Starting phenix.real_space_refine
on Wed Sep 17 09:15:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xda_38271/09_2025/8xda_38271_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xda_38271/09_2025/8xda_38271.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xda_38271/09_2025/8xda_38271.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xda_38271/09_2025/8xda_38271.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xda_38271/09_2025/8xda_38271_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xda_38271/09_2025/8xda_38271_neut.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.169
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      57      5.16       5
     C    5100      2.51       5
     N    1158      2.21       5
     O    1305      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7620
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2530
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 328, 2510
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 306}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
      Conformer: "B"
        Number of residues, atoms: 328, 2510
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 306}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
          bond proxies already assigned to first conformer: 2565
    Chain: "B"
      Number of atoms: 2530
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 328, 2510
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 306}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
      Conformer: "B"
        Number of residues, atoms: 328, 2510
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 306}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
          bond proxies already assigned to first conformer: 2565
    Chain: "C"
      Number of atoms: 2530
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 328, 2510
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 306}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
      Conformer: "B"
        Number of residues, atoms: 328, 2510
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 306}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
          bond proxies already assigned to first conformer: 2565
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 2, 8
          Unusual residues: {'URE': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 2, 8
          Unusual residues: {'URE': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 2, 8
          Unusual residues: {'URE': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 6
    residue:
      pdb=" N  APHE A 120 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 120 " occ=0.50
    residue:
      pdb=" N  APHE B 120 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE B 120 " occ=0.50
    residue:
      pdb=" N  APHE C 120 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE C 120 " occ=0.50
    residue:
      pdb=" C  AURE A 401 " occ=0.25
      ... (2 atoms not shown)
      pdb=" N2 AURE A 401 " occ=0.25
    residue:
      pdb=" C  AURE B 401 " occ=0.25
      ... (2 atoms not shown)
      pdb=" N2 AURE B 401 " occ=0.25
    residue:
      pdb=" C  AURE C 401 " occ=0.25
      ... (2 atoms not shown)
      pdb=" N2 AURE C 401 " occ=0.25
  Time building chain proxies: 3.38, per 1000 atoms: 0.44
  Number of scatterers: 7620
  At special positions: 0
  Unit cell: (94.76, 89.24, 71.76, 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      57     16.00
     O    1305      8.00
     N    1158      7.00
     C    5100      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 689.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1830

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 0 sheets defined
      77.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 52 through 68
      removed outlier: 3.867A  pdb=" N   VAL A  68 " --> pdb=" O   GLY A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 88
      removed outlier: 3.759A  pdb=" N   ASN A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 109
    Processing helix  chain 'A' and resid 112 through 117
    Processing helix  chain 'A' and resid 122 through 135
      removed outlier: 4.018A  pdb=" N   LEU A 127 " --> pdb=" O   TYR A 123 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL A 128 " --> pdb=" O   ASN A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 144
      No H-bonds generated for 'chain 'A' and resid 142 through 144'
    Processing helix  chain 'A' and resid 145 through 167
      Proline residue:  A 157  - end of helix
      removed outlier: 3.970A  pdb=" N   GLY A 164 " --> pdb=" O   SER A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 191
    Processing helix  chain 'A' and resid 212 through 216
      removed outlier: 3.885A  pdb=" N   VAL A 216 " --> pdb=" O   TRP A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 231
