet with id=AA6, first strand: chain 'a' and resid 199 through 204
      removed outlier: 3.516A  pdb=" N   ALA a 165 " --> pdb=" O   SER a 199 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   PHE a 231 " --> pdb=" O   LEU a 164 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU a 232 " --> pdb=" O   VAL a 279 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'a' and resid 243 through 244
    Processing sheet with id=AA8, first strand: chain 'b' and resid 340 through 341
    Processing sheet with id=AA9, first strand: chain 'C' and resid 24 through 25
      removed outlier: 3.721A  pdb=" N   ALA C 162 " --> pdb=" O   ILE C 173 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   LEU C 161 " --> pdb=" O   PHE C 187 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   PHE C 187 " --> pdb=" O   LEU C 161 " (cutoff:3.500A)
      removed outlier: 18.414A  pdb=" N   ILE C 185 " --> pdb=" O   SER C 153 " (cutoff:3.500A)
      removed outlier: 13.593A  pdb=" N   SER C 153 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   PHE C 187 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   PHE C 151 " --> pdb=" O   PHE C 187 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL C 189 " --> pdb=" O   MET C 149 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   MET C 149 " --> pdb=" O   VAL C 189 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ALA C  97 " --> pdb=" O   TYR C  88 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 46
      removed outlier: 5.857A  pdb=" N   SER C  46 " --> pdb=" O   THR C 188 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   GLN C 190 " --> pdb=" O   SER C  46 " (cutoff:3.500A)
      removed outlier: 18.414A  pdb=" N   ILE C 185 " --> pdb=" O   SER C 153 " (cutoff:3.500A)
      removed outlier: 13.593A  pdb=" N   SER C 153 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   PHE C 187 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   PHE C 151 " --> pdb=" O   PHE C 187 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL C 189 " --> pdb=" O   MET C 149 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   MET C 149 " --> pdb=" O   VAL C 189 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   ILE C 100 " --> pdb=" O   LEU C 110 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU C 110 " --> pdb=" O   ILE C 100 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'c' and resid 24 through 25
      removed outlier: 3.721A  pdb=" N   ALA c 162 " --> pdb=" O   ILE c 173 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   LEU c 161 " --> pdb=" O   PHE c 187 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   PHE c 187 " --> pdb=" O   LEU c 161 " (cutoff:3.500A)
      removed outlier: 18.414A  pdb=" N   ILE c 185 " --> pdb=" O   SER c 153 " (cutoff:3.500A)
      removed outlier: 13.592A  pdb=" N   SER c 153 " --> pdb=" O   ILE c 185 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   PHE c 187 " --> pdb=" O   PHE c 151 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   PHE c 151 " --> pdb=" O   PHE c 187 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL c 189 " --> pdb=" O   MET c 149 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   MET c 149 " --> pdb=" O   VAL c 189 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ALA c  97 " --> pdb=" O   TYR c  88 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'c' and resid 45 through 46
      removed outlier: 5.856A  pdb=" N   SER c  46 " --> pdb=" O   THR c 188 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   GLN c 190 " --> pdb=" O   SER c  46 " (cutoff:3.500A)
      removed outlier: 18.414A  pdb=" N   ILE c 185 " --> pdb=" O   SER c 153 " (cutoff:3.500A)
      removed outlier: 13.592A  pdb=" N   SER c 153 " --> pdb=" O   ILE c 185 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   PHE c 187 " --> pdb=" O   PHE c 151 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   PHE c 151 " --> pdb=" O   PHE c 187 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL c 189 " --> pdb=" O   MET c 149 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   MET c 149 " --> pdb=" O   VAL c 189 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   ILE c 100 " --> pdb=" O   LEU c 110 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU c 110 " --> pdb=" O   ILE c 100 " (cutoff:3.500A)

    199 hydrogen bonds defined for protein.
