Starting phenix.real_space_refine
on Thu Jul 24 19:34:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jnc_22404/07_2025/7jnc_22404.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jnc_22404/07_2025/7jnc_22404.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jnc_22404/07_2025/7jnc_22404.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jnc_22404/07_2025/7jnc_22404.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jnc_22404/07_2025/7jnc_22404.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jnc_22404/07_2025/7jnc_22404.cif"
  }
  resolution = 3.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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      24      5.16       5
     C    4287      2.51       5
     N    1080      2.21       5
     O    1182      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6573
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2121
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 63}
          Link IDs: {'PTRANS': 13, 'TRANS': 273}
          Unresolved non-hydrogen bonds: 218
          Unresolved non-hydrogen angles: 264
          Unresolved non-hydrogen dihedrals: 186
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 118
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Restraints were copied for chains:
    C, B, D, F
  Time building chain proxies: 4.13, per 1000 atoms: 0.63
  Number of scatterers: 6573
  At special positions: 0
  Unit cell: (84.132, 82.08, 126.198, 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      24     16.00
     O    1182      8.00
     N    1080      7.00
     C    4287      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 128 " - pdb=" SG  CYS A 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 128 " - pdb=" SG  CYS C 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 128 " - pdb=" SG  CYS B 149 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 401 " - " ASN A 148 "
      " NAG A 402 " - " ASN A 162 "
      " NAG A 403 " - " ASN A 190 "
      " NAG B 401 " - " ASN B 148 "
      " NAG B 402 " - " ASN B 162 "
      " NAG B 403 " - " ASN B 190 "
      " NAG C 401 " - " ASN C 148 "
      " NAG C 402 " - " ASN C 162 "
      " NAG C 403 " - " ASN C 190 "
      " NAG D   1 " - " ASN A 155 "
      " NAG E   1 " - " ASN B 155 "
      " NAG F   1 " - " ASN C 155 "
  Time building additional restraints: 1.67
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1662

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 12 sheets defined
      37.0% alpha, 22.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 53 through 96
      removed outlier: 4.215A  pdb=" N   PHE A  57 " --> pdb=" O   SER A  53 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   ALA A  60 " --> pdb=" O   ARG A  56 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   CYS A  61 " --> pdb=" O   PHE A  57 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LYS A  95 " --> pdb=" O   ASP A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 212
    Processing helix  chain 'A' and resid 215 through 226
    Processing helix  chain 'A' and resid 297 through 302
      removed outlier: 3.777A  pdb=" N   ASN A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 339
      removed outlier: 3.920A  pdb=" N   THR A 306 " --> pdb=" O   ASN A 302 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA A 308 " --> pdb=" O   TRP A 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 96
      removed outlier: 4.443A  pdb=" N   ALA B  60 " --> pdb=" O   ARG B  56 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   CYS B  61 " --> pdb=" O   PHE B  57 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LYS B  95 " --> pdb=" O   ASP B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 212
    Processing helix  chain 'B' and resid 215 through 226
    Processing helix  chain 'B' and resid 297 through 302
      removed outlier: 3.777A  pdb=" N   ASN B 302 " --> pdb=" O   ILE B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 339
      removed outlier: 3.920A  pdb=" N   THR B 306 " --> pdb=" O   ASN B 302 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA B 308 " --> pdb=" O   TRP B 304 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 96
      removed outlier: 4.442A  pdb=" N   ALA C  60 " --> pdb=" O   ARG C  56 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   CYS C  61 " --> pdb=" O   PHE C  57 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LYS C  95 " --> pdb=" O   ASP C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 212
    Processing helix  chain 'C' and resid 215 through 226
    Processing helix  chain 'C' and resid 297 through 302
      removed outlier: 3.777A  pdb=" N   ASN C 302 " --> pdb=" O   ILE C 298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 339
      removed outlier: 3.920A  pdb=" N   THR C 306 " --> pdb=" O   ASN C 302 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA C 308 " --> pdb=" O   TRP C 304 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 101
      removed outlier: 5.519A  pdb=" N   LEU B 244 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 258
      removed outlier: 5.519A  pdb=" N   LEU A 244 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119
      removed outlier: 4.023A  pdb=" N   ASP A 200 " --> pdb=" O   TYR A 119 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ILE A 199 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   PHE A 232 " --> pdb=" O   ILE A 199 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 131
      removed outlier: 6.383A  pdb=" N   GLN A 186 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   CYS A 128 " --> pdb=" O   PHE A 184 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   PHE A 184 " --> pdb=" O   CYS A 128 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   HIS A 130 " --> pdb=" O   LEU A 182 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LEU A 182 " --> pdb=" O   HIS A 130 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   PHE A 282 " --> pdb=" O   PHE A 236 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LYS A 241 " --> pdb=" O   GLU A 261 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU A 261 " --> pdb=" O   LYS A 241 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 157