      removed outlier: 4.334A  pdb=" N   ILE A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      Proline residue:  A 226  - end of helix
    Processing helix  chain 'A' and resid 232 through 234
      No H-bonds generated for 'chain 'A' and resid 232 through 234'
    Processing helix  chain 'A' and resid 237 through 252
      removed outlier: 3.642A  pdb=" N   SER A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 273
    Processing helix  chain 'A' and resid 276 through 283
      removed outlier: 3.535A  pdb=" N   ILE A 280 " --> pdb=" O   PRO A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 297
    Processing helix  chain 'A' and resid 304 through 330
    Processing helix  chain 'A' and resid 338 through 350
    Processing helix  chain 'A' and resid 362 through 366
    Processing helix  chain 'A' and resid 368 through 379
    Processing helix  chain 'B' and resid 53 through 67
    Processing helix  chain 'B' and resid 68 through 70
      No H-bonds generated for 'chain 'B' and resid 68 through 70'
    Processing helix  chain 'B' and resid 73 through 88
      removed outlier: 3.759A  pdb=" N   ASN B  88 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 109
    Processing helix  chain 'B' and resid 112 through 117
    Processing helix  chain 'B' and resid 122 through 135
      removed outlier: 4.018A  pdb=" N   LEU B 127 " --> pdb=" O   TYR B 123 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL B 128 " --> pdb=" O   ASN B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 144
      No H-bonds generated for 'chain 'B' and resid 142 through 144'
    Processing helix  chain 'B' and resid 145 through 167
      Proline residue:  B 157  - end of helix
      removed outlier: 3.969A  pdb=" N   GLY B 164 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 191
    Processing helix  chain 'B' and resid 212 through 216
      removed outlier: 3.885A  pdb=" N   VAL B 216 " --> pdb=" O   TRP B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 231
      removed outlier: 4.334A  pdb=" N   ILE B 225 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
      Proline residue:  B 226  - end of helix
    Processing helix  chain 'B' and resid 232 through 234
      No H-bonds generated for 'chain 'B' and resid 232 through 234'
    Processing helix  chain 'B' and resid 237 through 252
      removed outlier: 3.643A  pdb=" N   SER B 251 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 273
    Processing helix  chain 'B' and resid 276 through 283
      removed outlier: 3.535A  pdb=" N   ILE B 280 " --> pdb=" O   PRO B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 297
    Processing helix  chain 'B' and resid 304 through 330
    Processing helix  chain 'B' and resid 338 through 350
    Processing helix  chain 'B' and resid 362 through 366
    Processing helix  chain 'B' and resid 368 through 379
    Processing helix  chain 'C' and resid 53 through 67
    Processing helix  chain 'C' and resid 68 through 70
      No H-bonds generated for 'chain 'C' and resid 68 through 70'
    Processing helix  chain 'C' and resid 73 through 88
      removed outlier: 3.758A  pdb=" N   ASN C  88 " --> pdb=" O   LEU C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 88 through 109
    Processing helix  chain 'C' and resid 112 through 117
    Processing helix  chain 'C' and resid 122 through 135
      removed outlier: 4.018A  pdb=" N   LEU C 127 " --> pdb=" O   TYR C 123 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL C 128 " --> pdb=" O   ASN C 124 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 142 through 144
      No H-bonds generated for 'chain 'C' and resid 142 through 144'
    Processing helix  chain 'C' and resid 145 through 167
      Proline residue:  C 157  - end of helix
      removed outlier: 3.969A  pdb=" N   GLY C 164 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 191
    Processing helix  chain 'C' and resid 212 through 216
      removed outlier: 3.885A  pdb=" N   VAL C 216 " --> pdb=" O   TRP C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 217 through 231
      removed outlier: 4.334A  pdb=" N   ILE C 225 " --> pdb=" O   LEU C 221 " (cutoff:3.500A)
      Proline residue:  C 226  - end of helix
    Processing helix  chain 'C' and resid 232 through 234
      No H-bonds generated for 'chain 'C' and resid 232 through 234'
    Processing helix  chain 'C' and resid 237 through 252
      removed outlier: 3.642A  pdb=" N   SER C 251 " --> pdb=" O   ALA C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 252 through 273
    Processing helix  chain 'C' and resid 276 through 283
      removed outlier: 3.535A  pdb=" N   ILE C 280 " --> pdb=" O   PRO C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 297
    Processing helix  chain 'C' and resid 304 through 330
    Processing helix  chain 'C' and resid 338 through 350
    Processing helix  chain 'C' and resid 362 through 366
    Processing helix  chain 'C' and resid 368 through 379

    502 hydrogen bonds defined for protein.