    519 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: 0.93

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1983
        1.33 -     1.46: 1005
        1.46 -     1.58: 3378
        1.58 -     1.70: 0
        1.70 -     1.82: 84
  Bond restraints: 6450
  Sorted by residual:
  bond pdb=" N   PHE C  83 "
       pdb=" CA  PHE C  83 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.036 1.29e-02 6.01e+03 7.84e+00
  bond pdb=" N   PHE c  83 "
       pdb=" CA  PHE c  83 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.29e-02 6.01e+03 7.62e+00
  bond pdb=" N   MET C 122 "
       pdb=" CA  MET C 122 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.031 1.29e-02 6.01e+03 5.89e+00
  bond pdb=" N   MET c 122 "
       pdb=" CA  MET c 122 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.29e-02 6.01e+03 5.42e+00
  bond pdb=" C   ARG a 221 "
       pdb=" N   PRO a 222 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.018 9.40e-03 1.13e+04 3.67e+00
  ... (remaining 6445 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.47: 8629
        3.47 -     6.94: 44
        6.94 -    10.42: 7
       10.42 -    13.89: 0
       13.89 -    17.36: 2
  Bond angle restraints: 8682
  Sorted by residual:
  angle pdb=" N   ILE c  84 "
        pdb=" CA  ILE c  84 "
        pdb=" C   ILE c  84 "
      ideal   model   delta    sigma   weight residual
     109.30  125.39  -16.09 1.25e+00 6.40e-01 1.66e+02
  angle pdb=" N   ILE C  84 "
        pdb=" CA  ILE C  84 "
        pdb=" C   ILE C  84 "
      ideal   model   delta    sigma   weight residual
     109.37  126.73  -17.36 1.35e+00 5.49e-01 1.65e+02
  angle pdb=" N   ILE c  84 "
        pdb=" CA  ILE c  84 "
        pdb=" CB  ILE c  84 "
      ideal   model   delta    sigma   weight residual
     110.31  101.58    8.73 1.23e+00 6.61e-01 5.04e+01
  angle pdb=" N   ILE C  84 "
        pdb=" CA  ILE C  84 "
        pdb=" CB  ILE C  84 "
      ideal   model   delta    sigma   weight residual
     110.13  101.48    8.65 1.34e+00 5.57e-01 4.17e+01
  angle pdb=" CA  ARG b 383 "
        pdb=" C   ARG b 383 "
        pdb=" O   ARG b 383 "
      ideal   model   delta    sigma   weight residual
     122.36  118.10    4.26 1.21e+00 6.83e-01 1.24e+01
  ... (remaining 8677 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.05: 3240
       14.05 -    28.10: 475
       28.10 -    42.14: 187
       42.14 -    56.19: 37
       56.19 -    70.24: 15
  Dihedral angle restraints: 3954
    sinusoidal: 1636
      harmonic: 2318
  Sorted by residual:
  dihedral pdb=" CA  VAL C  47 "
           pdb=" C   VAL C  47 "
           pdb=" N   ILE C  48 "
           pdb=" CA  ILE C  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.06  -20.94     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" CA  VAL c  47 "
           pdb=" C   VAL c  47 "
           pdb=" N   ILE c  48 "
           pdb=" CA  ILE c  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.09  -20.91     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" CA  GLU C 105 "
           pdb=" C   GLU C 105 "
           pdb=" N   LYS C 106 "
           pdb=" CA  LYS C 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.83   17.17     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 3951 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 781
       0.058 -    0.116: 164
       0.116 -    0.175: 17
       0.175 -    0.233: 1
       0.233 -    0.291: 1
  Chirality restraints: 964
  Sorted by residual:
  chirality pdb=" CA  ILE C  84 "
            pdb=" N   ILE C  84 "
            pdb=" C   ILE C  84 "
            pdb=" CB  ILE C  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.14    0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CA  ILE c  84 "
            pdb=" N   ILE c  84 "
            pdb=" C   ILE c  84 "
            pdb=" CB  ILE c  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.21    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CB  ILE B 318 "
            pdb=" CA  ILE B 318 "
            pdb=" CG1 ILE B 318 "
            pdb=" CG2 ILE B 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.17 2.00e-01 2.50e+01 7.38e-01
  ... (remaining 961 not shown)

  Planarity restraints: 1122
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG c  49 "    0.474 9.50e-02 1.11e+02   2.13e-01 2.76e+01
        pdb=" NE  ARG c  49 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG c  49 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG c  49 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG c  49 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  49 "   -0.474 9.50e-02 1.11e+02   2.13e-01 2.76e+01
        pdb=" NE  ARG C  49 "    0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  49 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  49 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  49 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG b 383 "    0.415 9.50e-02 1.11e+02   1.86e-01 2.12e+01
        pdb=" NE  ARG b 383 "   -0.025 2.00e-02 2.50e+03
        pdb=" CZ  ARG b 383 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG b 383 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG b 383 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1119 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 883
        2.76 -     3.29: 6106
        3.29 -     3.83: 10062
        3.83 -     4.36: 11584
        4.36 -     4.90: 20099
  Nonbonded interactions: 48734
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 162 "
            pdb=" OG1 THR A 226 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OG  SER B 332 "
            pdb=" OG  SER B 339 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   THR a 162 "
            pdb=" OG1 THR a 162 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OH  TYR A 198 "
            pdb=" OG  SER A 229 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OE2 GLU b 324 "
            pdb=" NH2 ARG b 391 "
     model   vdw
     2.300 3.120