      removed outlier: 3.550A  pdb=" N   TYR A 156 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 101
      removed outlier: 5.520A  pdb=" N   LEU C 244 " --> pdb=" O   PHE C 291 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 118 through 119
      removed outlier: 4.023A  pdb=" N   ASP B 200 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ILE B 199 " --> pdb=" O   PHE B 232 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   PHE B 232 " --> pdb=" O   ILE B 199 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 131
      removed outlier: 6.383A  pdb=" N   GLN B 186 " --> pdb=" O   LEU B 126 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   CYS B 128 " --> pdb=" O   PHE B 184 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   PHE B 184 " --> pdb=" O   CYS B 128 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   HIS B 130 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   LEU B 182 " --> pdb=" O   HIS B 130 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   PHE B 282 " --> pdb=" O   PHE B 236 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LYS B 241 " --> pdb=" O   GLU B 261 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLU B 261 " --> pdb=" O   LYS B 241 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 157
      removed outlier: 3.550A  pdb=" N   TYR B 156 " --> pdb=" O   LYS B 166 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 118 through 119
      removed outlier: 4.023A  pdb=" N   ASP C 200 " --> pdb=" O   TYR C 119 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ILE C 199 " --> pdb=" O   PHE C 232 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   PHE C 232 " --> pdb=" O   ILE C 199 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 124 through 131
      removed outlier: 6.383A  pdb=" N   GLN C 186 " --> pdb=" O   LEU C 126 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   CYS C 128 " --> pdb=" O   PHE C 184 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   PHE C 184 " --> pdb=" O   CYS C 128 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   HIS C 130 " --> pdb=" O   LEU C 182 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   LEU C 182 " --> pdb=" O   HIS C 130 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   PHE C 282 " --> pdb=" O   PHE C 236 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LYS C 241 " --> pdb=" O   GLU C 261 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU C 261 " --> pdb=" O   LYS C 241 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 151 through 157
      removed outlier: 3.550A  pdb=" N   TYR C 156 " --> pdb=" O   LYS C 166 " (cutoff:3.500A)

    354 hydrogen bonds defined for protein.
    1035 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: 1.88

  Time building geometry restraints manager: 1.97 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2049
        1.35 -     1.47: 1758
        1.47 -     1.58: 2892
        1.58 -     1.70: 0
        1.70 -     1.82: 36
  Bond restraints: 6735
  Sorted by residual:
  bond pdb=" N   LYS B 319 "
       pdb=" CA  LYS B 319 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.20e-02 6.94e+03 5.52e+00
  bond pdb=" N   LYS C 319 "
       pdb=" CA  LYS C 319 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.20e-02 6.94e+03 5.31e+00
  bond pdb=" N   LYS A 319 "
       pdb=" CA  LYS A 319 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.027 1.20e-02 6.94e+03 5.22e+00
  bond pdb=" N   PHE A 318 "
       pdb=" CA  PHE A 318 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.17e-02 7.31e+03 4.92e+00
  bond pdb=" N   PHE B 318 "
       pdb=" CA  PHE B 318 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.17e-02 7.31e+03 4.87e+00
  ... (remaining 6730 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.09: 8405
        1.09 -     2.19: 619
        2.19 -     3.28: 134
        3.28 -     4.37: 17
        4.37 -     5.47: 20
  Bond angle restraints: 9195
  Sorted by residual:
  angle pdb=" CA  LYS B 319 "
        pdb=" C   LYS B 319 "
        pdb=" O   LYS B 319 "
      ideal   model   delta    sigma   weight residual
     120.90  118.00    2.90 1.07e+00 8.73e-01 7.36e+00
  angle pdb=" CA  LYS A 319 "
        pdb=" C   LYS A 319 "
        pdb=" O   LYS A 319 "
      ideal   model   delta    sigma   weight residual
     120.90  118.00    2.90 1.07e+00 8.73e-01 7.35e+00
  angle pdb=" CA  LYS C 319 "
        pdb=" C   LYS C 319 "
        pdb=" O   LYS C 319 "
      ideal   model   delta    sigma   weight residual
     120.90  118.03    2.87 1.07e+00 8.73e-01 7.19e+00
  angle pdb=" O   PHE B 318 "
        pdb=" C   PHE B 318 "
        pdb=" N   LYS B 319 "
      ideal   model   delta    sigma   weight residual
     122.03  124.55   -2.52 1.04e+00 9.25e-01 5.87e+00
  angle pdb=" O   PHE C 318 "
        pdb=" C   PHE C 318 "
        pdb=" N   LYS C 319 "
      ideal   model   delta    sigma   weight residual
     122.03  124.50   -2.47 1.04e+00 9.25e-01 5.64e+00
  ... (remaining 9190 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.08: 3763
       16.08 -    32.16: 299
       32.16 -    48.24: 66
       48.24 -    64.32: 30
       64.32 -    80.39: 3
  Dihedral angle restraints: 4161
    sinusoidal: 1611
      harmonic: 2550
  Sorted by residual:
  dihedral pdb=" CB  CYS C 128 "
           pdb=" SG  CYS C 128 "
           pdb=" SG  CYS C 149 "
           pdb=" CB  CYS C 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   41.20   51.80     1      1.00e+01 1.00e-02 3.66e+01
  dihedral pdb=" CB  CYS A 128 "
           pdb=" SG  CYS A 128 "