    1479 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: 1.21

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.11 -     1.25: 1113
        1.25 -     1.39: 2034
        1.39 -     1.53: 4350
        1.53 -     1.67: 273
        1.67 -     1.81: 87
  Bond restraints: 7857
  Sorted by residual:
  bond pdb=" C   URE A 402 "
       pdb=" O   URE A 402 "
    ideal  model  delta    sigma   weight residual
    1.225  1.115  0.110 2.00e-02 2.50e+03 3.05e+01
  bond pdb=" C   URE C 402 "
       pdb=" O   URE C 402 "
    ideal  model  delta    sigma   weight residual
    1.225  1.115  0.110 2.00e-02 2.50e+03 3.04e+01
  bond pdb=" C   URE B 402 "
       pdb=" O   URE B 402 "
    ideal  model  delta    sigma   weight residual
    1.225  1.115  0.110 2.00e-02 2.50e+03 3.04e+01
  bond pdb=" CA  SER C 168 "
       pdb=" C   SER C 168 "
    ideal  model  delta    sigma   weight residual
    1.523  1.449  0.074 1.41e-02 5.03e+03 2.72e+01
  bond pdb=" CA  SER A 168 "
       pdb=" C   SER A 168 "
    ideal  model  delta    sigma   weight residual
    1.523  1.449  0.073 1.41e-02 5.03e+03 2.70e+01
  ... (remaining 7852 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 10560
        2.60 -     5.20: 197
        5.20 -     7.80: 22
        7.80 -    10.40: 6
       10.40 -    13.00: 6
  Bond angle restraints: 10791
  Sorted by residual:
  angle pdb=" N   THR C 165 "
        pdb=" CA  THR C 165 "
        pdb=" C   THR C 165 "
      ideal   model   delta    sigma   weight residual
     114.31  101.31   13.00 1.29e+00 6.01e-01 1.02e+02
  angle pdb=" N   THR B 165 "
        pdb=" CA  THR B 165 "
        pdb=" C   THR B 165 "
      ideal   model   delta    sigma   weight residual
     114.31  101.33   12.98 1.29e+00 6.01e-01 1.01e+02
  angle pdb=" N   THR A 165 "
        pdb=" CA  THR A 165 "
        pdb=" C   THR A 165 "
      ideal   model   delta    sigma   weight residual
     114.31  101.34   12.97 1.29e+00 6.01e-01 1.01e+02
  angle pdb=" N   TRP B 170 "
        pdb=" CA  TRP B 170 "
        pdb=" C   TRP B 170 "
      ideal   model   delta    sigma   weight residual
     113.61  104.49    9.12 1.50e+00 4.44e-01 3.70e+01
  angle pdb=" N   TRP A 170 "
        pdb=" CA  TRP A 170 "
        pdb=" C   TRP A 170 "
      ideal   model   delta    sigma   weight residual
     113.61  104.49    9.12 1.50e+00 4.44e-01 3.70e+01
  ... (remaining 10786 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.31: 3836
       12.31 -    24.62: 442
       24.62 -    36.92: 133
       36.92 -    49.23: 29
       49.23 -    61.54: 18
  Dihedral angle restraints: 4458
    sinusoidal: 1593
      harmonic: 2865
  Sorted by residual:
  dihedral pdb=" C   THR A 338 "
           pdb=" N   THR A 338 "
           pdb=" CA  THR A 338 "
           pdb=" CB  THR A 338 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.47   13.47     0      2.50e+00 1.60e-01 2.90e+01
  dihedral pdb=" C   THR B 338 "
           pdb=" N   THR B 338 "
           pdb=" CA  THR B 338 "
           pdb=" CB  THR B 338 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.41   13.41     0      2.50e+00 1.60e-01 2.88e+01
  dihedral pdb=" C   THR C 338 "
           pdb=" N   THR C 338 "
           pdb=" CA  THR C 338 "
           pdb=" CB  THR C 338 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.37   13.37     0      2.50e+00 1.60e-01 2.86e+01
  ... (remaining 4455 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 1219
       0.107 -    0.214: 48
       0.214 -    0.321: 2
       0.321 -    0.428: 0
       0.428 -    0.534: 6
  Chirality restraints: 1275
  Sorted by residual:
  chirality pdb=" CA  PHE C  70 "
            pdb=" N   PHE C  70 "
            pdb=" C   PHE C  70 "
            pdb=" CB  PHE C  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 7.14e+00
  chirality pdb=" CA  PHE A  70 "
            pdb=" N   PHE A  70 "
            pdb=" C   PHE A  70 "
            pdb=" CB  PHE A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 7.10e+00
  chirality pdb=" CA  PHE B  70 "
            pdb=" N   PHE B  70 "
            pdb=" C   PHE B  70 "
            pdb=" CB  PHE B  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 7.09e+00
  ... (remaining 1272 not shown)

  Planarity restraints: 1314
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 305 "    0.010 2.00e-02 2.50e+03   1.96e-02 3.83e+00
        pdb=" C   TRP A 305 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   TRP A 305 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLN A 306 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 305 "   -0.010 2.00e-02 2.50e+03   1.94e-02 3.78e+00
        pdb=" C   TRP B 305 "    0.034 2.00e-02 2.50e+03
        pdb=" O   TRP B 305 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLN B 306 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP C 305 "    0.010 2.00e-02 2.50e+03   1.93e-02 3.71e+00
        pdb=" C   TRP C 305 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   TRP C 305 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLN C 306 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1311 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2295
        2.81 -     3.33: 7825
        3.33 -     3.86: 13491
        3.86 -     4.38: 16568
        4.38 -     4.90: 27256
  Nonbonded interactions: 67435
