Starting phenix.real_space_refine
on Fri Nov 15 12:35:41 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieq_35390/11_2024/8ieq_35390.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieq_35390/11_2024/8ieq_35390.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieq_35390/11_2024/8ieq_35390.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieq_35390/11_2024/8ieq_35390.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieq_35390/11_2024/8ieq_35390.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieq_35390/11_2024/8ieq_35390.cif"
  }
  resolution = 2.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=  -0.004 sd=   0.189
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: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      71      5.16       5
     C    5900      2.51       5
     N    1399      2.21       5
     O    1526      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 8900
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2135
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2135
          Classifications: {'peptide': 277}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 8, 'TRANS': 268}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 2230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2230
          Classifications: {'peptide': 286}
          Link IDs: {'PTRANS': 9, 'TRANS': 276}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2155
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 8, 'TRANS': 269}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 2172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2172
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 8, 'TRANS': 270}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 52
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 52
          Unusual residues: {'PC1': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
    Chain: "B"
      Number of atoms: 52
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 52
          Unusual residues: {'PC1': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
    Chain: "C"
      Number of atoms: 52
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 52
          Unusual residues: {'PC1': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
    Chain: "D"
      Number of atoms: 52
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 52
          Unusual residues: {'PC1': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
  Time building chain proxies: 6.74, per 1000 atoms: 0.76
  Number of scatterers: 8900
  At special positions: 0
  Unit cell: (76.95, 91.53, 149.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      71     16.00
     P       4     15.00
     O    1526      8.00
     N    1399      7.00
     C    5900      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 191 " - pdb=" SG  CYS A 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 191 " - pdb=" SG  CYS B 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 191 " - pdb=" SG  CYS C 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 191 " - pdb=" SG  CYS D 216 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.39
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2086

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 2 sheets defined
      78.7% alpha, 7.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 74
    Processing helix  chain 'A' and resid 77 through 82
    Processing helix  chain 'A' and resid 84 through 105
      removed outlier: 3.560A  pdb=" N   ILE A  89 " --> pdb=" O   PRO A  85 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   VAL A  90 " --> pdb=" O   ASN A  86 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   THR A  91 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 150
      Proline residue:  A 137  - end of helix
    Processing helix  chain 'A' and resid 161 through 187
      removed outlier: 3.782A  pdb=" N   LEU A 165 " --> pdb=" O   LYS A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 246
      removed outlier: 4.099A  pdb=" N   TRP A 224 " --> pdb=" O   TYR A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 281
      removed outlier: 3.558A  pdb=" N   ASN A 265 " --> pdb=" O   MET A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 327
      Proline residue:  A 310  - end of helix
    Processing helix  chain 'B' and resid 46 through 74
    Processing helix  chain 'B' and resid 77 through 83
      removed outlier: 3.692A  pdb=" N   SER B  83 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 105
      removed outlier: 3.664A  pdb=" N   VAL B  90 " --> pdb=" O   ASN B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 149
      Proline residue:  B 137  - end of helix
    Processing helix  chain 'B' and resid 157 through 168
    Processing helix  chain 'B' and resid 169 through 187
    Processing helix  chain 'B' and resid 220 through 246
      removed outlier: 3.597A  pdb=" N   TRP B 224 " --> pdb=" O   TYR B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 281
    Processing helix  chain 'B' and resid 284 through 332
      Proline residue:  B 310  - end of helix
    Processing helix  chain 'C' and resid 46 through 74
    Processing helix  chain 'C' and resid 77 through 82
    Processing helix  chain 'C' and resid 84 through 105
      removed outlier: 3.671A  pdb=" N   ILE C  89 " --> pdb=" O   PRO C  85 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   VAL C  90 " --> pdb=" O   ASN C  86 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   THR C  91 " --> pdb=" O   LEU C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 116 through 150
      Proline residue:  C 137  - end of helix
    Processing helix  chain 'C' and resid 161 through 187
      removed outlier: 3.599A  pdb=" N   LEU C 165 " --> pdb=" O   LYS C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 246
      removed outlier: 4.089A  pdb=" N   TRP C 224 " --> pdb=" O   TYR C 220 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 257 through 281
    Processing helix  chain 'C' and resid 284 through 332
      Proline residue:  C 310  - end of helix
    Processing helix  chain 'D' and resid 46 through 74
    Processing helix  chain 'D' and resid 77 through 83
    Processing helix  chain 'D' and resid 84 through 105
      removed outlier: 3.595A  pdb=" N   VAL D  90 " --> pdb=" O   ASN D  86 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   TYR D 103 " --> pdb=" O   TYR D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 116 through 149
      Proline residue:  D 137  - end of helix
    Processing helix  chain 'D' and resid 162 through 187
      removed outlier: 3.558A  pdb=" N   ASP D 176 " --> pdb=" O   LEU D 172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 220 through 246
      removed outlier: 3.539A  pdb=" N   TRP D 224 " --> pdb=" O   TYR D 220 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 256 through 281
    Processing helix  chain 'D' and resid 284 through 332
      Proline residue:  D 310  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 216
      removed outlier: 3.508A  pdb=" N   PHE A 215 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   LEU A 195 " --> pdb=" O   MET B 199 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   PHE B 215 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 206 through 216
      removed outlier: 3.604A  pdb=" N   PHE C 215 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   LEU C 195 " --> pdb=" O   MET D 199 " (cutoff:3.500A)

    766 hydrogen bonds defined for protein.