           pdb=" SG  CYS A 149 "
           pdb=" CB  CYS A 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   41.23   51.77     1      1.00e+01 1.00e-02 3.66e+01
  dihedral pdb=" CB  CYS B 128 "
           pdb=" SG  CYS B 128 "
           pdb=" SG  CYS B 149 "
           pdb=" CB  CYS B 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   41.24   51.76     1      1.00e+01 1.00e-02 3.66e+01
  ... (remaining 4158 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 837
       0.047 -    0.094: 224
       0.094 -    0.140: 40
       0.140 -    0.187: 3
       0.187 -    0.234: 3
  Chirality restraints: 1107
  Sorted by residual:
  chirality pdb=" CA  PHE A 318 "
            pdb=" N   PHE A 318 "
            pdb=" C   PHE A 318 "
            pdb=" CB  PHE A 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CA  PHE B 318 "
            pdb=" N   PHE B 318 "
            pdb=" C   PHE B 318 "
            pdb=" CB  PHE B 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  PHE C 318 "
            pdb=" N   PHE C 318 "
            pdb=" C   PHE C 318 "
            pdb=" CB  PHE C 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.33e+00
  ... (remaining 1104 not shown)

  Planarity restraints: 1164
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 232 "   -0.014 2.00e-02 2.50e+03   1.02e-02 1.82e+00
        pdb=" CG  PHE A 232 "    0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 232 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 232 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 232 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 232 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 232 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 232 "    0.014 2.00e-02 2.50e+03   1.02e-02 1.81e+00
        pdb=" CG  PHE B 232 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 232 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 232 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 232 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 232 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 232 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 232 "    0.014 2.00e-02 2.50e+03   1.01e-02 1.79e+00
        pdb=" CG  PHE C 232 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 232 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 232 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 232 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 232 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 232 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1161 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1760
        2.80 -     3.32: 6510
        3.32 -     3.85: 10764
        3.85 -     4.37: 12187
        4.37 -     4.90: 21104
  Nonbonded interactions: 52325
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 174 "
            pdb=" NE1 TRP A 287 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" O   PRO C 174 "
            pdb=" NE1 TRP C 287 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" O   PRO B 174 "
            pdb=" NE1 TRP B 287 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" CG  ARG A 259 "
            pdb=" OE2 GLU B 261 "
     model   vdw
     2.295 3.440
  nonbonded pdb=" CG  ARG B 259 "
            pdb=" OE2 GLU C 261 "
     model   vdw
     2.301 3.440
  ... (remaining 52320 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     19.260
  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:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
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      :  0.005   0.043   6753  Z= 0.236
  Angle     :  0.700   5.468   9246  Z= 0.376
  Chirality :  0.045   0.234   1107
  Planarity :  0.003   0.028   1152
  Dihedral  : 13.562  80.394   2490
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 17.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  6.74 %
    Favored  : 92.75 %
  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: -4.01 (0.24), residues: 855
  helix: -1.00 (0.24), residues: 291
  sheet: -3.58 (0.25), residues: 255
  loop : -3.22 (0.30), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 230 
 HIS   0.001   0.000   HIS C  98 
 PHE   0.022   0.002   PHE A 232 
 TYR   0.015   0.002   TYR A 267 
 ARG   0.002   0.000   ARG B 175 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00444 (   12)
  link_NAG-ASN         : angle       2.02114 (   36)
  link_BETA1-4         : bond        0.00166 (    3)
  link_BETA1-4         : angle       2.69943 (    9)
  hydrogen bonds       : bond        0.18701 (  354)
  hydrogen bonds       : angle       8.13157 ( 1035)
  SS BOND              : bond        0.00161 (    3)
  SS BOND              : angle       2.69178 (    6)
  covalent geometry    : bond        0.00488 ( 6735)
  covalent geometry    : angle       0.68217 ( 9195)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 220
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A  131 HIS cc_start: 0.8117 (m-70) cc_final: 0.7282 (m-70)
REVERT: A  220 MET cc_start: 0.6991 (tpp) cc_final: 0.6719 (tpp)
REVERT: A  286 GLU cc_start: 0.7176 (pt0) cc_final: 0.6612 (pt0)
REVERT: B  286 GLU cc_start: 0.7102 (pt0) cc_final: 0.6692 (pt0)
  outliers start: 3
  outliers final: 0
  residues processed: 220
  average time/residue: 0.1960
  time to fit residues: 55.6023
Evaluate side-chains
  163 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 63 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 42 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0030
   chunk 65 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0980
   chunk 76 optimal weight:    0.7980
   overall best weight:    1.1592

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

Flipped N/Q/H residues before XYZ refinement:
A 186 GLN
B 186 GLN
C  98 HIS