  ... (remaining 48729 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'
  selection = chain 'a'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'b'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'c'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.480
  Find NCS groups from input model:        0.050
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
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      :  0.003   0.036   6450  Z= 0.176
  Angle     :  0.755  17.360   8682  Z= 0.439
  Chirality :  0.046   0.291    964
  Planarity :  0.012   0.213   1122
  Dihedral  : 16.023  70.239   2438
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  6.19 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 17.69 %
    Favored  : 81.62 %
  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: -1.32 (0.29), residues: 776
  helix:  1.09 (0.43), residues: 136
  sheet: -0.71 (0.44), residues: 158
  loop : -1.59 (0.26), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 221 
 TYR   0.007   0.001   TYR c  88 
 PHE   0.010   0.001   PHE C  18 
 TRP   0.004   0.001   TRP b 340 
 HIS   0.005   0.001   HIS a 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 6450)
  covalent geometry    : angle       0.75463 ( 8682)
  hydrogen bonds       : bond        0.22246 (  187)
  hydrogen bonds       : angle       8.10325 (  519)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 258
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ARG cc_start: 0.7063 (ptt180) cc_final: 0.6776 (ptt180)
REVERT: A  283 GLN cc_start: 0.7597 (tm-30) cc_final: 0.6709 (tm-30)
REVERT: a  225 LYS cc_start: 0.8484 (tttt) cc_final: 0.8251 (mmtp)
REVERT: a  272 SER cc_start: 0.7953 (m) cc_final: 0.7554 (m)
REVERT: a  283 GLN cc_start: 0.7114 (tm-30) cc_final: 0.6670 (tm-30)
REVERT: a  296 LYS cc_start: 0.8569 (tppt) cc_final: 0.7754 (mtpt)
REVERT: C   50 ASN cc_start: 0.7295 (m110) cc_final: 0.7031 (m110)
REVERT: C  164 GLU cc_start: 0.5615 (tp30) cc_final: 0.5142 (tp30)
REVERT: c   50 ASN cc_start: 0.7226 (m110) cc_final: 0.6936 (m110)
REVERT: c  164 GLU cc_start: 0.5408 (tp30) cc_final: 0.5030 (tp30)
  outliers start: 5
  outliers final: 3
  residues processed: 259
  average time/residue: 0.0862
  time to fit residues: 28.5478
Evaluate side-chains
  233 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 230
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue  383 ARG
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain c residue   49 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0870
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.0770
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    8.9990
   overall best weight:    0.6120

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 337 ASN
C 147 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.231490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.160499 restraints weight = 6224.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.169221 restraints weight = 2842.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.174836 restraints weight = 1800.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.178189 restraints weight = 1355.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.180464 restraints weight = 1140.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.4204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6739
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6450  Z= 0.132
  Angle     :  0.626   8.054   8682  Z= 0.326
  Chirality :  0.046   0.172    964
  Planarity :  0.005   0.055   1122
  Dihedral  :  6.177  59.422    852
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 21.59 %
    Favored  : 75.77 %
  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: -1.23 (0.29), residues: 776
  helix:  1.10 (0.43), residues: 138
  sheet: -0.50 (0.45), residues: 148
  loop : -1.57 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 383 
 TYR   0.006   0.001   TYR c  88 
 PHE   0.025   0.001   PHE B 370 
 TRP   0.007   0.001   TRP a 294 
 HIS   0.003   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6450)
  covalent geometry    : angle       0.62640 ( 8682)
  hydrogen bonds       : bond        0.04061 (  187)
  hydrogen bonds       : angle       5.51968 (  519)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 224
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 GLN cc_start: 0.7481 (tm-30) cc_final: 0.6435 (tm-30)
REVERT: a  225 LYS cc_start: 0.8965 (tttt) cc_final: 0.8392 (mmtp)
REVERT: a  241 GLU cc_start: 0.8431 (mp0) cc_final: 0.8160 (mp0)
REVERT: a  283 GLN cc_start: 0.7425 (tm-30) cc_final: 0.6339 (tm-30)
REVERT: a  296 LYS cc_start: 0.8471 (tppt) cc_final: 0.7682 (mttt)
REVERT: C   50 ASN cc_start: 0.6978 (m110) cc_final: 0.6639 (m110)
REVERT: C  164 GLU cc_start: 0.5137 (tp30) cc_final: 0.4806 (tp30)
REVERT: c   50 ASN cc_start: 0.6763 (m110) cc_final: 0.6418 (m110)
REVERT: c  176 LYS cc_start: 0.8825 (mmtp) cc_final: 0.8163 (mtmt)
  outliers start: 19
  outliers final: 13
  residues processed: 230
  average time/residue: 0.0894
  time to fit residues: 26.3257
Evaluate side-chains
  224 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 211
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain a residue  249 SER
Chi-restraints excluded: chain b residue  348 VAL
Chi-restraints excluded: chain b residue  383 ARG
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain b residue  393 THR
Chi-restraints excluded: chain C residue   28 GLU
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain c residue   49 ARG
Chi-restraints excluded: chain c residue  160 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 15 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 55 optimal weight:    7.9990
   chunk 62 optimal weight:    8.9990