    2292 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: 2.84

  Time building geometry restraints manager: 2.75 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1282
        1.31 -     1.44: 2431
        1.44 -     1.56: 5242
        1.56 -     1.69: 24
        1.69 -     1.81: 102
  Bond restraints: 9081
  Sorted by residual:
  bond pdb=" C39 PC1 B 601 "
       pdb=" C3A PC1 B 601 "
    ideal  model  delta    sigma   weight residual
    1.524  1.324  0.200 2.00e-02 2.50e+03 9.99e+01
  bond pdb=" C39 PC1 A 601 "
       pdb=" C3A PC1 A 601 "
    ideal  model  delta    sigma   weight residual
    1.524  1.327  0.197 2.00e-02 2.50e+03 9.74e+01
  bond pdb=" C39 PC1 C 601 "
       pdb=" C3A PC1 C 601 "
    ideal  model  delta    sigma   weight residual
    1.524  1.327  0.197 2.00e-02 2.50e+03 9.72e+01
  bond pdb=" C39 PC1 D 601 "
       pdb=" C3A PC1 D 601 "
    ideal  model  delta    sigma   weight residual
    1.524  1.327  0.197 2.00e-02 2.50e+03 9.69e+01
  bond pdb=" C31 PC1 D 601 "
       pdb=" O31 PC1 D 601 "
    ideal  model  delta    sigma   weight residual
    1.330  1.427 -0.097 2.00e-02 2.50e+03 2.34e+01
  ... (remaining 9076 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.82: 12164
        2.82 -     5.63: 128
        5.63 -     8.45: 24
        8.45 -    11.26: 0
       11.26 -    14.08: 4
  Bond angle restraints: 12320
  Sorted by residual:
  angle pdb=" O12 PC1 B 601 "
        pdb=" P   PC1 B 601 "
        pdb=" O14 PC1 B 601 "
      ideal   model   delta    sigma   weight residual
     123.67  109.59   14.08 3.00e+00 1.11e-01 2.20e+01
  angle pdb=" O12 PC1 C 601 "
        pdb=" P   PC1 C 601 "
        pdb=" O14 PC1 C 601 "
      ideal   model   delta    sigma   weight residual
     123.67  109.62   14.05 3.00e+00 1.11e-01 2.19e+01
  angle pdb=" O12 PC1 D 601 "
        pdb=" P   PC1 D 601 "
        pdb=" O14 PC1 D 601 "
      ideal   model   delta    sigma   weight residual
     123.67  109.68   13.99 3.00e+00 1.11e-01 2.18e+01
  angle pdb=" O12 PC1 A 601 "
        pdb=" P   PC1 A 601 "
        pdb=" O14 PC1 A 601 "
      ideal   model   delta    sigma   weight residual
     123.67  109.95   13.72 3.00e+00 1.11e-01 2.09e+01
  angle pdb=" CB  TRP B 229 "
        pdb=" CG  TRP B 229 "
        pdb=" CD2 TRP B 229 "
      ideal   model   delta    sigma   weight residual
     126.80  131.57   -4.77 1.40e+00 5.10e-01 1.16e+01
  ... (remaining 12315 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 4889
       17.93 -    35.87: 385
       35.87 -    53.80: 78
       53.80 -    71.74: 11
       71.74 -    89.67: 12
  Dihedral angle restraints: 5375
    sinusoidal: 2148
      harmonic: 3227
  Sorted by residual:
  dihedral pdb=" CA  ILE D 228 "
           pdb=" C   ILE D 228 "
           pdb=" N   TRP D 229 "
           pdb=" CA  TRP D 229 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.79   21.21     0      5.00e+00 4.00e-02 1.80e+01
  dihedral pdb=" CA  ILE B 228 "
           pdb=" C   ILE B 228 "
           pdb=" N   TRP B 229 "
           pdb=" CA  TRP B 229 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.87   20.13     0      5.00e+00 4.00e-02 1.62e+01
  dihedral pdb=" CA  ILE A 307 "
           pdb=" C   ILE A 307 "
           pdb=" N   PHE A 308 "
           pdb=" CA  PHE A 308 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.00  -20.00     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 5372 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1168
       0.044 -    0.088: 276
       0.088 -    0.132: 64
       0.132 -    0.176: 3
       0.176 -    0.219: 3
  Chirality restraints: 1514
  Sorted by residual:
  chirality pdb=" CA  TRP C 229 "
            pdb=" N   TRP C 229 "
            pdb=" C   TRP C 229 "
            pdb=" CB  TRP C 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  TRP B 229 "
            pdb=" N   TRP B 229 "
            pdb=" C   TRP B 229 "
            pdb=" CB  TRP B 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.88e-01
  chirality pdb=" CA  TRP D 229 "
            pdb=" N   TRP D 229 "
            pdb=" C   TRP D 229 "
            pdb=" CB  TRP D 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.77e-01
  ... (remaining 1511 not shown)

  Planarity restraints: 1433
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 229 "   -0.028 2.00e-02 2.50e+03   2.95e-02 2.17e+01
        pdb=" CG  TRP B 229 "    0.080 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 229 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 229 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 229 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 229 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 229 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 229 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 229 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 229 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 229 "    0.026 2.00e-02 2.50e+03   2.85e-02 2.03e+01
        pdb=" CG  TRP D 229 "   -0.078 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 229 "    0.030 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 229 "    0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 229 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 229 "    0.008 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 229 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 229 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 229 "   -0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 229 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 229 "   -0.024 2.00e-02 2.50e+03   2.56e-02 1.64e+01
        pdb=" CG  TRP C 229 "    0.070 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 229 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 229 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 229 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 229 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 229 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 229 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 229 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 229 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1430 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 201