C 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.163306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.142929 restraints weight = 8983.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.143489 restraints weight = 8526.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 14)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.143489 restraints weight = 8266.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3543
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3543 r_free = 0.3543    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6753  Z= 0.184
  Angle     :  0.703  10.177   9246  Z= 0.351
  Chirality :  0.046   0.210   1107
  Planarity :  0.004   0.033   1152
  Dihedral  :  8.631  59.555   1233
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.76 %
    Favored  : 74.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.27), residues: 855
  helix:  0.39 (0.28), residues: 297
  sheet: -3.02 (0.26), residues: 309
  loop : -2.27 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 304 
 HIS   0.003   0.001   HIS C  98 
 PHE   0.030   0.002   PHE B 232 
 TYR   0.015   0.002   TYR A 201 
 ARG   0.010   0.001   ARG C 188 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00394 (   12)
  link_NAG-ASN         : angle       2.73686 (   36)
  link_BETA1-4         : bond        0.00625 (    3)
  link_BETA1-4         : angle       2.02726 (    9)
  hydrogen bonds       : bond        0.03872 (  354)
  hydrogen bonds       : angle       5.61809 ( 1035)
  SS BOND              : bond        0.00108 (    3)
  SS BOND              : angle       0.93986 (    6)
  covalent geometry    : bond        0.00418 ( 6735)
  covalent geometry    : angle       0.68090 ( 9195)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 165
  time to evaluate  : 0.812 
Fit side-chains
REVERT: A  220 MET cc_start: 0.6796 (tpp) cc_final: 0.6433 (tpp)
REVERT: A  318 PHE cc_start: 0.6732 (m-10) cc_final: 0.6494 (m-10)
REVERT: B  153 ARG cc_start: 0.7472 (mtp-110) cc_final: 0.6835 (mmm160)
REVERT: B  188 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7368 (ttm170)
REVERT: B  286 GLU cc_start: 0.7508 (pt0) cc_final: 0.7274 (pt0)
REVERT: B  318 PHE cc_start: 0.7057 (m-10) cc_final: 0.6775 (m-10)
  outliers start: 19
  outliers final: 12
  residues processed: 176
  average time/residue: 0.1726
  time to fit residues: 40.6365
Evaluate side-chains
  160 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 148
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 TYR
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain B residue  132 TYR
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain C residue  317 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 83 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 186 GLN
B 186 GLN
** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.163752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.137927 restraints weight = 9037.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.139833 restraints weight = 7131.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.140724 restraints weight = 6087.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3547
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3547 r_free = 0.3547    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3547 r_free = 0.3547    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3547
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.3610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6753  Z= 0.151
  Angle     :  0.611   6.272   9246  Z= 0.302
  Chirality :  0.043   0.204   1107
  Planarity :  0.003   0.029   1152
  Dihedral  :  7.833  57.296   1233
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  7.43 %
    Allowed  : 19.69 %
    Favored  : 72.88 %
  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: -1.82 (0.28), residues: 855
  helix:  1.10 (0.28), residues: 297
  sheet: -2.74 (0.26), residues: 285
  loop : -1.82 (0.37), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 304 
 HIS   0.001   0.000   HIS A  98 
 PHE   0.020   0.002   PHE C 232 
 TYR   0.021   0.002   TYR B 267 
 ARG   0.005   0.001   ARG A 188 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00646 (   12)
  link_NAG-ASN         : angle       1.79999 (   36)
  link_BETA1-4         : bond        0.00645 (    3)
  link_BETA1-4         : angle       1.82278 (    9)
  hydrogen bonds       : bond        0.03728 (  354)
  hydrogen bonds       : angle       5.26796 ( 1035)
  SS BOND              : bond        0.00093 (    3)
  SS BOND              : angle       0.66763 (    6)
  covalent geometry    : bond        0.00344 ( 6735)
  covalent geometry    : angle       0.59973 ( 9195)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 164
  time to evaluate  : 0.712 
Fit side-chains
REVERT: A  220 MET cc_start: 0.6979 (tpp) cc_final: 0.6631 (tpp)
REVERT: A  249 GLU cc_start: 0.6010 (pt0) cc_final: 0.5762 (pt0)
REVERT: A  318 PHE cc_start: 0.6951 (m-10) cc_final: 0.6655 (m-10)
REVERT: B  152 GLN cc_start: 0.6927 (mp10) cc_final: 0.6586 (tm-30)
REVERT: B  318 PHE cc_start: 0.7060 (m-10) cc_final: 0.6759 (m-10)
REVERT: C  152 GLN cc_start: 0.7230 (mp-120) cc_final: 0.6850 (tm-30)
REVERT: C  188 ARG cc_start: 0.7894 (ttm-80) cc_final: 0.7680 (ttm-80)
  outliers start: 43
  outliers final: 22
  residues processed: 192
  average time/residue: 0.1804
  time to fit residues: 45.6516
Evaluate side-chains
  177 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 155
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 TYR
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 TYR
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain C residue  149 CYS
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain C residue  245 VAL
Chi-restraints excluded: chain C residue  317 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0000
   chunk 65 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0980
   chunk 81 optimal weight:    2.9990
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 130 HIS
