Starting phenix.real_space_refine
on Wed Feb 12 02:08:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sqh_25385/02_2025/7sqh_25385.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sqh_25385/02_2025/7sqh_25385.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sqh_25385/02_2025/7sqh_25385.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sqh_25385/02_2025/7sqh_25385.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sqh_25385/02_2025/7sqh_25385.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sqh_25385/02_2025/7sqh_25385.cif"
  }
  resolution = 2.5
  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=   0.000 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     C    4500      2.51       5
     N    1134      2.21       5
     O    1287      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6954
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2255
          Classifications: {'peptide': 283}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 13, 'TRANS': 269}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "B"
      Number of atoms: 2255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2255
          Classifications: {'peptide': 283}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 13, 'TRANS': 269}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "C"
      Number of atoms: 2255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2255
          Classifications: {'peptide': 283}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 13, 'TRANS': 269}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 9
          Classifications: {'water': 9}
          Link IDs: {None: 8}
    Chain: "C"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
  Time building chain proxies: 4.87, per 1000 atoms: 0.70
  Number of scatterers: 6954
  At special positions: 0
  Unit cell: (81.4625, 81.4625, 126.35, 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      33     16.00
     O    1287      8.00
     N    1134      7.00
     C    4500      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
  Links applied
    NAG-ASN
      " NAG A 401 " - " ASN A 148 "
      " NAG A 402 " - " ASN A 162 "
      " NAG A 403 " - " ASN A 190 "
      " NAG A 404 " - " ASN A 155 "
      " NAG B 401 " - " ASN B 148 "
      " NAG B 402 " - " ASN B 162 "
      " NAG B 403 " - " ASN B 190 "
      " NAG B 404 " - " ASN B 155 "
      " NAG C 401 " - " ASN C 148 "
      " NAG C 402 " - " ASN C 162 "
      " NAG C 403 " - " ASN C 190 "
      " NAG C 404 " - " ASN C 155 "
  Time building additional restraints: 1.61
  Conformation dependent library (CDL) restraints added in 956.3 milliseconds
  

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1638

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 4 sheets defined
      38.6% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 95
      removed outlier: 3.793A  pdb=" N   LYS A  95 " --> pdb=" O   ASP A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 179
      removed outlier: 3.515A  pdb=" N   LYS A 179 " --> pdb=" O   GLU A 176 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 176 through 179'
    Processing helix  chain 'A' and resid 206 through 212
      removed outlier: 3.649A  pdb=" N   PHE A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 226
    Processing helix  chain 'A' and resid 272 through 278
      removed outlier: 4.305A  pdb=" N   SER A 277 " --> pdb=" O   ALA A 274 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ALA A 278 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 302
      removed outlier: 3.638A  pdb=" N   ASN A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 298 through 302'
    Processing helix  chain 'A' and resid 302 through 339
      removed outlier: 3.906A  pdb=" N   THR A 306 " --> pdb=" O   ASN A 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 95
      removed outlier: 3.793A  pdb=" N   LYS B  95 " --> pdb=" O   ASP B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 179
      removed outlier: 3.515A  pdb=" N   LYS B 179 " --> pdb=" O   GLU B 176 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 176 through 179'
    Processing helix  chain 'B' and resid 206 through 212
      removed outlier: 3.649A  pdb=" N   PHE B 210 " --> pdb=" O   SER B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 226
    Processing helix  chain 'B' and resid 272 through 278
      removed outlier: 4.305A  pdb=" N   SER B 277 " --> pdb=" O   ALA B 274 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ALA B 278 " --> pdb=" O   LYS B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 302
      removed outlier: 3.639A  pdb=" N   ASN B 302 " --> pdb=" O   ILE B 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 298 through 302'
    Processing helix  chain 'B' and resid 302 through 339
      removed outlier: 3.906A  pdb=" N   THR B 306 " --> pdb=" O   ASN B 302 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 95
      removed outlier: 3.793A  pdb=" N   LYS C  95 " --> pdb=" O   ASP C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 179
      removed outlier: 3.515A  pdb=" N   LYS C 179 " --> pdb=" O   GLU C 176 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 176 through 179'
    Processing helix  chain 'C' and resid 206 through 212
      removed outlier: 3.649A  pdb=" N   PHE C 210 " --> pdb=" O   SER C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 217 through 226
    Processing helix  chain 'C' and resid 272 through 278
      removed outlier: 4.305A  pdb=" N   SER C 277 " --> pdb=" O   ALA C 274 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ALA C 278 " --> pdb=" O   LYS C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 302
      removed outlier: 3.639A  pdb=" N   ASN C 302 " --> pdb=" O   ILE C 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 298 through 302'
    Processing helix  chain 'C' and resid 302 through 339
      removed outlier: 3.906A  pdb=" N   THR C 306 " --> pdb=" O   ASN C 302 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 107
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 100 through 107
    current: chain 'A' and resid 181 through 189
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 181 through 189
    current: chain 'A' and resid 254 through 266
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 254 through 266
    current: chain 'B' and resid 181 through 189
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 181 through 189
    current: chain 'B' and resid 254 through 266
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 254 through 266
    current: chain 'C' and resid 181 through 189
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 181 through 189
    current: chain 'C' and resid 254 through 266
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 157
      removed outlier: 4.120A  pdb=" N   ASP A 200 " --> pdb=" O   TYR A 119 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 151 through 157
      removed outlier: 4.121A  pdb=" N   ASP B 200 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 151 through 157
      removed outlier: 4.120A  pdb=" N   ASP C 200 " --> pdb=" O   TYR C 119 " (cutoff:3.500A)

    286 hydrogen bonds defined for protein.