   chunk 53 optimal weight:    8.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 190 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4577 r_free = 0.4577 target = 0.229824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.157574 restraints weight = 6161.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.165849 restraints weight = 2955.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.171097 restraints weight = 1926.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.174384 restraints weight = 1486.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.176353 restraints weight = 1265.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.4161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6851
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6450  Z= 0.132
  Angle     :  0.587   7.519   8682  Z= 0.305
  Chirality :  0.044   0.164    964
  Planarity :  0.005   0.055   1122
  Dihedral  :  6.073  57.655    852
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 21.59 %
    Favored  : 75.21 %
  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: -1.27 (0.29), residues: 776
  helix:  1.03 (0.43), residues: 138
  sheet: -0.57 (0.45), residues: 148
  loop : -1.56 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG b 352 
 TYR   0.013   0.001   TYR C  37 
 PHE   0.017   0.001   PHE B 370 
 TRP   0.023   0.003   TRP A 294 
 HIS   0.003   0.001   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6450)
  covalent geometry    : angle       0.58695 ( 8682)
  hydrogen bonds       : bond        0.03477 (  187)
  hydrogen bonds       : angle       4.99913 (  519)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 221
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 GLU cc_start: 0.7314 (tt0) cc_final: 0.6761 (tt0)
REVERT: A  283 GLN cc_start: 0.7503 (tm-30) cc_final: 0.6514 (tm-30)
REVERT: a  225 LYS cc_start: 0.8911 (tttt) cc_final: 0.8422 (mttm)
REVERT: a  241 GLU cc_start: 0.8429 (mp0) cc_final: 0.8115 (mp0)
REVERT: a  283 GLN cc_start: 0.7384 (tm-30) cc_final: 0.6289 (tm-30)
REVERT: a  296 LYS cc_start: 0.8451 (tppt) cc_final: 0.7656 (mttt)
REVERT: C   13 PHE cc_start: 0.7211 (m-80) cc_final: 0.6983 (m-80)
REVERT: C   34 GLU cc_start: 0.6995 (mp0) cc_final: 0.6782 (mp0)
REVERT: C   50 ASN cc_start: 0.7006 (m110) cc_final: 0.6678 (m110)
REVERT: c  164 GLU cc_start: 0.6138 (tp30) cc_final: 0.5689 (tp30)
  outliers start: 23
  outliers final: 16
  residues processed: 233
  average time/residue: 0.0786
  time to fit residues: 24.0002
Evaluate side-chains
  231 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 215
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain a residue  249 SER
Chi-restraints excluded: chain b residue  322 HIS
Chi-restraints excluded: chain b residue  348 VAL
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain b residue  393 THR
Chi-restraints excluded: chain C residue   46 SER
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue  108 SER
Chi-restraints excluded: chain C residue  161 LEU
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue  160 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 71 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 75 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 385 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.222982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.150072 restraints weight = 6271.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.158112 restraints weight = 2943.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.163210 restraints weight = 1910.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.166394 restraints weight = 1480.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.168072 restraints weight = 1262.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6882
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6450  Z= 0.235
  Angle     :  0.662   7.263   8682  Z= 0.347
  Chirality :  0.046   0.160    964
  Planarity :  0.005   0.059   1122
  Dihedral  :  5.574  56.200    844
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 22.98 %
    Favored  : 73.40 %
  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: -1.60 (0.28), residues: 776
  helix:  0.86 (0.43), residues: 138
  sheet: -0.89 (0.44), residues: 140
  loop : -1.77 (0.25), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG c  49 
 TYR   0.013   0.002   TYR C  37 
 PHE   0.036   0.002   PHE b 370 
 TRP   0.009   0.002   TRP A 294 
 HIS   0.005   0.002   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 6450)
  covalent geometry    : angle       0.66190 ( 8682)
  hydrogen bonds       : bond        0.03374 (  187)
  hydrogen bonds       : angle       4.90140 (  519)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 226
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 GLU cc_start: 0.7388 (tt0) cc_final: 0.6764 (tt0)
REVERT: A  272 SER cc_start: 0.8723 (OUTLIER) cc_final: 0.7979 (t)
REVERT: A  283 GLN cc_start: 0.7566 (tm-30) cc_final: 0.6473 (tm-30)
REVERT: a  225 LYS cc_start: 0.8973 (tttt) cc_final: 0.8351 (mmtp)
REVERT: a  283 GLN cc_start: 0.7349 (tm-30) cc_final: 0.6243 (tm-30)
REVERT: a  296 LYS cc_start: 0.8447 (tppt) cc_final: 0.7653 (mttt)
REVERT: b  372 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7815 (mmtp)
REVERT: C   34 GLU cc_start: 0.6970 (mp0) cc_final: 0.6675 (mp0)
REVERT: C   50 ASN cc_start: 0.6820 (m110) cc_final: 0.6498 (m110)
REVERT: C  165 LYS cc_start: 0.6937 (pptt) cc_final: 0.6505 (ptpp)
REVERT: c   47 VAL cc_start: 0.6193 (OUTLIER) cc_final: 0.5892 (p)
REVERT: c  164 GLU cc_start: 0.6228 (tp30) cc_final: 0.6002 (tp30)
  outliers start: 26
  outliers final: 18
  residues processed: 239
  average time/residue: 0.0889
  time to fit residues: 27.6055
Evaluate side-chains
  238 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 218
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ASN
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain a residue  205 ASN
Chi-restraints excluded: chain a residue  249 SER
Chi-restraints excluded: chain b residue  322 HIS
Chi-restraints excluded: chain b residue  334 THR
Chi-restraints excluded: chain b residue  348 VAL
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue  108 SER