        2.71 -     3.26: 8745
        3.26 -     3.80: 14261
        3.80 -     4.35: 17246
        4.35 -     4.90: 31039
  Nonbonded interactions: 71492
  Sorted by model distance:
  nonbonded pdb=" OG  SER C  58 "
            pdb=" OH  TYR C 103 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" O   TYR D 146 "
            pdb=" OG1 THR D 150 "
     model   vdw
     2.167 3.040
  nonbonded pdb=" OG1 THR C 202 "
            pdb=" OD1 ASP C 205 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OG  SER A  84 "
            pdb=" NH2 ARG A 144 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" OG  SER B  58 "
            pdb=" OH  TYR B 103 "
     model   vdw
     2.246 3.040
  ... (remaining 71487 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 44 through 110 or resid 115 through 152 or resid 161 throu \ 
gh 327 or resid 601))
  selection = (chain 'B' and (resid 44 through 110 or resid 115 through 151 or (resid 152 and  \ 
(name N or name CA or name C or name O or name CB )) or (resid 161 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 162 through 327 or resid 60 \ 
1))
  selection = (chain 'C' and (resid 44 through 152 or resid 161 through 327 or resid 601))
  selection = (chain 'D' and (resid 44 through 110 or resid 115 through 151 or (resid 152 thro \ 
ugh 161 and (name N or name CA or name C or name O or name CB )) or resid 162 th \ 
rough 327 or resid 601))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     24.360
  Find NCS groups from input model:        0.540
  Set up NCS constraints:                  0.040
  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:15.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
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      :  0.007   0.200   9081  Z= 0.457
  Angle     :  0.792  14.077  12320  Z= 0.379
  Chirality :  0.040   0.219   1514
  Planarity :  0.005   0.077   1433
  Dihedral  : 14.175  89.673   3277
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.06 (0.25), residues: 1100
  helix:  2.83 (0.16), residues: 846
  sheet:  1.86 (0.65), residues: 72
  loop : -2.15 (0.41), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.080   0.003   TRP B 229 
 HIS   0.002   0.001   HIS A 214 
 PHE   0.011   0.001   PHE A 308 
 TYR   0.010   0.001   TYR B 103 
 ARG   0.003   0.000   ARG A  75 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.7129 (tttt) cc_final: 0.6697 (tppt)
REVERT: A   96 CYS cc_start: 0.7326 (p) cc_final: 0.7075 (m)
REVERT: A  174 MET cc_start: 0.6355 (ttp) cc_final: 0.5891 (tpt)
REVERT: A  181 MET cc_start: 0.7052 (mtp) cc_final: 0.6577 (mmp)
REVERT: A  219 ARG cc_start: 0.7127 (mtp180) cc_final: 0.6634 (mtm110)
REVERT: A  222 ASP cc_start: 0.8359 (m-30) cc_final: 0.8128 (m-30)
REVERT: B   72 ILE cc_start: 0.7994 (mm) cc_final: 0.7695 (mt)
REVERT: B  246 THR cc_start: 0.8377 (m) cc_final: 0.7675 (p)
REVERT: B  275 PHE cc_start: 0.6930 (t80) cc_final: 0.6438 (t80)
REVERT: C   98 THR cc_start: 0.7428 (m) cc_final: 0.6897 (p)
REVERT: C  187 ASP cc_start: 0.8382 (p0) cc_final: 0.8178 (p0)
REVERT: C  199 MET cc_start: 0.7234 (ttt) cc_final: 0.6057 (mmt)
REVERT: C  219 ARG cc_start: 0.7415 (mtp180) cc_final: 0.6914 (mtp-110)
REVERT: C  222 ASP cc_start: 0.8482 (m-30) cc_final: 0.8179 (m-30)
REVERT: C  275 PHE cc_start: 0.7295 (t80) cc_final: 0.7086 (t80)
REVERT: C  328 MET cc_start: 0.5338 (mmm) cc_final: 0.4596 (ppp)
REVERT: D   81 LYS cc_start: 0.7678 (tttt) cc_final: 0.6773 (ttpt)
REVERT: D   82 MET cc_start: 0.7476 (ptt) cc_final: 0.7194 (ptp)
REVERT: D  190 GLN cc_start: 0.7663 (mt0) cc_final: 0.6624 (mm110)
REVERT: D  219 ARG cc_start: 0.7835 (ttp-170) cc_final: 0.7623 (ttp-110)
REVERT: D  235 LEU cc_start: 0.7175 (mm) cc_final: 0.6474 (tp)
  outliers start: 0
  outliers final: 1
  residues processed: 131
  average time/residue: 1.0970
  time to fit residues: 155.1066
Evaluate side-chains
  96 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  215 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 98 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 265 ASN
B 190 GLN
C 190 GLN
C 265 ASN
D  86 ASN
D 121 GLN
D 255 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.1237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9081  Z= 0.259
  Angle     :  0.567   6.977  12320  Z= 0.301
  Chirality :  0.041   0.189   1514
  Planarity :  0.005   0.072   1433
  Dihedral  : 11.310  87.813   1362
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  6.07 %
    Favored  : 92.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.47 (0.24), residues: 1100
  helix:  3.04 (0.16), residues: 852
  sheet:  3.07 (0.65), residues: 67
  loop : -2.08 (0.43), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 229 
 HIS   0.001   0.000   HIS D 214 
 PHE   0.013   0.002   PHE D 275 
 TYR   0.014   0.001   TYR D 103 
 ARG   0.004   0.000   ARG C  75 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 1.016 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.7436 (tttt) cc_final: 0.6951 (tppt)
REVERT: A   98 THR cc_start: 0.6973 (m) cc_final: 0.6504 (p)
REVERT: A  147 LYS cc_start: 0.6837 (mmmt) cc_final: 0.6497 (mmpt)
REVERT: A  174 MET cc_start: 0.6421 (ttp) cc_final: 0.5955 (tpt)
REVERT: A  181 MET cc_start: 0.7208 (mtp) cc_final: 0.6580 (mmp)
REVERT: A  219 ARG cc_start: 0.7194 (mtp180) cc_final: 0.6677 (mtm110)
REVERT: B   72 ILE cc_start: 0.7834 (mm) cc_final: 0.7591 (mt)
REVERT: B   81 LYS cc_start: 0.7283 (tttt) cc_final: 0.6981 (ttmt)
REVERT: B  123 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.6294 (ptp-170)
REVERT: B  174 MET cc_start: 0.5070 (OUTLIER) cc_final: 0.4495 (tmm)
REVERT: B  219 ARG cc_start: 0.7369 (ttt-90) cc_final: 0.6629 (ttp-110)
REVERT: B  246 THR cc_start: 0.8271 (m) cc_final: 0.7578 (p)