    831 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.82

  Time building geometry restraints manager: 1.89 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 1086
        1.27 -     1.41: 1809
        1.41 -     1.54: 4098
        1.54 -     1.67: 60
        1.67 -     1.81: 51
  Bond restraints: 7104
  Sorted by residual:
  bond pdb=" C   GLN C 152 "
       pdb=" O   GLN C 152 "
    ideal  model  delta    sigma   weight residual
    1.234  1.138  0.096 1.26e-02 6.30e+03 5.86e+01
  bond pdb=" C   ARG C 180 "
       pdb=" O   ARG C 180 "
    ideal  model  delta    sigma   weight residual
    1.235  1.146  0.090 1.26e-02 6.30e+03 5.07e+01
  bond pdb=" C   GLN B 152 "
       pdb=" O   GLN B 152 "
    ideal  model  delta    sigma   weight residual
    1.234  1.153  0.081 1.22e-02 6.72e+03 4.37e+01
  bond pdb=" C   TYR B 132 "
       pdb=" O   TYR B 132 "
    ideal  model  delta    sigma   weight residual
    1.235  1.163  0.072 1.14e-02 7.69e+03 3.95e+01
  bond pdb=" C   GLN A 152 "
       pdb=" O   GLN A 152 "
    ideal  model  delta    sigma   weight residual
    1.234  1.156  0.078 1.26e-02 6.30e+03 3.83e+01
  ... (remaining 7099 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 9094
        1.46 -     2.93: 438
        2.93 -     4.39: 58
        4.39 -     5.85: 17
        5.85 -     7.32: 14
  Bond angle restraints: 9621
  Sorted by residual:
  angle pdb=" CA  ARG B 180 "
        pdb=" C   ARG B 180 "
        pdb=" O   ARG B 180 "
      ideal   model   delta    sigma   weight residual
     122.14  114.88    7.26 1.24e+00 6.50e-01 3.43e+01
  angle pdb=" CA  ARG A 180 "
        pdb=" C   ARG A 180 "
        pdb=" O   ARG A 180 "
      ideal   model   delta    sigma   weight residual
     122.45  115.48    6.97 1.30e+00 5.92e-01 2.87e+01
  angle pdb=" O   HIS B 131 "
        pdb=" C   HIS B 131 "
        pdb=" N   TYR B 132 "
      ideal   model   delta    sigma   weight residual
     123.15  116.72    6.43 1.30e+00 5.92e-01 2.44e+01
  angle pdb=" O   HIS A 131 "
        pdb=" C   HIS A 131 "
        pdb=" N   TYR A 132 "
      ideal   model   delta    sigma   weight residual
     123.15  116.90    6.25 1.30e+00 5.92e-01 2.31e+01
  angle pdb=" O   HIS C 131 "
        pdb=" C   HIS C 131 "
        pdb=" N   TYR C 132 "
      ideal   model   delta    sigma   weight residual
     123.15  117.42    5.73 1.30e+00 5.92e-01 1.95e+01
  ... (remaining 9616 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.16: 3950
       21.16 -    42.32: 313
       42.32 -    63.48: 104
       63.48 -    84.65: 12
       84.65 -   105.81: 28
  Dihedral angle restraints: 4407
    sinusoidal: 1893
      harmonic: 2514
  Sorted by residual:
  dihedral pdb=" C2  NAG C 404 "
           pdb=" C3  NAG C 404 "
           pdb=" C4  NAG C 404 "
           pdb=" O4  NAG C 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   69.30  105.81     1      3.00e+01 1.11e-03 1.36e+01
  dihedral pdb=" C2  NAG A 404 "
           pdb=" C3  NAG A 404 "
           pdb=" C4  NAG A 404 "
           pdb=" O4  NAG A 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   69.33  105.78     1      3.00e+01 1.11e-03 1.36e+01
  dihedral pdb=" C2  NAG B 404 "
           pdb=" C3  NAG B 404 "
           pdb=" C4  NAG B 404 "
           pdb=" O4  NAG B 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   69.34  105.77     1      3.00e+01 1.11e-03 1.36e+01
  ... (remaining 4404 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 893
       0.057 -    0.114: 166
       0.114 -    0.170: 33
       0.170 -    0.227: 2
       0.227 -    0.284: 4
  Chirality restraints: 1098
  Sorted by residual:
  chirality pdb=" CA  ARG B 180 "
            pdb=" N   ARG B 180 "
            pdb=" C   ARG B 180 "
            pdb=" CB  ARG B 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.01e+00
  chirality pdb=" C1  NAG C 401 "
            pdb=" ND2 ASN C 148 "
            pdb=" C2  NAG C 401 "
            pdb=" O5  NAG C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.14   -0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" C1  NAG A 401 "
            pdb=" ND2 ASN A 148 "
            pdb=" C2  NAG A 401 "
            pdb=" O5  NAG A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.14   -0.26 2.00e-01 2.50e+01 1.71e+00
  ... (remaining 1095 not shown)

  Planarity restraints: 1212
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 132 "    0.018 2.00e-02 2.50e+03   3.67e-02 1.35e+01
        pdb=" C   TYR B 132 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   TYR B 132 "    0.024 2.00e-02 2.50e+03
        pdb=" N   GLU B 133 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 132 "    0.016 2.00e-02 2.50e+03   3.25e-02 1.06e+01
        pdb=" C   TYR A 132 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   TYR A 132 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLU A 133 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C 132 "    0.015 2.00e-02 2.50e+03   3.04e-02 9.23e+00
        pdb=" C   TYR C 132 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   TYR C 132 "    0.020 2.00e-02 2.50e+03
        pdb=" N   GLU C 133 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1209 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1410
        2.79 -     3.31: 6126
        3.31 -     3.84: 11152
        3.84 -     4.37: 13265
        4.37 -     4.90: 23067
  Nonbonded interactions: 55020
  Sorted by model distance:
  nonbonded pdb=" O   ASP C 269 "