Chi-restraints excluded: chain c residue   28 GLU
Chi-restraints excluded: chain c residue   47 VAL
Chi-restraints excluded: chain c residue  108 SER
Chi-restraints excluded: chain c residue  160 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0980
   chunk 72 optimal weight:   10.0000
   chunk 67 optimal weight:    0.2980
   chunk 6 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.228769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.157124 restraints weight = 6302.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.165819 restraints weight = 2847.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.171194 restraints weight = 1808.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.174757 restraints weight = 1378.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.176780 restraints weight = 1158.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.4159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6765
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6450  Z= 0.114
  Angle     :  0.620   8.804   8682  Z= 0.312
  Chirality :  0.044   0.158    964
  Planarity :  0.005   0.055   1122
  Dihedral  :  5.297  58.427    844
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 25.07 %
    Favored  : 72.01 %
  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: -1.45 (0.28), residues: 776
  helix:  0.82 (0.42), residues: 138
  sheet: -0.87 (0.44), residues: 140
  loop : -1.59 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG c  49 
 TYR   0.012   0.001   TYR C  37 
 PHE   0.015   0.001   PHE b 370 
 TRP   0.007   0.001   TRP b 340 
 HIS   0.003   0.001   HIS A 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6450)
  covalent geometry    : angle       0.62046 ( 8682)
  hydrogen bonds       : bond        0.03141 (  187)
  hydrogen bonds       : angle       4.68877 (  519)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 219
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 SER cc_start: 0.8651 (m) cc_final: 0.7857 (t)
REVERT: A  283 GLN cc_start: 0.7438 (tm-30) cc_final: 0.6399 (tm-30)
REVERT: B  357 MET cc_start: 0.8167 (mtp) cc_final: 0.7786 (mtt)
REVERT: B  370 PHE cc_start: 0.7834 (m-10) cc_final: 0.7558 (m-80)
REVERT: a  225 LYS cc_start: 0.8922 (tttt) cc_final: 0.8343 (mttm)
REVERT: a  241 GLU cc_start: 0.8446 (mp0) cc_final: 0.8189 (mp0)
REVERT: a  283 GLN cc_start: 0.7386 (tm-30) cc_final: 0.6261 (tm-30)
REVERT: a  296 LYS cc_start: 0.8459 (tppt) cc_final: 0.7690 (mttt)
REVERT: b  372 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7646 (mmtp)
REVERT: C   13 PHE cc_start: 0.7285 (m-80) cc_final: 0.7048 (m-80)
REVERT: C   34 GLU cc_start: 0.6977 (mp0) cc_final: 0.6618 (mp0)
REVERT: C   50 ASN cc_start: 0.6850 (m110) cc_final: 0.6539 (m110)
REVERT: C  140 ARG cc_start: 0.7605 (mpt-90) cc_final: 0.7071 (mpt90)
REVERT: C  165 LYS cc_start: 0.6996 (pptt) cc_final: 0.6556 (ptpp)
  outliers start: 21
  outliers final: 18
  residues processed: 231
  average time/residue: 0.0888
  time to fit residues: 26.6422
Evaluate side-chains
  228 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 210
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain a residue  171 GLU
Chi-restraints excluded: chain a residue  249 SER
Chi-restraints excluded: chain b residue  322 HIS
Chi-restraints excluded: chain b residue  334 THR
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain b residue  393 THR
Chi-restraints excluded: chain C residue   46 SER
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue  160 PHE
Chi-restraints excluded: chain c residue  161 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 56 optimal weight:    8.9990
   chunk 14 optimal weight:    4.9990
   chunk 71 optimal weight:    9.9990
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    0.3980
   chunk 45 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 28 optimal weight:    0.2980
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 237 HIS
** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 147 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.223693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.157817 restraints weight = 6163.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.165349 restraints weight = 2969.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.170153 restraints weight = 1918.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.173335 restraints weight = 1461.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.175309 restraints weight = 1224.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6873
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6450  Z= 0.142
  Angle     :  0.646   8.859   8682  Z= 0.323
  Chirality :  0.045   0.282    964
  Planarity :  0.005   0.057   1122
  Dihedral  :  5.303  59.390    844
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 24.79 %
    Favored  : 71.59 %
  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: -1.47 (0.29), residues: 776
  helix:  0.88 (0.43), residues: 138
  sheet: -1.00 (0.43), residues: 140
  loop : -1.59 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG c  49 
 TYR   0.013   0.001   TYR C  37 
 PHE   0.013   0.001   PHE b 327 
 TRP   0.013   0.002   TRP b 340 
 HIS   0.005   0.001   HIS A 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6450)
  covalent geometry    : angle       0.64604 ( 8682)
  hydrogen bonds       : bond        0.03046 (  187)
  hydrogen bonds       : angle       4.58544 (  519)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 223
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 GLU cc_start: 0.7411 (tt0) cc_final: 0.6810 (tt0)
REVERT: A  272 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.7783 (t)
REVERT: A  283 GLN cc_start: 0.7474 (tm-30) cc_final: 0.6495 (tm-30)
REVERT: B  370 PHE cc_start: 0.7834 (m-10) cc_final: 0.7542 (m-10)
REVERT: a  225 LYS cc_start: 0.8874 (tttt) cc_final: 0.8362 (mttm)
REVERT: a  241 GLU cc_start: 0.8414 (mp0) cc_final: 0.8127 (mp0)