B 130 HIS
C 130 HIS
** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.162551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.143338 restraints weight = 9294.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.141453 restraints weight = 8195.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.141217 restraints weight = 9317.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3510
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3510 r_free = 0.3510    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3510 r_free = 0.3510    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3510
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.4169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6753  Z= 0.130
  Angle     :  0.599   8.276   9246  Z= 0.293
  Chirality :  0.043   0.186   1107
  Planarity :  0.003   0.033   1152
  Dihedral  :  7.396  55.249   1233
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  6.91 %
    Allowed  : 21.59 %
    Favored  : 71.50 %
  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: -1.55 (0.28), residues: 855
  helix:  1.20 (0.27), residues: 312
  sheet: -2.59 (0.27), residues: 285
  loop : -1.67 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C 304 
 HIS   0.002   0.001   HIS C 130 
 PHE   0.020   0.001   PHE C 232 
 TYR   0.016   0.002   TYR B 267 
 ARG   0.003   0.000   ARG C 188 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00276 (   12)
  link_NAG-ASN         : angle       1.64335 (   36)
  link_BETA1-4         : bond        0.00515 (    3)
  link_BETA1-4         : angle       1.74000 (    9)
  hydrogen bonds       : bond        0.03422 (  354)
  hydrogen bonds       : angle       5.11723 ( 1035)
  SS BOND              : bond        0.00063 (    3)
  SS BOND              : angle       0.52196 (    6)
  covalent geometry    : bond        0.00293 ( 6735)
  covalent geometry    : angle       0.58961 ( 9195)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 165
  time to evaluate  : 0.691 
Fit side-chains
REVERT: A   72 PHE cc_start: 0.7686 (m-10) cc_final: 0.7453 (m-10)
REVERT: A  220 MET cc_start: 0.7016 (tpp) cc_final: 0.6665 (tpp)
REVERT: A  309 LEU cc_start: 0.7675 (tp) cc_final: 0.7433 (tp)
REVERT: A  318 PHE cc_start: 0.6936 (m-10) cc_final: 0.6620 (m-10)
REVERT: B   94 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6900 (tm-30)
REVERT: B  124 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.6135 (pm20)
REVERT: B  152 GLN cc_start: 0.7009 (mp10) cc_final: 0.6636 (tm-30)
REVERT: B  188 ARG cc_start: 0.8235 (ttm110) cc_final: 0.7460 (ttm-80)
REVERT: B  286 GLU cc_start: 0.7440 (pt0) cc_final: 0.7029 (pt0)
REVERT: B  318 PHE cc_start: 0.6968 (m-10) cc_final: 0.6715 (m-10)
REVERT: C  152 GLN cc_start: 0.7179 (mp-120) cc_final: 0.6739 (tm-30)
REVERT: C  250 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6071 (pt0)
  outliers start: 40
  outliers final: 18
  residues processed: 193
  average time/residue: 0.1912
  time to fit residues: 47.9519
Evaluate side-chains
  183 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 163
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  132 TYR
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain B residue  124 GLN
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 TYR
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  149 CYS
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain C residue  245 VAL
Chi-restraints excluded: chain C residue  250 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 64 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 186 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.161643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.139396 restraints weight = 9219.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.137267 restraints weight = 8238.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.137196 restraints weight = 8991.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3465
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3465
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.4812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   6753  Z= 0.184
  Angle     :  0.660   9.698   9246  Z= 0.319
  Chirality :  0.044   0.166   1107
  Planarity :  0.004   0.033   1152
  Dihedral  :  6.834  52.488   1233
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  7.43 %
    Allowed  : 23.14 %
    Favored  : 69.43 %
  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: -1.40 (0.28), residues: 855
  helix:  1.48 (0.27), residues: 297
  sheet: -2.61 (0.27), residues: 273
  loop : -1.59 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP C 304 
 HIS   0.001   0.001   HIS A  98 
 PHE   0.031   0.002   PHE B 219 
 TYR   0.017   0.002   TYR C 227 
 ARG   0.004   0.001   ARG C 188 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00943 (   12)
  link_NAG-ASN         : angle       2.81902 (   36)
  link_BETA1-4         : bond        0.00653 (    3)
  link_BETA1-4         : angle       1.65992 (    9)
  hydrogen bonds       : bond        0.03581 (  354)
  hydrogen bonds       : angle       5.17267 ( 1035)
  SS BOND              : bond        0.00156 (    3)
  SS BOND              : angle       0.62910 (    6)
  covalent geometry    : bond        0.00418 ( 6735)
  covalent geometry    : angle       0.63530 ( 9195)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 165
  time to evaluate  : 0.717 
Fit side-chains
REVERT: A   75 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7264 (mm)
REVERT: A  220 MET cc_start: 0.7036 (tpp) cc_final: 0.6743 (tpp)
REVERT: A  250 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5648 (pt0)
REVERT: A  309 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7094 (tp)
REVERT: A  318 PHE cc_start: 0.6909 (m-10) cc_final: 0.6606 (m-10)
REVERT: B  124 GLN cc_start: 0.6873 (OUTLIER) cc_final: 0.6284 (pm20)