            pdb=" OD1 ASP C 269 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   ASP B 269 "
            pdb=" OD1 ASP B 269 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   ASP A 269 "
            pdb=" OD1 ASP A 269 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OH  TYR C 119 "
            pdb=" OH  TYR C 156 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OH  TYR B 119 "
            pdb=" OH  TYR B 156 "
     model   vdw
     2.266 3.040
  ... (remaining 55015 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             2.490
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.470
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
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      :  0.006   0.096   7104  Z= 0.361
  Angle     :  0.740   7.318   9621  Z= 0.465
  Chirality :  0.050   0.284   1098
  Planarity :  0.004   0.037   1200
  Dihedral  : 19.411 105.807   2769
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.75 %
    Favored  : 79.25 %
  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:  1.93 (0.29), residues: 843
  helix:  3.21 (0.27), residues: 312
  sheet:  0.58 (0.27), residues: 312
  loop : -0.53 (0.44), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 330 
 HIS   0.003   0.001   HIS B 130 
 PHE   0.014   0.001   PHE C 204 
 TYR   0.022   0.001   TYR A 132 
 ARG   0.003   0.000   ARG C 188 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.7058 (t80) cc_final: 0.6852 (t80)
REVERT: A  122 GLN cc_start: 0.8847 (mm110) cc_final: 0.8488 (mm110)
REVERT: A  153 ARG cc_start: 0.7453 (mtp85) cc_final: 0.7166 (mtp85)
REVERT: A  180 ARG cc_start: 0.7846 (mtp180) cc_final: 0.7618 (mtp180)
REVERT: A  253 ARG cc_start: 0.7686 (ptm-80) cc_final: 0.7002 (ptm-80)
REVERT: A  297 ASP cc_start: 0.8455 (t0) cc_final: 0.8182 (t0)
REVERT: A  325 LYS cc_start: 0.7909 (ttmt) cc_final: 0.7692 (ttmt)
REVERT: B   72 PHE cc_start: 0.6920 (m-10) cc_final: 0.6677 (m-80)
REVERT: B   87 ARG cc_start: 0.7355 (tpm-80) cc_final: 0.7111 (tpp80)
REVERT: B   91 ASP cc_start: 0.8205 (m-30) cc_final: 0.7920 (m-30)
REVERT: B  247 THR cc_start: 0.9088 (m) cc_final: 0.8847 (t)
REVERT: B  275 LYS cc_start: 0.8027 (mttm) cc_final: 0.7747 (ttmm)
REVERT: B  296 GLN cc_start: 0.8308 (tt0) cc_final: 0.8092 (tp40)
REVERT: C   72 PHE cc_start: 0.7282 (m-10) cc_final: 0.6994 (m-80)
REVERT: C  266 ASN cc_start: 0.8740 (t0) cc_final: 0.8452 (t0)
REVERT: C  275 LYS cc_start: 0.8050 (mttm) cc_final: 0.7809 (ttmm)
REVERT: C  297 ASP cc_start: 0.8530 (t0) cc_final: 0.8229 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 256
  average time/residue: 1.8332
  time to fit residues: 484.9216
Evaluate side-chains
  184 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
A 143 GLN
A 152 GLN
A 266 ASN
B 152 GLN
B 212 GLN
B 266 ASN
C 143 GLN
C 152 GLN
C 279 GLN
C 293 GLN
C 296 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.105675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.090156 restraints weight = 12395.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 2.70
r_work: 0.3151 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3156
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3154
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   7104  Z= 0.310
  Angle     :  0.609   7.102   9621  Z= 0.303
  Chirality :  0.048   0.344   1098
  Planarity :  0.004   0.046   1200
  Dihedral  : 12.892  71.126   1164
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 26.00 %
    Favored  : 71.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.01 (0.29), residues: 843
  helix:  3.30 (0.27), residues: 312
  sheet:  0.68 (0.27), residues: 306
  loop : -0.60 (0.43), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 230 
 HIS   0.005   0.002   HIS A  98 
 PHE   0.023   0.002   PHE C  92 
 TYR   0.008   0.001   TYR C 227 
 ARG   0.013   0.001   ARG B 110 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 193
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.7685 (t80) cc_final: 0.7475 (t80)
REVERT: A   95 LYS cc_start: 0.8686 (mttt) cc_final: 0.8350 (mtmm)
REVERT: A  124 GLN cc_start: 0.7926 (mm110) cc_final: 0.7714 (mm110)
REVERT: A  153 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7823 (mtp85)
REVERT: A  156 TYR cc_start: 0.8473 (p90) cc_final: 0.8139 (p90)
REVERT: A  180 ARG cc_start: 0.8416 (mtp180) cc_final: 0.8187 (mtp180)
REVERT: A  224 GLU cc_start: 0.7764 (tp30) cc_final: 0.7416 (tp30)
REVERT: A  275 LYS cc_start: 0.8252 (ttmm) cc_final: 0.8046 (mtpp)
REVERT: B   77 LEU cc_start: 0.8528 (mm) cc_final: 0.8303 (mm)
REVERT: B  208 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7899 (mp10)
REVERT: B  224 GLU cc_start: 0.7754 (tp30) cc_final: 0.7512 (tp30)
REVERT: B  275 LYS cc_start: 0.8304 (mttm) cc_final: 0.8090 (mttm)
REVERT: C   72 PHE cc_start: 0.7905 (m-10) cc_final: 0.7697 (m-80)
REVERT: C   95 LYS cc_start: 0.8711 (mttt) cc_final: 0.8470 (mtmm)
REVERT: C  133 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7383 (tm-30)
REVERT: C  147 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8106 (tpp)
REVERT: C  266 ASN cc_start: 0.9033 (t0) cc_final: 0.8691 (t0)
REVERT: C  326 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8253 (mm)
REVERT: C  333 LYS cc_start: 0.8583 (tttt) cc_final: 0.8182 (ttpt)
  outliers start: 16
  outliers final: 5
  residues processed: 199
  average time/residue: 1.7384
  time to fit residues: 358.3076
Evaluate side-chains
  203 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 195
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain B residue  208 GLN