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 180 "
            pdb=" O   CYS A 337 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" ND2 ASN B 180 "
            pdb=" O   CYS B 337 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" ND2 ASN C 180 "
            pdb=" O   CYS C 337 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" OG  SER A 102 "
            pdb=" O   HIS A 121 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" OG  SER B 102 "
            pdb=" O   HIS B 121 "
     model   vdw
     2.326 3.040
  ... (remaining 67430 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.25 max=1.00 mean=0.99
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:             1.530
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.610
  Find NCS groups from input model:        0.070
  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:6.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
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      :  0.008   0.110   7857  Z= 0.434
  Angle     :  0.862  13.001  10791  Z= 0.495
  Chirality :  0.061   0.534   1275
  Planarity :  0.006   0.040   1314
  Dihedral  : 12.749  61.536   2628
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  0.73 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.33 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.27), residues: 990
  helix:  0.66 (0.19), residues: 693
  sheet:  None (None), residues: 0
  loop : -0.04 (0.39), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 223 
 TYR   0.014   0.002   TYR C 123 
 PHE   0.013   0.002   PHE B 287 
 TRP   0.007   0.001   TRP C 305 
 HIS   0.004   0.002   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00827 ( 7857)
  covalent geometry    : angle       0.86158 (10791)
  hydrogen bonds       : bond        0.15194 (  502)
  hydrogen bonds       : angle       6.66378 ( 1479)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.259 
Fit side-chains
  outliers start: 8
  outliers final: 0
  residues processed: 57
  average time/residue: 0.4847
  time to fit residues: 29.7532
Evaluate side-chains
  45 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  72 ASN
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  72 ASN
C  72 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.127104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.111772 restraints weight = 22026.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.18
r_work: 0.3206 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3070
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3067
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7857  Z= 0.174
  Angle     :  0.617   7.173  10791  Z= 0.306
  Chirality :  0.044   0.140   1275
  Planarity :  0.005   0.038   1314
  Dihedral  :  4.690  18.746   1044
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  5.01 %
    Favored  : 94.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.26), residues: 990
  helix:  0.82 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop :  0.12 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  63 
 TYR   0.008   0.001   TYR C 123 
 PHE   0.015   0.001   PHE A 287 
 TRP   0.013   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 7857)
  covalent geometry    : angle       0.61662 (10791)
  hydrogen bonds       : bond        0.03947 (  502)
  hydrogen bonds       : angle       4.42536 ( 1479)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.279 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 62
  average time/residue: 0.4350
  time to fit residues: 29.3334
Evaluate side-chains
  55 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain C residue  160 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 75 optimal weight:    0.5980
   chunk 59 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.118579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.101683 restraints weight = 39246.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.86
r_work: 0.3078 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3126
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3126
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7857  Z= 0.175
  Angle     :  0.590   7.761  10791  Z= 0.295
  Chirality :  0.043   0.121   1275
  Planarity :  0.005   0.041   1314
  Dihedral  :  4.496  16.490   1044
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  7.57 %
    Favored  : 91.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.27), residues: 990
  helix:  1.03 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.20 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 223 
 TYR   0.009   0.001   TYR C 123 
 PHE   0.012   0.001   PHE A 287 
 TRP   0.013   0.001   TRP B 170 
 HIS   0.003   0.001   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 7857)
  covalent geometry    : angle       0.58984 (10791)
  hydrogen bonds       : bond        0.04196 (  502)
  hydrogen bonds       : angle       4.37726 ( 1479)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8096 (pt)
REVERT: A  202 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8284 (mp)
REVERT: B   84 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7929 (pt)
  outliers start: 6
  outliers final: 3
  residues processed: 72
  average time/residue: 0.3918
  time to fit residues: 30.8889
Evaluate side-chains