REVERT: a  283 GLN cc_start: 0.7351 (tm-30) cc_final: 0.6300 (tm-30)
REVERT: C   34 GLU cc_start: 0.7173 (mp0) cc_final: 0.6812 (mp0)
REVERT: C   50 ASN cc_start: 0.6812 (m110) cc_final: 0.6514 (m110)
REVERT: C  165 LYS cc_start: 0.7156 (pptt) cc_final: 0.6731 (ptpp)
REVERT: c  165 LYS cc_start: 0.7629 (ptpt) cc_final: 0.7319 (ptmt)
REVERT: c  176 LYS cc_start: 0.8081 (mmtt) cc_final: 0.6405 (mttt)
  outliers start: 26
  outliers final: 19
  residues processed: 238
  average time/residue: 0.0875
  time to fit residues: 26.8980
Evaluate side-chains
  239 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 219
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain a residue  171 GLU
Chi-restraints excluded: chain a residue  249 SER
Chi-restraints excluded: chain b residue  322 HIS
Chi-restraints excluded: chain b residue  323 ILE
Chi-restraints excluded: chain b residue  334 THR
Chi-restraints excluded: chain b residue  348 VAL
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain b residue  393 THR
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue  142 VAL
Chi-restraints excluded: chain c residue  160 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 48 optimal weight:    6.9990
   chunk 45 optimal weight:   10.0000
   chunk 47 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0770
   chunk 63 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    1.2942

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.225417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.153339 restraints weight = 6248.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.161585 restraints weight = 2888.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.166880 restraints weight = 1862.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.170164 restraints weight = 1426.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.172325 restraints weight = 1213.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.4115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6825
moved from start:          0.3263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6450  Z= 0.171
  Angle     :  0.665  11.980   8682  Z= 0.333
  Chirality :  0.047   0.435    964
  Planarity :  0.005   0.057   1122
  Dihedral  :  5.357  59.310    844
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 25.77 %
    Favored  : 70.47 %
  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: -1.57 (0.28), residues: 776
  helix:  0.82 (0.43), residues: 138
  sheet: -1.17 (0.43), residues: 140
  loop : -1.62 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG c 140 
 TYR   0.013   0.001   TYR C  37 
 PHE   0.015   0.001   PHE b 327 
 TRP   0.010   0.002   TRP b 340 
 HIS   0.003   0.001   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 6450)
  covalent geometry    : angle       0.66548 ( 8682)
  hydrogen bonds       : bond        0.03022 (  187)
  hydrogen bonds       : angle       4.55708 (  519)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 224
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 GLU cc_start: 0.7449 (tt0) cc_final: 0.6818 (tt0)
REVERT: A  272 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.7908 (t)
REVERT: A  283 GLN cc_start: 0.7475 (tm-30) cc_final: 0.6422 (tm-30)
REVERT: B  357 MET cc_start: 0.8219 (mtp) cc_final: 0.7800 (mtt)
REVERT: B  370 PHE cc_start: 0.7919 (m-10) cc_final: 0.7261 (m-10)
REVERT: B  374 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6529 (mtm110)
REVERT: a  225 LYS cc_start: 0.8979 (tttt) cc_final: 0.8323 (mmtp)
REVERT: a  241 GLU cc_start: 0.8439 (mp0) cc_final: 0.8150 (mp0)
REVERT: a  283 GLN cc_start: 0.7298 (tm-30) cc_final: 0.6160 (tm-30)
REVERT: b  370 PHE cc_start: 0.7873 (m-10) cc_final: 0.7585 (m-80)
REVERT: C   34 GLU cc_start: 0.7152 (mp0) cc_final: 0.6679 (mp0)
REVERT: C   50 ASN cc_start: 0.6780 (m110) cc_final: 0.6440 (m110)
REVERT: C  140 ARG cc_start: 0.7455 (mpt-90) cc_final: 0.7212 (mpt90)
REVERT: C  165 LYS cc_start: 0.6986 (pptt) cc_final: 0.6557 (ptpp)
REVERT: c  122 MET cc_start: 0.5890 (ptt) cc_final: 0.5352 (ppp)
REVERT: c  164 GLU cc_start: 0.6254 (tp30) cc_final: 0.6022 (tp30)
REVERT: c  176 LYS cc_start: 0.8162 (mmtt) cc_final: 0.6498 (mttt)
  outliers start: 27
  outliers final: 22
  residues processed: 239
  average time/residue: 0.0790
  time to fit residues: 24.4813
Evaluate side-chains
  245 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 221
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  374 ARG
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain a residue  171 GLU
Chi-restraints excluded: chain a residue  272 SER
Chi-restraints excluded: chain b residue  322 HIS
Chi-restraints excluded: chain b residue  323 ILE
Chi-restraints excluded: chain b residue  334 THR
Chi-restraints excluded: chain b residue  348 VAL
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain b residue  393 THR
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue  108 SER
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain c residue  108 SER
Chi-restraints excluded: chain c residue  142 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 74 optimal weight:    9.9990
   chunk 8 optimal weight:    0.8980
   chunk 52 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 75 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.225255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.154306 restraints weight = 6219.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.162552 restraints weight = 2864.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.167825 restraints weight = 1837.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.171049 restraints weight = 1403.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.173272 restraints weight = 1193.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6806
moved from start:          0.3481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6450  Z= 0.152
  Angle     :  0.696  11.842   8682  Z= 0.344
  Chirality :  0.047   0.365    964