REVERT: B  152 GLN cc_start: 0.7172 (mp10) cc_final: 0.6754 (tm-30)
REVERT: B  188 ARG cc_start: 0.8173 (ttm110) cc_final: 0.7454 (ttm-80)
REVERT: B  286 GLU cc_start: 0.7685 (pt0) cc_final: 0.7294 (pt0)
REVERT: B  318 PHE cc_start: 0.7081 (m-10) cc_final: 0.6749 (m-10)
REVERT: C  101 MET cc_start: 0.8797 (mtt) cc_final: 0.8577 (mtt)
REVERT: C  152 GLN cc_start: 0.7140 (mp-120) cc_final: 0.6663 (tm-30)
REVERT: C  182 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9103 (pp)
REVERT: C  250 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6295 (pt0)
  outliers start: 43
  outliers final: 29
  residues processed: 197
  average time/residue: 0.2161
  time to fit residues: 54.6654
Evaluate side-chains
  194 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 159
  time to evaluate  : 1.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  132 TYR
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  250 GLU
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  124 GLN
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 TYR
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  149 CYS
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  245 VAL
Chi-restraints excluded: chain C residue  250 GLU
Chi-restraints excluded: chain C residue  317 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 70 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 82 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 44 optimal weight:    0.6980
   chunk 12 optimal weight:    0.2980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** C 152 GLN ** 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 = 0.3794 r_free = 0.3794 target = 0.163004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.142563 restraints weight = 8921.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.143074 restraints weight = 8423.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.143074 restraints weight = 7985.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3538
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3538 r_free = 0.3538    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3538 r_free = 0.3538    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3538
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.5198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6753  Z= 0.137
  Angle     :  0.637  11.036   9246  Z= 0.304
  Chirality :  0.043   0.179   1107
  Planarity :  0.004   0.036   1152
  Dihedral  :  6.449  52.094   1233
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  6.39 %
    Allowed  : 26.42 %
    Favored  : 67.18 %
  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: -1.33 (0.28), residues: 855
  helix:  1.41 (0.27), residues: 312
  sheet: -2.56 (0.27), residues: 279
  loop : -1.50 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 304 
 HIS   0.001   0.000   HIS C 130 
 PHE   0.019   0.001   PHE C 232 
 TYR   0.014   0.001   TYR B 267 
 ARG   0.003   0.000   ARG A 188 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00850 (   12)
  link_NAG-ASN         : angle       2.83794 (   36)
  link_BETA1-4         : bond        0.00413 (    3)
  link_BETA1-4         : angle       1.56787 (    9)
  hydrogen bonds       : bond        0.03355 (  354)
  hydrogen bonds       : angle       4.97330 ( 1035)
  SS BOND              : bond        0.00120 (    3)
  SS BOND              : angle       0.51523 (    6)
  covalent geometry    : bond        0.00307 ( 6735)
  covalent geometry    : angle       0.61153 ( 9195)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 164
  time to evaluate  : 0.947 
Fit side-chains
REVERT: A   75 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7399 (mm)
REVERT: A  220 MET cc_start: 0.7058 (tpp) cc_final: 0.6615 (tpp)
REVERT: A  250 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5616 (pt0)
REVERT: A  309 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.6953 (tp)
REVERT: A  318 PHE cc_start: 0.6837 (m-10) cc_final: 0.6557 (m-10)
REVERT: B  124 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6415 (pm20)
REVERT: B  152 GLN cc_start: 0.7154 (mp10) cc_final: 0.6732 (tm-30)
REVERT: B  188 ARG cc_start: 0.8163 (ttm110) cc_final: 0.7702 (ttm-80)
REVERT: B  318 PHE cc_start: 0.6900 (m-10) cc_final: 0.6589 (m-10)
REVERT: C   75 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7280 (mm)
REVERT: C   94 GLU cc_start: 0.7332 (tm-30) cc_final: 0.7126 (tm-30)
REVERT: C  182 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9043 (pp)
REVERT: C  241 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8669 (mtmm)
REVERT: C  250 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6224 (pt0)
REVERT: C  259 ARG cc_start: 0.7917 (mtp85) cc_final: 0.7673 (mtp85)
  outliers start: 37
  outliers final: 23
  residues processed: 192
  average time/residue: 0.2496
  time to fit residues: 60.3796
Evaluate side-chains
  187 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 156
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  132 TYR
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  250 GLU
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  124 GLN
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 TYR
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  149 CYS
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain C residue  241 LYS
Chi-restraints excluded: chain C residue  245 VAL
Chi-restraints excluded: chain C residue  250 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 27 optimal weight:   10.0000
   chunk 54 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 55 optimal weight:   10.0000
   chunk 44 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3786 r_free = 0.3786 target = 0.162408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.140430 restraints weight = 8957.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.140985 restraints weight = 8296.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.141252 restraints weight = 7904.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3516