REVERT: B  275 PHE cc_start: 0.7102 (t80) cc_final: 0.6404 (t80)
REVERT: B  328 MET cc_start: 0.4558 (mtp) cc_final: 0.3891 (mtp)
REVERT: C   81 LYS cc_start: 0.7489 (ttmt) cc_final: 0.6620 (tptt)
REVERT: C   98 THR cc_start: 0.7501 (m) cc_final: 0.6917 (p)
REVERT: C  174 MET cc_start: 0.6667 (mmm) cc_final: 0.6417 (tpt)
REVERT: C  187 ASP cc_start: 0.8447 (p0) cc_final: 0.7967 (p0)
REVERT: C  199 MET cc_start: 0.7247 (ttt) cc_final: 0.5988 (mmt)
REVERT: C  219 ARG cc_start: 0.7417 (mtp180) cc_final: 0.6954 (mtp-110)
REVERT: C  328 MET cc_start: 0.5545 (mmm) cc_final: 0.4739 (ppp)
REVERT: D   81 LYS cc_start: 0.7792 (tttt) cc_final: 0.6906 (ttpt)
REVERT: D  190 GLN cc_start: 0.7374 (mt0) cc_final: 0.6722 (mm110)
REVERT: D  235 LEU cc_start: 0.7180 (mm) cc_final: 0.6464 (tp)
REVERT: D  328 MET cc_start: 0.3356 (mtm) cc_final: 0.2493 (pmt)
  outliers start: 16
  outliers final: 9
  residues processed: 114
  average time/residue: 1.2081
  time to fit residues: 147.8800
Evaluate side-chains
  111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain B residue  123 ARG
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain C residue  132 SER
Chi-restraints excluded: chain C residue  181 MET
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  282 HIS
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  259 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 99 optimal weight:    0.7980
   chunk 107 optimal weight:    0.7980
   chunk 88 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 190 GLN
D 121 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9081  Z= 0.238
  Angle     :  0.547   8.089  12320  Z= 0.291
  Chirality :  0.040   0.218   1514
  Planarity :  0.006   0.075   1433
  Dihedral  : 11.486  89.181   1360
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  7.79 %
    Favored  : 89.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.49 (0.24), residues: 1100
  helix:  3.13 (0.15), residues: 853
  sheet:  3.13 (0.79), residues: 42
  loop : -1.85 (0.41), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 315 
 HIS   0.001   0.000   HIS C  73 
 PHE   0.027   0.002   PHE B 215 
 TYR   0.011   0.001   TYR B 280 
 ARG   0.006   0.001   ARG B 279 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 1.062 
Fit side-chains
REVERT: A   81 LYS cc_start: 0.7471 (tttt) cc_final: 0.6942 (tppt)
REVERT: A   98 THR cc_start: 0.7150 (m) cc_final: 0.6689 (p)
REVERT: A  116 MET cc_start: 0.7828 (tpt) cc_final: 0.7418 (tpt)
REVERT: A  147 LYS cc_start: 0.6853 (mmmt) cc_final: 0.6520 (mmpt)
REVERT: A  174 MET cc_start: 0.6418 (ttp) cc_final: 0.5974 (tpt)
REVERT: A  181 MET cc_start: 0.7160 (mtp) cc_final: 0.6681 (tpt)
REVERT: A  219 ARG cc_start: 0.7181 (mtp180) cc_final: 0.6574 (mtm-85)
REVERT: B   81 LYS cc_start: 0.7272 (tttt) cc_final: 0.6965 (ttmt)
REVERT: B  123 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.6207 (ptp-170)
REVERT: B  174 MET cc_start: 0.5121 (OUTLIER) cc_final: 0.4531 (tmm)
REVERT: B  219 ARG cc_start: 0.7307 (ttt-90) cc_final: 0.6701 (ttp-110)
REVERT: B  222 ASP cc_start: 0.8437 (m-30) cc_final: 0.8107 (m-30)
REVERT: B  246 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.7655 (p)
REVERT: B  275 PHE cc_start: 0.7147 (t80) cc_final: 0.6321 (t80)
REVERT: C   98 THR cc_start: 0.7536 (m) cc_final: 0.6927 (p)
REVERT: C  117 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7473 (mp0)
REVERT: C  174 MET cc_start: 0.6601 (mmm) cc_final: 0.6325 (tpt)
REVERT: C  187 ASP cc_start: 0.8372 (p0) cc_final: 0.7983 (p0)
REVERT: C  199 MET cc_start: 0.7229 (ttt) cc_final: 0.5981 (mmt)
REVERT: C  219 ARG cc_start: 0.7441 (mtp180) cc_final: 0.6923 (mtp-110)
REVERT: C  328 MET cc_start: 0.5563 (mmm) cc_final: 0.4698 (ppp)
REVERT: D   81 LYS cc_start: 0.7784 (tttt) cc_final: 0.6872 (ttpt)
REVERT: D  190 GLN cc_start: 0.7406 (mt0) cc_final: 0.6719 (mm110)
REVERT: D  235 LEU cc_start: 0.7180 (mm) cc_final: 0.6424 (tp)
REVERT: D  328 MET cc_start: 0.3398 (mtm) cc_final: 0.2438 (pmt)
  outliers start: 25
  outliers final: 8
  residues processed: 119
  average time/residue: 1.1641
  time to fit residues: 148.9335
Evaluate side-chains
  111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain B residue  123 ARG
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  246 THR
Chi-restraints excluded: chain C residue  117 GLU
Chi-restraints excluded: chain C residue  132 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  259 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 47 optimal weight:    0.4980
   chunk 66 optimal weight:    0.6980
   chunk 99 optimal weight:    0.9990
   chunk 105 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 87 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:
B 190 GLN
B 304 ASN
D  86 ASN
D 121 GLN
D 255 ASN
D 304 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9081  Z= 0.226
  Angle     :  0.526   6.831  12320  Z= 0.282
  Chirality :  0.040   0.241   1514
  Planarity :  0.006   0.076   1433
  Dihedral  : 11.621  86.093   1360
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  :  8.20 %
    Favored  : 88.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.62 (0.24), residues: 1100
  helix:  3.18 (0.15), residues: 855
  sheet:  3.37 (0.73), residues: 48
  loop : -1.84 (0.42), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 315 
 HIS   0.001   0.000   HIS C  73 
 PHE   0.027   0.002   PHE B 215 
 TYR   0.011   0.001   TYR B 280 
 ARG   0.009   0.000   ARG C  75 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.7442 (tttt) cc_final: 0.6931 (tppt)
REVERT: A   98 THR cc_start: 0.7092 (m) cc_final: 0.6631 (p)
REVERT: A  147 LYS cc_start: 0.6870 (mmmt) cc_final: 0.6547 (mmpt)
REVERT: A  174 MET cc_start: 0.6471 (ttp) cc_final: 0.5991 (tpt)
REVERT: A  181 MET cc_start: 0.7184 (mtp) cc_final: 0.6718 (tpt)
REVERT: A  219 ARG cc_start: 0.7154 (mtp180) cc_final: 0.6556 (mtm-85)
REVERT: B   81 LYS cc_start: 0.7249 (tttt) cc_final: 0.6930 (ttmt)
REVERT: B  123 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.6279 (ptp-170)