  Planarity :  0.004   0.058   1122
  Dihedral  :  5.340  59.861    844
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 26.18 %
    Favored  : 69.78 %
  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: -1.50 (0.28), residues: 776
  helix:  0.90 (0.43), residues: 138
  sheet: -1.15 (0.43), residues: 140
  loop : -1.57 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG c  49 
 TYR   0.013   0.001   TYR C  37 
 PHE   0.015   0.001   PHE b 327 
 TRP   0.007   0.001   TRP b 340 
 HIS   0.003   0.001   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6450)
  covalent geometry    : angle       0.69596 ( 8682)
  hydrogen bonds       : bond        0.02979 (  187)
  hydrogen bonds       : angle       4.50383 (  519)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 217
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 GLU cc_start: 0.7396 (tt0) cc_final: 0.6768 (tt0)
REVERT: A  283 GLN cc_start: 0.7469 (tm-30) cc_final: 0.6391 (tm-30)
REVERT: B  370 PHE cc_start: 0.7903 (m-10) cc_final: 0.7215 (m-10)
REVERT: B  374 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6486 (mtm110)
REVERT: a  225 LYS cc_start: 0.8977 (tttt) cc_final: 0.8380 (mttm)
REVERT: a  241 GLU cc_start: 0.8496 (mp0) cc_final: 0.8174 (mp0)
REVERT: a  283 GLN cc_start: 0.7303 (tm-30) cc_final: 0.6154 (tm-30)
REVERT: a  296 LYS cc_start: 0.8382 (tppt) cc_final: 0.7597 (mttm)
REVERT: b  370 PHE cc_start: 0.7851 (m-10) cc_final: 0.7574 (m-80)
REVERT: C   34 GLU cc_start: 0.7179 (mp0) cc_final: 0.6689 (mp0)
REVERT: C   50 ASN cc_start: 0.6507 (m110) cc_final: 0.6170 (m110)
REVERT: C  164 GLU cc_start: 0.5632 (tp30) cc_final: 0.5372 (tp30)
REVERT: C  165 LYS cc_start: 0.7090 (pptt) cc_final: 0.6653 (ptpp)
REVERT: c  122 MET cc_start: 0.5867 (ptt) cc_final: 0.5294 (ppp)
REVERT: c  164 GLU cc_start: 0.6214 (tp30) cc_final: 0.6005 (tp30)
REVERT: c  176 LYS cc_start: 0.8215 (mmtt) cc_final: 0.6631 (mttt)
  outliers start: 29
  outliers final: 25
  residues processed: 231
  average time/residue: 0.0771
  time to fit residues: 23.1333
Evaluate side-chains
  243 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 217
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  374 ARG
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain a residue  171 GLU
Chi-restraints excluded: chain b residue  322 HIS
Chi-restraints excluded: chain b residue  323 ILE
Chi-restraints excluded: chain b residue  334 THR
Chi-restraints excluded: chain b residue  348 VAL
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain b residue  393 THR
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue  108 SER
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue  121 GLU
Chi-restraints excluded: chain c residue  142 VAL
Chi-restraints excluded: chain c residue  160 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 66 optimal weight:    9.9990
   chunk 8 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.4537 r_free = 0.4537 target = 0.225069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.153239 restraints weight = 6332.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.161569 restraints weight = 2882.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.166885 restraints weight = 1839.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.170122 restraints weight = 1404.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.172276 restraints weight = 1194.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6813
moved from start:          0.3569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6450  Z= 0.158
  Angle     :  0.707  14.011   8682  Z= 0.348
  Chirality :  0.048   0.404    964
  Planarity :  0.005   0.058   1122
  Dihedral  :  5.402  59.758    844
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 26.32 %
    Favored  : 69.50 %
  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: -1.53 (0.28), residues: 776
  helix:  0.82 (0.42), residues: 138
  sheet: -1.20 (0.44), residues: 140
  loop : -1.57 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG c 140 
 TYR   0.013   0.001   TYR C  37 
 PHE   0.017   0.001   PHE b 327 
 TRP   0.006   0.001   TRP b 340 
 HIS   0.003   0.001   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 6450)
  covalent geometry    : angle       0.70703 ( 8682)
  hydrogen bonds       : bond        0.02936 (  187)
  hydrogen bonds       : angle       4.55707 (  519)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 216
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 GLU cc_start: 0.7428 (tt0) cc_final: 0.6780 (tt0)
REVERT: A  283 GLN cc_start: 0.7454 (tm-30) cc_final: 0.6363 (tm-30)
REVERT: B  370 PHE cc_start: 0.7904 (m-10) cc_final: 0.7212 (m-10)
REVERT: B  374 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6481 (mtm110)
REVERT: a  225 LYS cc_start: 0.8976 (tttt) cc_final: 0.8372 (mttm)
REVERT: a  241 GLU cc_start: 0.8504 (mp0) cc_final: 0.8190 (mp0)
REVERT: a  283 GLN cc_start: 0.7291 (tm-30) cc_final: 0.6168 (tm-30)
REVERT: a  296 LYS cc_start: 0.8373 (tppt) cc_final: 0.7588 (mttm)
REVERT: b  370 PHE cc_start: 0.7848 (m-10) cc_final: 0.7553 (m-80)
REVERT: C   34 GLU cc_start: 0.7189 (mp0) cc_final: 0.6662 (mp0)
REVERT: C   50 ASN cc_start: 0.6153 (m110) cc_final: 0.5815 (m110)
REVERT: C  165 LYS cc_start: 0.7050 (pptt) cc_final: 0.6615 (ptpp)
REVERT: c   28 GLU cc_start: 0.5887 (OUTLIER) cc_final: 0.5633 (pp20)
REVERT: c  122 MET cc_start: 0.5910 (ptt) cc_final: 0.5310 (ppp)
REVERT: c  164 GLU cc_start: 0.6184 (tp30) cc_final: 0.5983 (tp30)
REVERT: c  176 LYS cc_start: 0.8254 (mmtt) cc_final: 0.6673 (mttt)
  outliers start: 30
  outliers final: 27
  residues processed: 233
  average time/residue: 0.0896
  time to fit residues: 27.1637
Evaluate side-chains
  242 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 213
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  374 ARG
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain a residue  171 GLU
Chi-restraints excluded: chain a residue  276 LYS
Chi-restraints excluded: chain b residue  322 HIS