  66 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain C residue  166 ILE
Chi-restraints excluded: chain C residue  250 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 71 optimal weight:    0.5980
   overall best weight:    0.8584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.117287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.102524 restraints weight = 22473.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.09
r_work: 0.3106 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3034
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3034
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.3476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7857  Z= 0.173
  Angle     :  0.577   7.446  10791  Z= 0.285
  Chirality :  0.043   0.121   1275
  Planarity :  0.005   0.042   1314
  Dihedral  :  4.492  15.671   1044
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  9.52 %
    Favored  : 88.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.26), residues: 990
  helix:  1.04 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.35 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 223 
 TYR   0.009   0.001   TYR C 123 
 PHE   0.013   0.001   PHE C 287 
 TRP   0.010   0.001   TRP A 170 
 HIS   0.003   0.001   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 7857)
  covalent geometry    : angle       0.57724 (10791)
  hydrogen bonds       : bond        0.03893 (  502)
  hydrogen bonds       : angle       4.25977 ( 1479)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A  202 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8220 (mp)
REVERT: A  273 ILE cc_start: 0.7707 (tp) cc_final: 0.7464 (tp)
REVERT: B   84 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7905 (pt)
REVERT: B  168 SER cc_start: 0.8274 (t) cc_final: 0.8007 (p)
REVERT: C   84 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8218 (pp)
REVERT: C  273 ILE cc_start: 0.7933 (tp) cc_final: 0.7659 (tp)
  outliers start: 14
  outliers final: 5
  residues processed: 67
  average time/residue: 0.4154
  time to fit residues: 30.3427
Evaluate side-chains
  67 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  250 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 61 optimal weight:    0.0980
   chunk 9 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 77 optimal weight:    0.5980
   chunk 91 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 83 optimal weight:    0.7980
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.119613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.104079 restraints weight = 28442.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.37
r_work: 0.3119 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3052
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3052
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7857  Z= 0.137
  Angle     :  0.536   6.628  10791  Z= 0.265
  Chirality :  0.041   0.121   1275
  Planarity :  0.005   0.043   1314
  Dihedral  :  4.314  14.941   1044
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 10.01 %
    Favored  : 88.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.27), residues: 990
  helix:  1.24 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.44 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A  63 
 TYR   0.008   0.001   TYR C 123 
 PHE   0.011   0.001   PHE C 287 
 TRP   0.010   0.001   TRP B 339 
 HIS   0.002   0.001   HIS C 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 7857)
  covalent geometry    : angle       0.53594 (10791)
  hydrogen bonds       : bond        0.03655 (  502)
  hydrogen bonds       : angle       4.06552 ( 1479)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8035 (pt)
REVERT: A  236 ASP cc_start: 0.7782 (p0) cc_final: 0.7578 (p0)
REVERT: A  273 ILE cc_start: 0.7667 (tp) cc_final: 0.7430 (tp)
REVERT: B   84 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7832 (pt)
REVERT: C   84 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8060 (pt)
REVERT: C  273 ILE cc_start: 0.7824 (tp) cc_final: 0.7510 (tp)
  outliers start: 14
  outliers final: 5
  residues processed: 63
  average time/residue: 0.4563
  time to fit residues: 31.1960
Evaluate side-chains
  66 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  250 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0980
   chunk 75 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 180 ASN
C 180 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.117654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.101636 restraints weight = 33070.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 2.56
r_work: 0.3078 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2990
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2990 r_free = 0.2990    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2990 r_free = 0.2990    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2990
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.3718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7857  Z= 0.163
  Angle     :  0.563   7.534  10791  Z= 0.277
  Chirality :  0.043   0.119   1275
  Planarity :  0.005   0.043   1314
  Dihedral  :  4.388  15.555   1044
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  :  9.65 %
    Favored  : 88.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.27), residues: 990