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  147 MET
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  326 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0980
   chunk 20 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 74 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 212 GLN
C 279 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.104470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.088926 restraints weight = 12415.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 2.71
r_work: 0.3123 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3126
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3125
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7104  Z= 0.292
  Angle     :  0.579   7.039   9621  Z= 0.289
  Chirality :  0.047   0.334   1098
  Planarity :  0.003   0.035   1200
  Dihedral  :  8.206  57.578   1164
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 26.56 %
    Favored  : 70.54 %
  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:  1.89 (0.29), residues: 843
  helix:  3.12 (0.27), residues: 315
  sheet:  0.61 (0.28), residues: 312
  loop : -0.61 (0.44), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 230 
 HIS   0.002   0.001   HIS B 130 
 PHE   0.025   0.002   PHE B  72 
 TYR   0.007   0.001   TYR C 201 
 ARG   0.013   0.001   ARG C 259 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 203
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A   63 LYS cc_start: 0.8056 (tptp) cc_final: 0.7775 (tmmt)
REVERT: A   92 PHE cc_start: 0.7863 (t80) cc_final: 0.7640 (t80)
REVERT: A  124 GLN cc_start: 0.8032 (mm110) cc_final: 0.7744 (mm110)
REVERT: A  153 ARG cc_start: 0.8203 (mtp85) cc_final: 0.7805 (mtp85)
REVERT: A  180 ARG cc_start: 0.8409 (mtp180) cc_final: 0.8160 (mtp180)
REVERT: A  224 GLU cc_start: 0.7816 (tp30) cc_final: 0.7333 (tp30)
REVERT: A  294 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8424 (tmmt)
REVERT: A  333 LYS cc_start: 0.8716 (tttt) cc_final: 0.8209 (ttpp)
REVERT: B   77 LEU cc_start: 0.8586 (mm) cc_final: 0.8345 (mm)
REVERT: B   91 ASP cc_start: 0.8546 (m-30) cc_final: 0.8340 (m-30)
REVERT: B  212 GLN cc_start: 0.8285 (pt0) cc_final: 0.8055 (mt0)
REVERT: B  224 GLU cc_start: 0.7879 (tp30) cc_final: 0.7625 (tp30)
REVERT: B  333 LYS cc_start: 0.8742 (tttt) cc_final: 0.8220 (ttpp)
REVERT: C   87 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7811 (tpm-80)
REVERT: C   95 LYS cc_start: 0.8754 (mttt) cc_final: 0.8518 (mttm)
REVERT: C  133 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7240 (tm-30)
REVERT: C  176 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8176 (mt-10)
REVERT: C  180 ARG cc_start: 0.8273 (mtp180) cc_final: 0.7851 (mtp180)
REVERT: C  266 ASN cc_start: 0.9015 (t0) cc_final: 0.8741 (t0)
REVERT: C  275 LYS cc_start: 0.8353 (mtpp) cc_final: 0.8140 (mtpp)
REVERT: C  326 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8299 (mm)
REVERT: C  333 LYS cc_start: 0.8691 (tttt) cc_final: 0.8344 (ttpt)
  outliers start: 21
  outliers final: 6
  residues processed: 213
  average time/residue: 1.7456
  time to fit residues: 385.3618
Evaluate side-chains
  205 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 197
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  302 ASN
Chi-restraints excluded: chain C residue   87 ARG
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  326 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 143 GLN
C 143 GLN
C 279 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.103406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.088044 restraints weight = 12538.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.70
r_work: 0.3116 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3121
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062   7104  Z= 0.372
  Angle     :  0.605   7.668   9621  Z= 0.303
  Chirality :  0.047   0.343   1098
  Planarity :  0.004   0.045   1200
  Dihedral  :  7.142  56.574   1164
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 27.25 %
    Favored  : 69.85 %
  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:  1.83 (0.29), residues: 843
  helix:  3.06 (0.27), residues: 312
  sheet:  0.64 (0.29), residues: 312
  loop : -0.67 (0.43), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 230 
 HIS   0.002   0.001   HIS A  98 
 PHE   0.027   0.002   PHE C  72 
 TYR   0.010   0.001   TYR B 111 
 ARG   0.011   0.001   ARG C 259 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 210
  time to evaluate  : 0.863 
Fit side-chains
REVERT: A   63 LYS cc_start: 0.8141 (tptp) cc_final: 0.7884 (tmmt)
REVERT: A  122 GLN cc_start: 0.9072 (mm110) cc_final: 0.8788 (mm110)
REVERT: A  124 GLN cc_start: 0.8060 (mm110) cc_final: 0.7743 (mm110)
REVERT: A  153 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7814 (mtp85)
REVERT: A  180 ARG cc_start: 0.8407 (mtp180) cc_final: 0.8188 (mtp180)
REVERT: A  224 GLU cc_start: 0.7809 (tp30) cc_final: 0.7323 (tp30)
REVERT: A  329 LYS cc_start: 0.8551 (tttt) cc_final: 0.8291 (tttt)
REVERT: A  333 LYS cc_start: 0.8785 (tttt) cc_final: 0.8348 (ttpp)
REVERT: B  162 ASN cc_start: 0.5827 (OUTLIER) cc_final: 0.5449 (m-40)
REVERT: B  212 GLN cc_start: 0.8277 (pt0) cc_final: 0.8068 (mt0)
REVERT: B  224 GLU cc_start: 0.7971 (tp30) cc_final: 0.7708 (tp30)
REVERT: B  227 TYR cc_start: 0.8700 (m-80) cc_final: 0.8432 (m-80)
REVERT: B  294 LYS cc_start: 0.8343 (tmmt) cc_final: 0.8130 (tmmt)
REVERT: B  333 LYS cc_start: 0.8813 (tttt) cc_final: 0.8360 (ttpp)