REVERT: B  199 MET cc_start: 0.7064 (tpt) cc_final: 0.6800 (tmt)
REVERT: B  219 ARG cc_start: 0.7303 (ttt-90) cc_final: 0.6675 (ttp-110)
REVERT: B  222 ASP cc_start: 0.8469 (m-30) cc_final: 0.8123 (m-30)
REVERT: B  246 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.7622 (p)
REVERT: B  275 PHE cc_start: 0.7183 (t80) cc_final: 0.6314 (t80)
REVERT: B  328 MET cc_start: 0.4613 (mtp) cc_final: 0.4039 (mtp)
REVERT: C   98 THR cc_start: 0.7526 (m) cc_final: 0.6932 (p)
REVERT: C  174 MET cc_start: 0.6510 (mmm) cc_final: 0.6296 (tpt)
REVERT: C  187 ASP cc_start: 0.8304 (p0) cc_final: 0.7981 (p0)
REVERT: C  199 MET cc_start: 0.7209 (ttt) cc_final: 0.6022 (mmt)
REVERT: C  219 ARG cc_start: 0.7499 (mtp180) cc_final: 0.6984 (mtp-110)
REVERT: C  328 MET cc_start: 0.5496 (mmm) cc_final: 0.4692 (ppp)
REVERT: D   81 LYS cc_start: 0.7662 (tttt) cc_final: 0.6726 (ttpt)
REVERT: D  190 GLN cc_start: 0.7390 (mt0) cc_final: 0.6693 (mm110)
REVERT: D  235 LEU cc_start: 0.7243 (mm) cc_final: 0.6431 (tp)
REVERT: D  328 MET cc_start: 0.3465 (mtm) cc_final: 0.2554 (pmt)
  outliers start: 30
  outliers final: 14
  residues processed: 120
  average time/residue: 1.0917
  time to fit residues: 141.2975
Evaluate side-chains
  116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain B residue  123 ARG
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  246 THR
Chi-restraints excluded: chain C residue  132 SER
Chi-restraints excluded: chain C residue  181 MET
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  181 MET
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  259 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
B 190 GLN
D  86 ASN
D 121 GLN
D 255 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9081  Z= 0.304
  Angle     :  0.585   7.277  12320  Z= 0.308
  Chirality :  0.042   0.304   1514
  Planarity :  0.006   0.079   1433
  Dihedral  : 11.856  88.545   1360
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  :  8.91 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.36 (0.24), residues: 1100
  helix:  2.96 (0.15), residues: 857
  sheet:  3.51 (0.73), residues: 48
  loop : -1.89 (0.43), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C 315 
 HIS   0.001   0.000   HIS C  73 
 PHE   0.029   0.002   PHE B 215 
 TYR   0.014   0.001   TYR B 280 
 ARG   0.009   0.001   ARG C  75 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 98
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.7437 (tttt) cc_final: 0.6888 (tppt)
REVERT: A   98 THR cc_start: 0.7260 (m) cc_final: 0.6804 (p)
REVERT: A  147 LYS cc_start: 0.6867 (mmmt) cc_final: 0.6635 (mmpt)
REVERT: A  174 MET cc_start: 0.6582 (ttp) cc_final: 0.6086 (tpt)
REVERT: A  181 MET cc_start: 0.7236 (mtp) cc_final: 0.6704 (tpt)
REVERT: A  219 ARG cc_start: 0.7117 (mtp180) cc_final: 0.6560 (mtm-85)
REVERT: A  228 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.7055 (mp)
REVERT: B   81 LYS cc_start: 0.7380 (tttt) cc_final: 0.7026 (ttmt)
REVERT: B  123 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.6435 (ptp-170)
REVERT: B  199 MET cc_start: 0.7109 (tpt) cc_final: 0.6706 (tmt)
REVERT: B  222 ASP cc_start: 0.8497 (m-30) cc_final: 0.8172 (m-30)
REVERT: B  246 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.7810 (p)
REVERT: B  275 PHE cc_start: 0.7286 (t80) cc_final: 0.6349 (t80)
REVERT: B  328 MET cc_start: 0.4751 (mtp) cc_final: 0.4197 (mtp)
REVERT: C   75 ARG cc_start: 0.7377 (ttm110) cc_final: 0.7122 (ttp80)
REVERT: C   98 THR cc_start: 0.7651 (m) cc_final: 0.7073 (p)
REVERT: C  117 GLU cc_start: 0.7792 (mp0) cc_final: 0.7512 (mp0)
REVERT: C  187 ASP cc_start: 0.8471 (p0) cc_final: 0.8037 (p0)
REVERT: C  199 MET cc_start: 0.7223 (ttt) cc_final: 0.6042 (mmt)
REVERT: C  219 ARG cc_start: 0.7597 (mtp180) cc_final: 0.7052 (mtp-110)
REVERT: C  328 MET cc_start: 0.5473 (mmm) cc_final: 0.4628 (ppp)
REVERT: D   81 LYS cc_start: 0.7691 (tttt) cc_final: 0.6761 (ttpt)
REVERT: D  190 GLN cc_start: 0.7410 (mt0) cc_final: 0.6686 (mm110)
REVERT: D  235 LEU cc_start: 0.7385 (mm) cc_final: 0.6546 (tp)
REVERT: D  328 MET cc_start: 0.3426 (mtm) cc_final: 0.2824 (ppp)
  outliers start: 31
  outliers final: 13
  residues processed: 118
  average time/residue: 1.1715
  time to fit residues: 148.6439
Evaluate side-chains
  113 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain B residue  123 ARG
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  246 THR
Chi-restraints excluded: chain C residue  132 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  282 HIS
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  181 MET
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  259 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 61 optimal weight:    0.1980
   chunk 26 optimal weight:    0.6980
   chunk 105 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 190 GLN
B 256 GLN
B 314 GLN
D  86 ASN
D 121 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9081  Z= 0.204
  Angle     :  0.508   6.756  12320  Z= 0.274
  Chirality :  0.039   0.274   1514
  Planarity :  0.006   0.076   1433
  Dihedral  : 11.291  85.060   1360
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  :  9.62 %
    Favored  : 87.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.68 (0.24), residues: 1100
  helix:  3.19 (0.16), residues: 857
  sheet:  3.76 (0.72), residues: 46
  loop : -1.72 (0.43), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 315 
 HIS   0.001   0.000   HIS A 214 
 PHE   0.027   0.001   PHE B 215 
 TYR   0.011   0.001   TYR C 280 
 ARG   0.004   0.000   ARG C  75 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.7477 (tttt) cc_final: 0.6918 (tppt)
REVERT: A   98 THR cc_start: 0.7143 (m) cc_final: 0.6697 (p)
REVERT: A  147 LYS cc_start: 0.6877 (mmmt) cc_final: 0.6656 (mmpt)
REVERT: A  174 MET cc_start: 0.6523 (ttp) cc_final: 0.6105 (tpt)
REVERT: A  181 MET cc_start: 0.7208 (mtp) cc_final: 0.6712 (tpt)
REVERT: A  199 MET cc_start: 0.7862 (ttt) cc_final: 0.7195 (ttp)