  helix:  1.24 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.53 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 223 
 TYR   0.009   0.001   TYR C 123 
 PHE   0.012   0.001   PHE C 287 
 TRP   0.009   0.001   TRP C 170 
 HIS   0.003   0.001   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 7857)
  covalent geometry    : angle       0.56308 (10791)
  hydrogen bonds       : bond        0.03810 (  502)
  hydrogen bonds       : angle       4.13976 ( 1479)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  273 ILE cc_start: 0.7634 (tp) cc_final: 0.7356 (tp)
REVERT: B   84 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7967 (pt)
REVERT: C  168 SER cc_start: 0.8157 (t) cc_final: 0.7855 (p)
REVERT: C  273 ILE cc_start: 0.7860 (tp) cc_final: 0.7544 (tp)
  outliers start: 17
  outliers final: 8
  residues processed: 68
  average time/residue: 0.4279
  time to fit residues: 31.6292
Evaluate side-chains
  66 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain C residue  250 ILE
Chi-restraints excluded: chain C residue  374 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.117674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.102449 restraints weight = 25793.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 2.22
r_work: 0.3106 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2798
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2798 r_free = 0.2798    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2798 r_free = 0.2798    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2798
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.3771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7857  Z= 0.164
  Angle     :  0.575   7.396  10791  Z= 0.286
  Chirality :  0.043   0.122   1275
  Planarity :  0.005   0.043   1314
  Dihedral  :  4.369  15.413   1044
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.26 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.27), residues: 990
  helix:  1.28 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.58 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 223 
 TYR   0.009   0.001   TYR C 123 
 PHE   0.012   0.001   PHE C 287 
 TRP   0.008   0.001   TRP C 170 
 HIS   0.003   0.001   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 7857)
  covalent geometry    : angle       0.57491 (10791)
  hydrogen bonds       : bond        0.03833 (  502)
  hydrogen bonds       : angle       4.14930 ( 1479)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  273 ILE cc_start: 0.7636 (tp) cc_final: 0.7368 (tp)
REVERT: B   84 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7979 (pt)
REVERT: C  168 SER cc_start: 0.8155 (t) cc_final: 0.7857 (p)
REVERT: C  273 ILE cc_start: 0.7869 (tp) cc_final: 0.7553 (tp)
  outliers start: 16
  outliers final: 8
  residues processed: 67
  average time/residue: 0.4265
  time to fit residues: 30.9847
Evaluate side-chains
  67 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  250 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 76 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.118359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.102652 restraints weight = 29695.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 2.41
r_work: 0.3103 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.3811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7857  Z= 0.153
  Angle     :  0.568   7.075  10791  Z= 0.283
  Chirality :  0.042   0.141   1275
  Planarity :  0.005   0.043   1314
  Dihedral  :  4.340  18.749   1044
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 10.74 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.27), residues: 990
  helix:  1.35 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.60 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  63 
 TYR   0.009   0.001   TYR C 123 
 PHE   0.012   0.001   PHE C 287 
 TRP   0.008   0.001   TRP B 339 
 HIS   0.003   0.001   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 7857)
  covalent geometry    : angle       0.56776 (10791)
  hydrogen bonds       : bond        0.03772 (  502)
  hydrogen bonds       : angle       4.10318 ( 1479)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  273 ILE cc_start: 0.7618 (tp) cc_final: 0.7341 (tp)
REVERT: B   84 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7941 (pt)
REVERT: C  273 ILE cc_start: 0.7862 (tp) cc_final: 0.7515 (tp)
  outliers start: 12
  outliers final: 8
  residues processed: 58
  average time/residue: 0.4951
  time to fit residues: 30.9660
Evaluate side-chains
  65 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  208 MET
Chi-restraints excluded: chain C residue  250 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 79 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 11 optimal weight:    0.1980
   chunk 93 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0670
   overall best weight:    0.4118

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.121143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.106524 restraints weight = 21868.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 2.04
r_work: 0.3166 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2867
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2867 r_free = 0.2867    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2867 r_free = 0.2867    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2867