REVERT: C   95 LYS cc_start: 0.8713 (mttt) cc_final: 0.8500 (mttm)
REVERT: C  133 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7336 (tm-30)
REVERT: C  180 ARG cc_start: 0.8264 (mtp180) cc_final: 0.7834 (mtp180)
REVERT: C  326 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8355 (mm)
REVERT: C  333 LYS cc_start: 0.8784 (tttt) cc_final: 0.8350 (ttpp)
  outliers start: 21
  outliers final: 9
  residues processed: 217
  average time/residue: 1.7574
  time to fit residues: 394.9395
Evaluate side-chains
  214 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 203
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  302 ASN
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain B residue  302 ASN
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  328 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 7 optimal weight:    0.2980
   chunk 53 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 60 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 293 GLN
C 279 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.105351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.088756 restraints weight = 12206.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.89
r_work: 0.3114 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3115
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3115
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7104  Z= 0.242
  Angle     :  0.568   7.605   9621  Z= 0.287
  Chirality :  0.045   0.324   1098
  Planarity :  0.004   0.037   1200
  Dihedral  :  6.397  54.868   1164
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 27.52 %
    Favored  : 69.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.89 (0.29), residues: 843
  helix:  3.17 (0.27), residues: 312
  sheet:  0.67 (0.29), residues: 306
  loop : -0.70 (0.43), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 230 
 HIS   0.002   0.001   HIS A  98 
 PHE   0.033   0.002   PHE C  72 
 TYR   0.007   0.001   TYR C 201 
 ARG   0.007   0.000   ARG A 110 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 207
  time to evaluate  : 0.819 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7859 (tmmt)
REVERT: A  124 GLN cc_start: 0.8053 (mm110) cc_final: 0.7735 (mm110)
REVERT: A  153 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7915 (mtp85)
REVERT: A  170 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8529 (mm)
REVERT: A  224 GLU cc_start: 0.7823 (tp30) cc_final: 0.7347 (tp30)
REVERT: A  329 LYS cc_start: 0.8567 (tttt) cc_final: 0.8353 (tttt)
REVERT: A  333 LYS cc_start: 0.8815 (tttt) cc_final: 0.8357 (ttpp)
REVERT: B  224 GLU cc_start: 0.7984 (tp30) cc_final: 0.7711 (tp30)
REVERT: B  227 TYR cc_start: 0.8639 (m-80) cc_final: 0.8407 (m-80)
REVERT: B  333 LYS cc_start: 0.8822 (tttt) cc_final: 0.8364 (ttpp)
REVERT: C   95 LYS cc_start: 0.8730 (mttt) cc_final: 0.8517 (mttm)
REVERT: C  133 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7361 (tm-30)
REVERT: C  180 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7835 (mtp180)
REVERT: C  326 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8329 (mm)
REVERT: C  333 LYS cc_start: 0.8800 (tttt) cc_final: 0.8335 (ttpp)
  outliers start: 21
  outliers final: 11
  residues processed: 215
  average time/residue: 1.7420
  time to fit residues: 387.7757
Evaluate side-chains
  226 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 212
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 LYS
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain B residue   94 GLU
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain B residue  302 ASN
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  302 ASN
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  328 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 82 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0040
   chunk 76 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
C 143 GLN
C 279 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.103905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.086983 restraints weight = 12212.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.90
r_work: 0.3103 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3107
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3107
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7104  Z= 0.268
  Angle     :  0.576   8.263   9621  Z= 0.289
  Chirality :  0.045   0.331   1098
  Planarity :  0.003   0.037   1200
  Dihedral  :  6.043  52.091   1164
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 28.08 %
    Favored  : 69.02 %
  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:  1.86 (0.29), residues: 843
  helix:  3.10 (0.27), residues: 312
  sheet:  0.59 (0.29), residues: 312
  loop : -0.57 (0.44), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 230 
 HIS   0.002   0.001   HIS A 130 
 PHE   0.030   0.002   PHE C  72 
 TYR   0.008   0.001   TYR C 201 
 ARG   0.008   0.001   ARG C 259 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 217
  time to evaluate  : 0.823 
Fit side-chains
REVERT: A   63 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7859 (tmmt)
REVERT: A  122 GLN cc_start: 0.9101 (mm110) cc_final: 0.8824 (mm110)
REVERT: A  124 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7694 (mm-40)
REVERT: A  133 GLU cc_start: 0.7545 (tm-30) cc_final: 0.6446 (tm-30)
REVERT: A  153 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7902 (mtp85)
REVERT: A  170 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8533 (mm)