REVERT: A  219 ARG cc_start: 0.7120 (mtp180) cc_final: 0.6667 (mtm110)
REVERT: A  228 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6906 (mp)
REVERT: B   81 LYS cc_start: 0.7199 (tttt) cc_final: 0.6861 (ttmt)
REVERT: B  123 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.6143 (ptp-170)
REVERT: B  199 MET cc_start: 0.7080 (tpt) cc_final: 0.6767 (tmt)
REVERT: B  219 ARG cc_start: 0.7365 (ttt180) cc_final: 0.6572 (ttp-110)
REVERT: B  222 ASP cc_start: 0.8465 (m-30) cc_final: 0.8110 (m-30)
REVERT: B  246 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7671 (p)
REVERT: B  275 PHE cc_start: 0.7179 (t80) cc_final: 0.6319 (t80)
REVERT: B  328 MET cc_start: 0.4751 (mtp) cc_final: 0.4193 (mtp)
REVERT: C   81 LYS cc_start: 0.7513 (ttmt) cc_final: 0.6662 (tptt)
REVERT: C   98 THR cc_start: 0.7505 (m) cc_final: 0.6918 (p)
REVERT: C  117 GLU cc_start: 0.7696 (mp0) cc_final: 0.7432 (mp0)
REVERT: C  187 ASP cc_start: 0.8235 (p0) cc_final: 0.7977 (p0)
REVERT: C  199 MET cc_start: 0.7262 (ttt) cc_final: 0.6110 (mmt)
REVERT: C  219 ARG cc_start: 0.7524 (mtp180) cc_final: 0.6977 (mtp-110)
REVERT: C  282 HIS cc_start: 0.7733 (OUTLIER) cc_final: 0.7308 (t70)
REVERT: C  328 MET cc_start: 0.5456 (mmm) cc_final: 0.4644 (ppp)
REVERT: D   81 LYS cc_start: 0.7636 (tttt) cc_final: 0.6692 (ttpt)
REVERT: D  190 GLN cc_start: 0.7365 (mt0) cc_final: 0.6655 (mm110)
REVERT: D  235 LEU cc_start: 0.7373 (mm) cc_final: 0.6523 (tp)
REVERT: D  328 MET cc_start: 0.3458 (mtm) cc_final: 0.2857 (ppp)
  outliers start: 27
  outliers final: 11
  residues processed: 117
  average time/residue: 1.1627
  time to fit residues: 146.6903
Evaluate side-chains
  112 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain B residue  123 ARG
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  246 THR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  282 HIS
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  197 VAL
Chi-restraints excluded: chain D residue  259 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 77 optimal weight:    0.0870
   chunk 59 optimal weight:    0.7980
   chunk 88 optimal weight:    0.1980
   chunk 58 optimal weight:    0.9980
   chunk 105 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 64 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
B 190 GLN
C 255 ASN
D  86 ASN
D 121 GLN
D 256 GLN
D 304 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9081  Z= 0.171
  Angle     :  0.482   6.473  12320  Z= 0.260
  Chirality :  0.038   0.251   1514
  Planarity :  0.005   0.075   1433
  Dihedral  : 10.807  87.180   1360
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  9.92 %
    Favored  : 87.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.92 (0.24), residues: 1100
  helix:  3.34 (0.15), residues: 858
  sheet:  3.74 (0.75), residues: 44
  loop : -1.50 (0.44), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 315 
 HIS   0.001   0.000   HIS C 214 
 PHE   0.028   0.001   PHE B 215 
 TYR   0.012   0.001   TYR C 280 
 ARG   0.003   0.000   ARG D  75 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 2.704 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.7476 (tttt) cc_final: 0.6887 (tppt)
REVERT: A   98 THR cc_start: 0.7082 (m) cc_final: 0.6631 (p)
REVERT: A  147 LYS cc_start: 0.6849 (mmmt) cc_final: 0.6638 (mmpt)
REVERT: A  174 MET cc_start: 0.6526 (ttp) cc_final: 0.6108 (tpt)
REVERT: A  181 MET cc_start: 0.7164 (mtp) cc_final: 0.6691 (tpt)
REVERT: A  199 MET cc_start: 0.7902 (ttt) cc_final: 0.7264 (ttp)
REVERT: A  219 ARG cc_start: 0.7095 (mtp180) cc_final: 0.6644 (mtm110)
REVERT: B   81 LYS cc_start: 0.7148 (tttt) cc_final: 0.6822 (ttmt)
REVERT: B  123 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6060 (ptp-170)
REVERT: B  199 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6444 (tpp)
REVERT: B  219 ARG cc_start: 0.7336 (ttt180) cc_final: 0.6556 (ttp-110)
REVERT: B  222 ASP cc_start: 0.8305 (m-30) cc_final: 0.7996 (m-30)
REVERT: B  246 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7559 (p)
REVERT: B  275 PHE cc_start: 0.7126 (t80) cc_final: 0.6286 (t80)
REVERT: B  328 MET cc_start: 0.4715 (mtp) cc_final: 0.4137 (mtp)
REVERT: C   81 LYS cc_start: 0.7458 (ttmt) cc_final: 0.6601 (tptt)
REVERT: C   98 THR cc_start: 0.7456 (m) cc_final: 0.6875 (p)
REVERT: C  199 MET cc_start: 0.7203 (ttt) cc_final: 0.6492 (mtp)
REVERT: C  219 ARG cc_start: 0.7428 (mtp180) cc_final: 0.6888 (mtp-110)
REVERT: C  282 HIS cc_start: 0.7694 (OUTLIER) cc_final: 0.7303 (t70)
REVERT: C  328 MET cc_start: 0.5453 (mmm) cc_final: 0.4662 (ppp)
REVERT: D   81 LYS cc_start: 0.7602 (tttt) cc_final: 0.6584 (ttpt)
REVERT: D   82 MET cc_start: 0.7420 (ptt) cc_final: 0.7083 (ptm)
REVERT: D  190 GLN cc_start: 0.7312 (mt0) cc_final: 0.6631 (mm110)
REVERT: D  195 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6995 (pt)
REVERT: D  235 LEU cc_start: 0.7177 (mm) cc_final: 0.6387 (tp)
REVERT: D  328 MET cc_start: 0.3474 (mtm) cc_final: 0.2892 (ppp)
  outliers start: 25
  outliers final: 12
  residues processed: 122
  average time/residue: 1.1373
  time to fit residues: 150.1952
Evaluate side-chains
  117 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain B residue  123 ARG
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  199 MET
Chi-restraints excluded: chain B residue  246 THR
Chi-restraints excluded: chain C residue  132 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  282 HIS
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  197 VAL
Chi-restraints excluded: chain D residue  259 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0970
   chunk 51 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 100 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
B 190 GLN
D 121 GLN
D 255 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.2227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9081  Z= 0.203
  Angle     :  0.518   9.985  12320  Z= 0.275
  Chirality :  0.039   0.280   1514
  Planarity :  0.006   0.076   1433
  Dihedral  : 10.837  89.945   1360