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3516 r_free = 0.3516    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3516 r_free = 0.3516    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3516
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.5434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6753  Z= 0.153
  Angle     :  0.643  10.809   9246  Z= 0.308
  Chirality :  0.044   0.206   1107
  Planarity :  0.004   0.035   1152
  Dihedral  :  6.316  52.467   1233
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  7.25 %
    Allowed  : 26.77 %
    Favored  : 65.98 %
  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: -1.25 (0.28), residues: 855
  helix:  1.53 (0.27), residues: 312
  sheet: -2.57 (0.27), residues: 279
  loop : -1.47 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 304 
 HIS   0.001   0.000   HIS B 130 
 PHE   0.033   0.002   PHE A 219 
 TYR   0.013   0.002   TYR B 267 
 ARG   0.002   0.000   ARG C 216 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00766 (   12)
  link_NAG-ASN         : angle       2.68576 (   36)
  link_BETA1-4         : bond        0.00517 (    3)
  link_BETA1-4         : angle       1.53194 (    9)
  hydrogen bonds       : bond        0.03317 (  354)
  hydrogen bonds       : angle       4.92893 ( 1035)
  SS BOND              : bond        0.00124 (    3)
  SS BOND              : angle       0.61095 (    6)
  covalent geometry    : bond        0.00343 ( 6735)
  covalent geometry    : angle       0.62091 ( 9195)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 153
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7320 (mm)
REVERT: A  156 TYR cc_start: 0.8528 (p90) cc_final: 0.8094 (p90)
REVERT: A  220 MET cc_start: 0.7118 (tpp) cc_final: 0.6645 (tpp)
REVERT: A  250 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5674 (pt0)
REVERT: A  309 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.6999 (tp)
REVERT: A  318 PHE cc_start: 0.6875 (m-10) cc_final: 0.6580 (m-10)
REVERT: B  124 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6320 (pm20)
REVERT: B  188 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7662 (ttm-80)
REVERT: B  318 PHE cc_start: 0.6914 (m-10) cc_final: 0.6611 (m-10)
REVERT: C   75 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7276 (mm)
REVERT: C   94 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7279 (tm-30)
REVERT: C  152 GLN cc_start: 0.6990 (mp10) cc_final: 0.6512 (tm-30)
REVERT: C  182 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9037 (pp)
REVERT: C  220 MET cc_start: 0.7282 (ttm) cc_final: 0.6761 (tpp)
REVERT: C  250 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6210 (pt0)
  outliers start: 42
  outliers final: 29
  residues processed: 185
  average time/residue: 0.2485
  time to fit residues: 58.2415
Evaluate side-chains
  185 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 149
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  132 TYR
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  250 GLU
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  124 GLN
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 TYR
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  149 CYS
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  245 VAL
Chi-restraints excluded: chain C residue  250 GLU
Chi-restraints excluded: chain C residue  310 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 75 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   chunk 45 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3767 r_free = 0.3767 target = 0.160672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.135475 restraints weight = 9024.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.136486 restraints weight = 7577.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.137685 restraints weight = 6778.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3502
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3502 r_free = 0.3502    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3502 r_free = 0.3502    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3502
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.5689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6753  Z= 0.179
  Angle     :  0.687  12.998   9246  Z= 0.329
  Chirality :  0.044   0.183   1107
  Planarity :  0.004   0.037   1152
  Dihedral  :  6.640  52.400   1233
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  7.08 %
    Allowed  : 27.46 %
    Favored  : 65.46 %
  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: -1.35 (0.28), residues: 855
  helix:  1.51 (0.27), residues: 312
  sheet: -2.70 (0.26), residues: 297
  loop : -1.37 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 304 
 HIS   0.001   0.001   HIS B  98 
 PHE   0.025   0.002   PHE C 232 
 TYR   0.017   0.002   TYR C 267 
 ARG   0.002   0.000   ARG C 216 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00948 (   12)
  link_NAG-ASN         : angle       2.69132 (   36)
  link_BETA1-4         : bond        0.00478 (    3)
  link_BETA1-4         : angle       1.46759 (    9)
  hydrogen bonds       : bond        0.03390 (  354)
  hydrogen bonds       : angle       4.97525 ( 1035)
  SS BOND              : bond        0.00197 (    3)
  SS BOND              : angle       0.73736 (    6)
  covalent geometry    : bond        0.00402 ( 6735)
  covalent geometry    : angle       0.66665 ( 9195)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 151
  time to evaluate  : 0.916 
Fit side-chains
REVERT: A  156 TYR cc_start: 0.8573 (p90) cc_final: 0.8345 (p90)
REVERT: A  250 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5670 (pt0)
REVERT: A  309 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7052 (tp)
REVERT: A  318 PHE cc_start: 0.6870 (m-10) cc_final: 0.6570 (m-10)