REVERT: A  180 ARG cc_start: 0.8080 (mtp180) cc_final: 0.7528 (ttp-170)
REVERT: A  224 GLU cc_start: 0.7851 (tp30) cc_final: 0.7382 (tp30)
REVERT: A  329 LYS cc_start: 0.8585 (tttt) cc_final: 0.8370 (tttt)
REVERT: A  333 LYS cc_start: 0.8846 (tttt) cc_final: 0.8398 (ttpp)
REVERT: B  147 MET cc_start: 0.8650 (tpt) cc_final: 0.8429 (tpp)
REVERT: B  162 ASN cc_start: 0.5936 (OUTLIER) cc_final: 0.5633 (m-40)
REVERT: B  224 GLU cc_start: 0.8001 (tp30) cc_final: 0.7738 (tp30)
REVERT: B  227 TYR cc_start: 0.8646 (m-80) cc_final: 0.8369 (m-80)
REVERT: B  333 LYS cc_start: 0.8803 (tttt) cc_final: 0.8351 (ttpp)
REVERT: C   95 LYS cc_start: 0.8748 (mttt) cc_final: 0.8535 (mttm)
REVERT: C  180 ARG cc_start: 0.8305 (mtp180) cc_final: 0.7845 (mtp180)
REVERT: C  326 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8338 (mm)
REVERT: C  333 LYS cc_start: 0.8800 (tttt) cc_final: 0.8383 (ttpp)
  outliers start: 21
  outliers final: 10
  residues processed: 226
  average time/residue: 1.7332
  time to fit residues: 405.8595
Evaluate side-chains
  223 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 209
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 LYS
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  302 ASN
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain B residue  302 ASN
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  302 ASN
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  328 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 81 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 52 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 293 GLN
B 143 GLN
B 212 GLN
B 296 GLN
C 279 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.101641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.084728 restraints weight = 12088.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.83
r_work: 0.3098 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3105
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3105
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   7104  Z= 0.310
  Angle     :  0.600   9.770   9621  Z= 0.303
  Chirality :  0.046   0.335   1098
  Planarity :  0.004   0.054   1200
  Dihedral  :  5.758  47.933   1164
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 28.77 %
    Favored  : 68.05 %
  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:  1.77 (0.29), residues: 843
  helix:  3.05 (0.27), residues: 312
  sheet:  0.69 (0.29), residues: 312
  loop : -0.91 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 304 
 HIS   0.003   0.001   HIS C 130 
 PHE   0.027   0.002   PHE C  72 
 TYR   0.009   0.001   TYR B  74 
 ARG   0.011   0.001   ARG A 110 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 206
  time to evaluate  : 0.735 
Fit side-chains
REVERT: A   63 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7962 (tmmt)
REVERT: A  124 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7767 (mm-40)
REVERT: A  133 GLU cc_start: 0.7595 (tm-30) cc_final: 0.6242 (tm-30)
REVERT: A  170 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8551 (mm)
REVERT: A  180 ARG cc_start: 0.8055 (mtp180) cc_final: 0.7429 (ttp-170)
REVERT: A  224 GLU cc_start: 0.7891 (tp30) cc_final: 0.7409 (tp30)
REVERT: A  329 LYS cc_start: 0.8595 (tttt) cc_final: 0.8379 (tttt)
REVERT: A  333 LYS cc_start: 0.8851 (tttt) cc_final: 0.8431 (ttpp)
REVERT: B  147 MET cc_start: 0.8678 (tpt) cc_final: 0.8452 (tpp)
REVERT: B  162 ASN cc_start: 0.6081 (OUTLIER) cc_final: 0.5832 (m-40)
REVERT: B  188 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8367 (ppp80)
REVERT: B  224 GLU cc_start: 0.8059 (tp30) cc_final: 0.7796 (tp30)
REVERT: B  227 TYR cc_start: 0.8650 (m-80) cc_final: 0.8370 (m-80)
REVERT: B  333 LYS cc_start: 0.8816 (tttt) cc_final: 0.8363 (ttpp)
REVERT: C   95 LYS cc_start: 0.8737 (mttt) cc_final: 0.8520 (mttm)
REVERT: C  180 ARG cc_start: 0.8304 (mtp180) cc_final: 0.7848 (mtp180)
REVERT: C  188 ARG cc_start: 0.8547 (ttt90) cc_final: 0.8191 (ttt90)
REVERT: C  326 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8349 (mm)
REVERT: C  333 LYS cc_start: 0.8821 (tttt) cc_final: 0.8395 (ttpp)
  outliers start: 23
  outliers final: 13
  residues processed: 213
  average time/residue: 1.7439
  time to fit residues: 384.4614
Evaluate side-chains
  216 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 198
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 LYS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  302 ASN
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain B residue  188 ARG
Chi-restraints excluded: chain B residue  302 ASN
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  302 ASN
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  328 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0060
   chunk 38 optimal weight:    0.9980
   chunk 71 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
A 143 GLN
B 143 GLN
B 212 GLN
B 293 GLN
B 296 GLN
C 143 GLN
C 279 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.101442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.084749 restraints weight = 12152.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.81
r_work: 0.3111 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3114
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3114
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7104  Z= 0.283
  Angle     :  0.608  10.439   9621  Z= 0.302
  Chirality :  0.046   0.331   1098
  Planarity :  0.004   0.055   1200
  Dihedral  :  5.523  44.018   1164