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 10.22 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.87 (0.24), residues: 1100
  helix:  3.29 (0.15), residues: 859
  sheet:  3.77 (0.74), residues: 44
  loop : -1.50 (0.44), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 315 
 HIS   0.001   0.000   HIS A 214 
 PHE   0.027   0.001   PHE B 215 
 TYR   0.011   0.001   TYR C 280 
 ARG   0.003   0.000   ARG C  75 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 102
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.7484 (tttt) cc_final: 0.6894 (tppt)
REVERT: A   98 THR cc_start: 0.7171 (m) cc_final: 0.6728 (p)
REVERT: A  147 LYS cc_start: 0.6853 (mmmt) cc_final: 0.6640 (mmpt)
REVERT: A  174 MET cc_start: 0.6491 (ttp) cc_final: 0.6076 (tpt)
REVERT: A  181 MET cc_start: 0.7158 (mtp) cc_final: 0.6661 (tpt)
REVERT: A  199 MET cc_start: 0.7912 (ttt) cc_final: 0.7269 (ttp)
REVERT: A  219 ARG cc_start: 0.7119 (mtp180) cc_final: 0.6688 (mtm110)
REVERT: A  228 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6821 (mp)
REVERT: B   81 LYS cc_start: 0.7173 (tttt) cc_final: 0.6833 (ttmt)
REVERT: B  123 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6229 (ptp-170)
REVERT: B  199 MET cc_start: 0.6894 (OUTLIER) cc_final: 0.6382 (tpp)
REVERT: B  219 ARG cc_start: 0.7341 (ttt180) cc_final: 0.6563 (ttp-110)
REVERT: B  222 ASP cc_start: 0.8412 (m-30) cc_final: 0.8084 (m-30)
REVERT: B  235 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6858 (mm)
REVERT: B  246 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.7651 (p)
REVERT: B  275 PHE cc_start: 0.7165 (t80) cc_final: 0.6319 (t80)
REVERT: B  328 MET cc_start: 0.4754 (mtp) cc_final: 0.4166 (mtp)
REVERT: C   81 LYS cc_start: 0.7447 (ttmt) cc_final: 0.6588 (tptt)
REVERT: C   98 THR cc_start: 0.7515 (m) cc_final: 0.6950 (p)
REVERT: C  199 MET cc_start: 0.7206 (ttt) cc_final: 0.6492 (mtp)
REVERT: C  219 ARG cc_start: 0.7440 (mtp180) cc_final: 0.6915 (mtp-110)
REVERT: C  282 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7315 (t70)
REVERT: C  328 MET cc_start: 0.5474 (mmm) cc_final: 0.4685 (ppp)
REVERT: D   81 LYS cc_start: 0.7639 (tttt) cc_final: 0.6609 (ttpt)
REVERT: D  181 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.7025 (ttp)
REVERT: D  190 GLN cc_start: 0.7322 (mt0) cc_final: 0.6616 (mm110)
REVERT: D  195 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6993 (pt)
REVERT: D  235 LEU cc_start: 0.7274 (mm) cc_final: 0.6478 (tp)
REVERT: D  328 MET cc_start: 0.3535 (mtm) cc_final: 0.2932 (ppp)
  outliers start: 28
  outliers final: 13
  residues processed: 118
  average time/residue: 1.1093
  time to fit residues: 140.9352
Evaluate side-chains
  122 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  261 MET
Chi-restraints excluded: chain B residue  123 ARG
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  199 MET
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain B residue  246 THR
Chi-restraints excluded: chain C residue  132 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  282 HIS
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  181 MET
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  197 VAL
Chi-restraints excluded: chain D residue  259 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    8.9990
   chunk 100 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 76 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0770
   chunk 88 optimal weight:    0.8980
   chunk 92 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 103 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
B 190 GLN
C 164 GLN
D  86 ASN
D 121 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9081  Z= 0.214
  Angle     :  0.527   9.206  12320  Z= 0.280
  Chirality :  0.039   0.280   1514
  Planarity :  0.006   0.076   1433
  Dihedral  : 10.646  84.432   1360
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 10.32 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.84 (0.24), residues: 1100
  helix:  3.26 (0.15), residues: 860
  sheet:  3.81 (0.75), residues: 44
  loop : -1.47 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  54 
 HIS   0.002   0.000   HIS C 214 
 PHE   0.027   0.001   PHE B 215 
 TYR   0.012   0.001   TYR C 280 
 ARG   0.004   0.000   ARG C  75 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 101
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.7490 (tttt) cc_final: 0.6919 (tppt)
REVERT: A   98 THR cc_start: 0.7184 (m) cc_final: 0.6747 (p)
REVERT: A  147 LYS cc_start: 0.6914 (mmmt) cc_final: 0.6691 (mmpt)
REVERT: A  174 MET cc_start: 0.6481 (ttp) cc_final: 0.6052 (tpt)
REVERT: A  181 MET cc_start: 0.7199 (mtp) cc_final: 0.6696 (tpt)
REVERT: A  199 MET cc_start: 0.7876 (ttt) cc_final: 0.7253 (ttp)
REVERT: A  219 ARG cc_start: 0.7145 (mtp180) cc_final: 0.6689 (mtm110)
REVERT: A  228 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6865 (mp)
REVERT: B   81 LYS cc_start: 0.7288 (tttt) cc_final: 0.6928 (ttmt)
REVERT: B  123 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.6254 (ptp-170)
REVERT: B  199 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6376 (tpp)
REVERT: B  222 ASP cc_start: 0.8481 (m-30) cc_final: 0.8120 (m-30)
REVERT: B  235 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6880 (mm)
REVERT: B  246 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.7655 (p)
REVERT: B  275 PHE cc_start: 0.7191 (t80) cc_final: 0.6326 (t80)
REVERT: B  328 MET cc_start: 0.4767 (mtp) cc_final: 0.4175 (mtp)
REVERT: C   98 THR cc_start: 0.7528 (m) cc_final: 0.6961 (p)
REVERT: C  187 ASP cc_start: 0.8194 (p0) cc_final: 0.7856 (p0)
REVERT: C  199 MET cc_start: 0.7216 (ttt) cc_final: 0.6503 (mtp)
REVERT: C  219 ARG cc_start: 0.7531 (mtp180) cc_final: 0.6963 (mtp-110)
REVERT: C  282 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7305 (t70)
REVERT: C  328 MET cc_start: 0.5473 (mmm) cc_final: 0.4681 (ppp)
REVERT: D   81 LYS cc_start: 0.7650 (tttt) cc_final: 0.6701 (ttpt)
REVERT: D  181 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6991 (ttp)