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7857  Z= 0.125
  Angle     :  0.543   7.579  10791  Z= 0.270
  Chirality :  0.041   0.157   1275
  Planarity :  0.005   0.043   1314
  Dihedral  :  4.204  18.975   1044
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 11.11 %
    Favored  : 87.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.27), residues: 990
  helix:  1.48 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.66 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  63 
 TYR   0.008   0.001   TYR B 123 
 PHE   0.010   0.001   PHE C 287 
 TRP   0.011   0.001   TRP B 339 
 HIS   0.002   0.001   HIS C 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 7857)
  covalent geometry    : angle       0.54311 (10791)
  hydrogen bonds       : bond        0.03598 (  502)
  hydrogen bonds       : angle       3.95205 ( 1479)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7941 (pt)
REVERT: A  132 MET cc_start: 0.9007 (ptp) cc_final: 0.8803 (ptt)
REVERT: A  273 ILE cc_start: 0.7582 (tp) cc_final: 0.7284 (tp)
REVERT: B   84 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7817 (pt)
REVERT: C  273 ILE cc_start: 0.7750 (tp) cc_final: 0.7417 (tp)
  outliers start: 11
  outliers final: 8
  residues processed: 60
  average time/residue: 0.4705
  time to fit residues: 30.4945
Evaluate side-chains
  63 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  250 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0980
   chunk 9 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0060
   chunk 80 optimal weight:    0.8980
   chunk 90 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9990
   chunk 78 optimal weight:    0.2980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.3596

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.119887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.104544 restraints weight = 29554.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.34
r_work: 0.3101 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3057
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3057 r_free = 0.3057    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3057 r_free = 0.3057    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3057
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.3916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7857  Z= 0.120
  Angle     :  0.533   6.358  10791  Z= 0.265
  Chirality :  0.041   0.153   1275
  Planarity :  0.005   0.043   1314
  Dihedral  :  4.115  18.200   1044
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 11.23 %
    Favored  : 87.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.27), residues: 990
  helix:  1.58 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.67 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  63 
 TYR   0.008   0.001   TYR C 123 
 PHE   0.010   0.001   PHE C 287 
 TRP   0.012   0.001   TRP B 339 
 HIS   0.002   0.001   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7857)
  covalent geometry    : angle       0.53334 (10791)
  hydrogen bonds       : bond        0.03525 (  502)
  hydrogen bonds       : angle       3.87821 ( 1479)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7942 (pt)
REVERT: A  273 ILE cc_start: 0.7600 (tp) cc_final: 0.7315 (tp)
REVERT: B   84 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7782 (pt)
REVERT: C   84 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8003 (pt)
REVERT: C  273 ILE cc_start: 0.7751 (tp) cc_final: 0.7435 (tp)
  outliers start: 11
  outliers final: 6
  residues processed: 59
  average time/residue: 0.4737
  time to fit residues: 30.2099
Evaluate side-chains
  63 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  250 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0970
   chunk 38 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0870
   chunk 35 optimal weight:    0.0980
   chunk 62 optimal weight:    0.4980
   chunk 93 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.2756

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.121062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.105977 restraints weight = 27607.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.25
r_work: 0.3124 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.3951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7857  Z= 0.114
  Angle     :  0.533   7.680  10791  Z= 0.264
  Chirality :  0.040   0.136   1275
  Planarity :  0.004   0.043   1314
  Dihedral  :  4.061  17.862   1044
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 11.60 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.27), residues: 990
  helix:  1.65 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.73 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  63 
 TYR   0.008   0.001   TYR C 123 
 PHE   0.009   0.001   PHE C 287 
 TRP   0.013   0.001   TRP B 339 
 HIS   0.002   0.001   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7857)
  covalent geometry    : angle       0.53331 (10791)
  hydrogen bonds       : bond        0.03478 (  502)
  hydrogen bonds       : angle       3.83985 ( 1479)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2444.70 seconds
wall clock time: 42 minutes 40.11 seconds (2560.11 seconds total)