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 28.91 %
    Favored  : 68.74 %
  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:  1.75 (0.29), residues: 843
  helix:  3.01 (0.27), residues: 312
  sheet:  0.69 (0.29), residues: 312
  loop : -0.91 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 304 
 HIS   0.002   0.001   HIS B  98 
 PHE   0.028   0.002   PHE C  72 
 TYR   0.008   0.001   TYR C 201 
 ARG   0.012   0.001   ARG A 110 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 213
  time to evaluate  : 0.708 
Fit side-chains
REVERT: A   63 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7991 (tmmt)
REVERT: A  122 GLN cc_start: 0.9119 (mm110) cc_final: 0.8852 (mm110)
REVERT: A  124 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7777 (mm-40)
REVERT: A  133 GLU cc_start: 0.7608 (tm-30) cc_final: 0.6348 (tm-30)
REVERT: A  170 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8553 (mm)
REVERT: A  180 ARG cc_start: 0.8041 (mtp180) cc_final: 0.7456 (ttp-170)
REVERT: A  224 GLU cc_start: 0.7913 (tp30) cc_final: 0.7420 (tp30)
REVERT: A  294 LYS cc_start: 0.8389 (tmmt) cc_final: 0.8157 (tmmt)
REVERT: A  329 LYS cc_start: 0.8574 (tttt) cc_final: 0.8359 (tttt)
REVERT: A  333 LYS cc_start: 0.8864 (tttt) cc_final: 0.8444 (ttpp)
REVERT: B  147 MET cc_start: 0.8673 (tpt) cc_final: 0.8452 (tpp)
REVERT: B  156 TYR cc_start: 0.8677 (p90) cc_final: 0.8443 (p90)
REVERT: B  162 ASN cc_start: 0.6166 (OUTLIER) cc_final: 0.5937 (m-40)
REVERT: B  188 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8352 (ppp80)
REVERT: B  224 GLU cc_start: 0.8071 (tp30) cc_final: 0.7843 (tp30)
REVERT: B  227 TYR cc_start: 0.8646 (m-80) cc_final: 0.8339 (m-80)
REVERT: B  333 LYS cc_start: 0.8837 (tttt) cc_final: 0.8381 (ttpp)
REVERT: C   95 LYS cc_start: 0.8728 (mttt) cc_final: 0.8505 (mttm)
REVERT: C  180 ARG cc_start: 0.8293 (mtp180) cc_final: 0.7836 (mtp180)
REVERT: C  188 ARG cc_start: 0.8551 (ttt90) cc_final: 0.8350 (ttt90)
REVERT: C  275 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8163 (mtpp)
REVERT: C  326 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8340 (mm)
REVERT: C  333 LYS cc_start: 0.8807 (tttt) cc_final: 0.8411 (ttpp)
  outliers start: 17
  outliers final: 9
  residues processed: 218
  average time/residue: 1.7678
  time to fit residues: 399.3660
Evaluate side-chains
  219 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 205
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 LYS
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  302 ASN
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain B residue  188 ARG
Chi-restraints excluded: chain B residue  302 ASN
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  302 ASN
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  328 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 56 optimal weight:    6.9990
   chunk 57 optimal weight:    0.3980
   chunk 23 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0870
   chunk 16 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 293 GLN
B 130 HIS
B 143 GLN
B 212 GLN
B 293 GLN
B 296 GLN
C 279 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.103180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.086338 restraints weight = 12329.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.88
r_work: 0.3116 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3121
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3121
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7104  Z= 0.242
  Angle     :  0.600   9.362   9621  Z= 0.301
  Chirality :  0.046   0.323   1098
  Planarity :  0.004   0.049   1200
  Dihedral  :  5.123  35.828   1164
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 30.57 %
    Favored  : 67.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.78 (0.29), residues: 843
  helix:  3.06 (0.26), residues: 312
  sheet:  0.67 (0.29), residues: 312
  loop : -0.89 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 304 
 HIS   0.002   0.001   HIS B  98 
 PHE   0.026   0.002   PHE B  92 
 TYR   0.009   0.001   TYR B  74 
 ARG   0.011   0.001   ARG C 259 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 208
  time to evaluate  : 0.827 
Fit side-chains
REVERT: A   63 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7999 (tmmt)
REVERT: A  124 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7808 (mm-40)
REVERT: A  153 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7871 (mtp85)
REVERT: A  170 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8555 (mm)
REVERT: A  180 ARG cc_start: 0.8037 (mtp180) cc_final: 0.7410 (ttp-170)
REVERT: A  224 GLU cc_start: 0.7896 (tp30) cc_final: 0.7388 (tp30)
REVERT: A  329 LYS cc_start: 0.8554 (tttt) cc_final: 0.8347 (tttt)
REVERT: A  331 MET cc_start: 0.7428 (tmm) cc_final: 0.7094 (tmm)
REVERT: A  333 LYS cc_start: 0.8866 (tttt) cc_final: 0.8448 (ttpp)
REVERT: B  156 TYR cc_start: 0.8676 (p90) cc_final: 0.8441 (p90)
REVERT: B  162 ASN cc_start: 0.6202 (OUTLIER) cc_final: 0.5976 (m-40)
REVERT: B  188 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8317 (ppp80)
REVERT: B  224 GLU cc_start: 0.8056 (tp30) cc_final: 0.7827 (tp30)
REVERT: B  227 TYR cc_start: 0.8599 (m-80) cc_final: 0.8378 (m-80)
REVERT: B  333 LYS cc_start: 0.8817 (tttt) cc_final: 0.8354 (ttpp)
REVERT: C   95 LYS cc_start: 0.8690 (mttt) cc_final: 0.8459 (mttm)
REVERT: C  180 ARG cc_start: 0.8267 (mtp180) cc_final: 0.7815 (mtp180)
REVERT: C  275 LYS cc_start: 0.8399 (mtpp) cc_final: 0.8173 (mtpp)