REVERT: D  190 GLN cc_start: 0.7314 (mt0) cc_final: 0.6618 (mm110)
REVERT: D  195 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6994 (pt)
REVERT: D  235 LEU cc_start: 0.7332 (mm) cc_final: 0.6523 (tp)
REVERT: D  328 MET cc_start: 0.3533 (mtm) cc_final: 0.2898 (ppp)
  outliers start: 28
  outliers final: 15
  residues processed: 118
  average time/residue: 1.1438
  time to fit residues: 145.3151
Evaluate side-chains
  122 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  261 MET
Chi-restraints excluded: chain B residue  123 ARG
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  199 MET
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain B residue  246 THR
Chi-restraints excluded: chain C residue  132 SER
Chi-restraints excluded: chain C residue  178 ILE
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  282 HIS
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  181 MET
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  197 VAL
Chi-restraints excluded: chain D residue  259 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 49 optimal weight:    0.1980
   chunk 71 optimal weight:    0.5980
   chunk 108 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 68 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 190 GLN
D  86 ASN
D 121 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9081  Z= 0.189
  Angle     :  0.522  10.907  12320  Z= 0.275
  Chirality :  0.039   0.271   1514
  Planarity :  0.006   0.076   1433
  Dihedral  : 10.481  82.285   1360
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 10.73 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.89 (0.24), residues: 1100
  helix:  3.30 (0.15), residues: 859
  sheet:  3.84 (0.75), residues: 44
  loop : -1.48 (0.44), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  54 
 HIS   0.001   0.000   HIS C 214 
 PHE   0.024   0.001   PHE B 215 
 TYR   0.011   0.001   TYR C 280 
 ARG   0.004   0.000   ARG C  75 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.7486 (tttt) cc_final: 0.6886 (tppt)
REVERT: A   98 THR cc_start: 0.7161 (m) cc_final: 0.6721 (p)
REVERT: A  147 LYS cc_start: 0.6908 (mmmt) cc_final: 0.6690 (mmpt)
REVERT: A  174 MET cc_start: 0.6492 (ttp) cc_final: 0.6096 (tpt)
REVERT: A  181 MET cc_start: 0.7160 (mtp) cc_final: 0.6664 (tpt)
REVERT: A  199 MET cc_start: 0.7866 (ttt) cc_final: 0.7245 (ttp)
REVERT: A  219 ARG cc_start: 0.7127 (mtp180) cc_final: 0.6668 (mtm110)
REVERT: A  228 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6800 (mp)
REVERT: B   81 LYS cc_start: 0.7162 (tttt) cc_final: 0.6828 (ttmt)
REVERT: B  123 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.6234 (ptp-170)
REVERT: B  219 ARG cc_start: 0.7311 (ttt180) cc_final: 0.6547 (ttp-110)
REVERT: B  222 ASP cc_start: 0.8464 (m-30) cc_final: 0.8090 (m-30)
REVERT: B  235 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6860 (mm)
REVERT: B  246 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.7632 (p)
REVERT: B  275 PHE cc_start: 0.7155 (t80) cc_final: 0.6303 (t80)
REVERT: B  328 MET cc_start: 0.4786 (mtp) cc_final: 0.4188 (mtp)
REVERT: C   81 LYS cc_start: 0.7445 (ttmt) cc_final: 0.6585 (tptt)
REVERT: C   98 THR cc_start: 0.7522 (m) cc_final: 0.6947 (p)
REVERT: C  187 ASP cc_start: 0.8181 (p0) cc_final: 0.7847 (p0)
REVERT: C  199 MET cc_start: 0.7229 (ttt) cc_final: 0.6534 (mtp)
REVERT: C  219 ARG cc_start: 0.7520 (mtp180) cc_final: 0.6966 (mtp-110)
REVERT: C  282 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.7312 (t70)
REVERT: C  328 MET cc_start: 0.5451 (mmm) cc_final: 0.4659 (ppp)
REVERT: D   81 LYS cc_start: 0.7602 (tttt) cc_final: 0.6569 (ttpt)
REVERT: D  181 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.7035 (ttp)
REVERT: D  190 GLN cc_start: 0.7310 (mt0) cc_final: 0.6615 (mm110)
REVERT: D  195 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6996 (pt)
REVERT: D  235 LEU cc_start: 0.7301 (mm) cc_final: 0.6495 (tp)
REVERT: D  328 MET cc_start: 0.3539 (mtm) cc_final: 0.2924 (ppp)
  outliers start: 26
  outliers final: 15
  residues processed: 118
  average time/residue: 1.1289
  time to fit residues: 143.7872
Evaluate side-chains
  121 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  261 MET
Chi-restraints excluded: chain B residue  123 ARG
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain B residue  246 THR
Chi-restraints excluded: chain C residue  132 SER
Chi-restraints excluded: chain C residue  178 ILE
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  282 HIS
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  181 MET
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  197 VAL
Chi-restraints excluded: chain D residue  259 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   chunk 88 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0370
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.5660

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

Flipped N/Q/H residues before XYZ refinement:
B 190 GLN
D 121 GLN
D 304 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.163248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.119018 restraints weight = 8582.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 1.69
r_work: 0.3112 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9081  Z= 0.191
  Angle     :  0.536  13.547  12320  Z= 0.277
  Chirality :  0.039   0.272   1514
  Planarity :  0.006   0.076   1433
  Dihedral  : 10.370  81.192   1360
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 10.83 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.90 (0.24), residues: 1100
  helix:  3.31 (0.15), residues: 859
  sheet:  3.86 (0.76), residues: 44
  loop : -1.45 (0.44), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  54 
 HIS   0.001   0.000   HIS C 214 
 PHE   0.023   0.001   PHE B 215 
 TYR   0.011   0.001   TYR C 280 
 ARG   0.004   0.000   ARG C  75 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3189.91 seconds
wall clock time: 58 minutes 12.86 seconds (3492.86 seconds total)