Chi-restraints excluded: chain b residue  323 ILE
Chi-restraints excluded: chain b residue  334 THR
Chi-restraints excluded: chain b residue  348 VAL
Chi-restraints excluded: chain b residue  366 VAL
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain b residue  393 THR
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue  108 SER
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain c residue   28 GLU
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue  108 SER
Chi-restraints excluded: chain c residue  121 GLU
Chi-restraints excluded: chain c residue  142 VAL
Chi-restraints excluded: chain c residue  160 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 67 optimal weight:    9.9990
   chunk 42 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   chunk 7 optimal weight:    5.9990
   chunk 49 optimal weight:    0.4980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.226874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.155673 restraints weight = 6144.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.163916 restraints weight = 2813.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.169303 restraints weight = 1809.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.172699 restraints weight = 1377.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.174665 restraints weight = 1164.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.4139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6773
moved from start:          0.3688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6450  Z= 0.135
  Angle     :  0.714  14.893   8682  Z= 0.348
  Chirality :  0.047   0.412    964
  Planarity :  0.005   0.058   1122
  Dihedral  :  5.307  59.874    844
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 27.58 %
    Favored  : 68.52 %
  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: -1.45 (0.29), residues: 776
  helix:  0.82 (0.42), residues: 138
  sheet: -1.17 (0.44), residues: 140
  loop : -1.49 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 352 
 TYR   0.012   0.001   TYR C  37 
 PHE   0.016   0.001   PHE b 327 
 TRP   0.005   0.001   TRP b 340 
 HIS   0.003   0.001   HIS B 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6450)
  covalent geometry    : angle       0.71422 ( 8682)
  hydrogen bonds       : bond        0.02868 (  187)
  hydrogen bonds       : angle       4.59874 (  519)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 216
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 GLU cc_start: 0.7450 (tt0) cc_final: 0.6801 (tt0)
REVERT: A  283 GLN cc_start: 0.7408 (tm-30) cc_final: 0.6382 (tm-30)
REVERT: B  370 PHE cc_start: 0.7864 (m-10) cc_final: 0.7558 (m-10)
REVERT: a  225 LYS cc_start: 0.8952 (tttt) cc_final: 0.8335 (mttm)
REVERT: a  241 GLU cc_start: 0.8521 (mp0) cc_final: 0.8206 (mp0)
REVERT: a  283 GLN cc_start: 0.7298 (tm-30) cc_final: 0.6177 (tm-30)
REVERT: a  296 LYS cc_start: 0.8351 (tppt) cc_final: 0.7575 (mttm)
REVERT: b  370 PHE cc_start: 0.7844 (m-10) cc_final: 0.7553 (m-80)
REVERT: C   34 GLU cc_start: 0.7217 (mp0) cc_final: 0.6698 (mp0)
REVERT: c  122 MET cc_start: 0.5933 (ptt) cc_final: 0.5316 (ppp)
REVERT: c  176 LYS cc_start: 0.8253 (mmtt) cc_final: 0.6697 (mttt)
  outliers start: 28
  outliers final: 27
  residues processed: 233
  average time/residue: 0.0839
  time to fit residues: 25.2129
Evaluate side-chains
  240 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 213
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain a residue  171 GLU
Chi-restraints excluded: chain a residue  276 LYS
Chi-restraints excluded: chain b residue  322 HIS
Chi-restraints excluded: chain b residue  323 ILE
Chi-restraints excluded: chain b residue  334 THR
Chi-restraints excluded: chain b residue  348 VAL
Chi-restraints excluded: chain b residue  366 VAL
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain b residue  393 THR
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue  108 SER
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue  108 SER
Chi-restraints excluded: chain c residue  121 GLU
Chi-restraints excluded: chain c residue  142 VAL
Chi-restraints excluded: chain c residue  160 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 23 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0470
   chunk 66 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 145 HIS
C 147 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.227950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.156850 restraints weight = 6206.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.165003 restraints weight = 2930.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.170156 restraints weight = 1898.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.173495 restraints weight = 1466.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.175508 restraints weight = 1246.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6840
moved from start:          0.3813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6450  Z= 0.133
  Angle     :  0.724  13.890   8682  Z= 0.355
  Chirality :  0.048   0.383    964
  Planarity :  0.005   0.058   1122
  Dihedral  :  5.278  59.587    844
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 27.58 %
    Favored  : 68.66 %
  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: -1.47 (0.28), residues: 776
  helix:  0.79 (0.42), residues: 138
  sheet: -1.17 (0.45), residues: 140
  loop : -1.49 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 140 
 TYR   0.014   0.001   TYR c 156 
 PHE   0.015   0.001   PHE b 327 
 TRP   0.005   0.001   TRP b 340 
 HIS   0.002   0.001   HIS A 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6450)
  covalent geometry    : angle       0.72395 ( 8682)
  hydrogen bonds       : bond        0.02835 (  187)
  hydrogen bonds       : angle       4.69164 (  519)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1598.07 seconds
wall clock time: 28 minutes 2.45 seconds (1682.45 seconds total)