REVERT: C  326 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8304 (mm)
REVERT: C  329 LYS cc_start: 0.8450 (tttt) cc_final: 0.7952 (ttpp)
REVERT: C  333 LYS cc_start: 0.8794 (tttt) cc_final: 0.8399 (ttpp)
  outliers start: 14
  outliers final: 6
  residues processed: 211
  average time/residue: 1.8042
  time to fit residues: 394.0463
Evaluate side-chains
  212 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 201
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 LYS
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  302 ASN
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain B residue  188 ARG
Chi-restraints excluded: chain B residue  302 ASN
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  302 ASN
Chi-restraints excluded: chain C residue  326 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0970
   chunk 3 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0570
   chunk 52 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.4096

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

Flipped N/Q/H residues before XYZ refinement:
A 143 GLN
B 143 GLN
B 212 GLN
B 293 GLN
B 296 GLN
C 143 GLN
C 279 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.104793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.088068 restraints weight = 12296.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 2.91
r_work: 0.3123 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.3318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7104  Z= 0.211
  Angle     :  0.591  11.565   9621  Z= 0.296
  Chirality :  0.045   0.321   1098
  Planarity :  0.004   0.065   1200
  Dihedral  :  4.818  27.532   1164
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 30.84 %
    Favored  : 67.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.79 (0.29), residues: 843
  helix:  3.10 (0.27), residues: 312
  sheet:  0.64 (0.29), residues: 312
  loop : -0.87 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 304 
 HIS   0.002   0.001   HIS B  98 
 PHE   0.029   0.002   PHE C  72 
 TYR   0.007   0.001   TYR C 201 
 ARG   0.014   0.001   ARG A 110 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 216
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7991 (tmmt)
REVERT: A  122 GLN cc_start: 0.9125 (mm110) cc_final: 0.8850 (mm110)
REVERT: A  124 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7797 (mm-40)
REVERT: A  153 ARG cc_start: 0.8246 (mtp85) cc_final: 0.7893 (mtp85)
REVERT: A  224 GLU cc_start: 0.7888 (tp30) cc_final: 0.7376 (tp30)
REVERT: A  294 LYS cc_start: 0.8540 (tmmt) cc_final: 0.8276 (tmmt)
REVERT: A  329 LYS cc_start: 0.8549 (tttt) cc_final: 0.8342 (tttt)
REVERT: A  331 MET cc_start: 0.7444 (tmm) cc_final: 0.7115 (tmm)
REVERT: A  333 LYS cc_start: 0.8872 (tttt) cc_final: 0.8459 (ttpp)
REVERT: B  156 TYR cc_start: 0.8675 (p90) cc_final: 0.8439 (p90)
REVERT: B  188 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8297 (ppp80)
REVERT: B  224 GLU cc_start: 0.8069 (tp30) cc_final: 0.7850 (tp30)
REVERT: B  294 LYS cc_start: 0.8528 (tmmt) cc_final: 0.8242 (tmmt)
REVERT: B  333 LYS cc_start: 0.8829 (tttt) cc_final: 0.8358 (ttpp)
REVERT: C   95 LYS cc_start: 0.8714 (mttt) cc_final: 0.8480 (mttm)
REVERT: C  180 ARG cc_start: 0.8274 (mtp180) cc_final: 0.7819 (mtp180)
REVERT: C  275 LYS cc_start: 0.8408 (mtpp) cc_final: 0.8205 (mtpp)
REVERT: C  326 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8327 (mm)
REVERT: C  333 LYS cc_start: 0.8816 (tttt) cc_final: 0.8427 (ttpp)
  outliers start: 9
  outliers final: 5
  residues processed: 218
  average time/residue: 1.7703
  time to fit residues: 399.3680
Evaluate side-chains
  213 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 205
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 LYS
Chi-restraints excluded: chain B residue  188 ARG
Chi-restraints excluded: chain B residue  302 ASN
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  302 ASN
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  326 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0980
   chunk 82 optimal weight:    0.5980
   chunk 35 optimal weight:    0.3980
   chunk 32 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 81 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 212 GLN
A 296 GLN
B 130 HIS
B 212 GLN
B 293 GLN
B 296 GLN
C 279 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.104082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.088707 restraints weight = 12305.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.67
r_work: 0.3133 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3136
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3136
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.3422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7104  Z= 0.224
  Angle     :  0.608  11.216   9621  Z= 0.302
  Chirality :  0.047   0.324   1098
  Planarity :  0.004   0.065   1200
  Dihedral  :  4.713  22.772   1164
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 30.57 %
    Favored  : 67.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.79 (0.29), residues: 843
  helix:  3.07 (0.27), residues: 312
  sheet:  0.66 (0.29), residues: 312
  loop : -0.85 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 304 
 HIS   0.002   0.001   HIS B  98 
 PHE   0.029   0.002   PHE B  72 
 TYR   0.007   0.001   TYR C 201 
 ARG   0.014   0.001   ARG A 110 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7519.39 seconds
wall clock time: 132 minutes 50.48 seconds (7970.48 seconds total)