REVERT: B  124 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6450 (pm20)
REVERT: B  188 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7574 (ttm-80)
REVERT: B  318 PHE cc_start: 0.6929 (m-10) cc_final: 0.6606 (m-10)
REVERT: C   75 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7198 (mm)
REVERT: C   94 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7390 (tm-30)
REVERT: C  153 ARG cc_start: 0.7382 (mmm160) cc_final: 0.7132 (mmm160)
REVERT: C  182 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9043 (pp)
REVERT: C  254 GLU cc_start: 0.7725 (pt0) cc_final: 0.7522 (pm20)
REVERT: C  259 ARG cc_start: 0.7806 (mtp85) cc_final: 0.7359 (mtt90)
  outliers start: 41
  outliers final: 31
  residues processed: 182
  average time/residue: 0.2224
  time to fit residues: 51.7051
Evaluate side-chains
  184 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 148
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  132 TYR
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  250 GLU
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  124 GLN
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 TYR
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue  149 CYS
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  245 VAL
Chi-restraints excluded: chain C residue  310 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 18 optimal weight:    0.2980
   chunk 68 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0070
   chunk 11 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 56 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.5598

-------------------------------------------------------------------------------
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 = 0.3801 r_free = 0.3801 target = 0.163721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.145030 restraints weight = 9054.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.142803 restraints weight = 7721.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.142465 restraints weight = 8325.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3534
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3534 r_free = 0.3534    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3534 r_free = 0.3534    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3534
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.5877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6753  Z= 0.135
  Angle     :  0.643  10.497   9246  Z= 0.311
  Chirality :  0.044   0.220   1107
  Planarity :  0.004   0.038   1152
  Dihedral  :  6.073  52.240   1233
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 30.22 %
    Favored  : 64.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.28), residues: 855
  helix:  1.61 (0.27), residues: 312
  sheet: -2.59 (0.27), residues: 297
  loop : -1.22 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 304 
 HIS   0.001   0.000   HIS B 130 
 PHE   0.025   0.001   PHE A 219 
 TYR   0.018   0.001   TYR C 267 
 ARG   0.002   0.000   ARG C 188 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00969 (   12)
  link_NAG-ASN         : angle       3.21246 (   36)
  link_BETA1-4         : bond        0.00374 (    3)
  link_BETA1-4         : angle       1.45561 (    9)
  hydrogen bonds       : bond        0.03298 (  354)
  hydrogen bonds       : angle       4.81023 ( 1035)
  SS BOND              : bond        0.00088 (    3)
  SS BOND              : angle       0.58882 (    6)
  covalent geometry    : bond        0.00307 ( 6735)
  covalent geometry    : angle       0.61048 ( 9195)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 158
  time to evaluate  : 0.711 
Fit side-chains
REVERT: A  250 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5816 (pt0)
REVERT: A  309 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7129 (tp)
REVERT: A  318 PHE cc_start: 0.6816 (m-10) cc_final: 0.6563 (m-10)
REVERT: B  188 ARG cc_start: 0.8225 (ttm110) cc_final: 0.7875 (ttm-80)
REVERT: B  309 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7242 (tp)
REVERT: B  318 PHE cc_start: 0.6888 (m-10) cc_final: 0.6580 (m-10)
REVERT: C   94 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7358 (tm-30)
REVERT: C  182 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8978 (pp)
REVERT: C  259 ARG cc_start: 0.7765 (mtp85) cc_final: 0.7394 (mtt90)
  outliers start: 29
  outliers final: 22
  residues processed: 177
  average time/residue: 0.2319
  time to fit residues: 51.8464
Evaluate side-chains
  179 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 153
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  132 TYR
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  250 GLU
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 TYR
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue  149 CYS
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  245 VAL
Chi-restraints excluded: chain C residue  310 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 4 optimal weight:    0.0970
   chunk 75 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 20 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 = 0.3789 r_free = 0.3789 target = 0.162893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.140320 restraints weight = 9051.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.139995 restraints weight = 8048.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.140208 restraints weight = 7663.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.6043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6753  Z= 0.135
  Angle     :  0.650   8.952   9246  Z= 0.320
  Chirality :  0.044   0.285   1107
  Planarity :  0.004   0.039   1152
  Dihedral  :  6.082  52.752   1233
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 30.92 %
    Favored  : 64.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.06 (0.28), residues: 855
  helix:  1.70 (0.27), residues: 312
  sheet: -2.51 (0.27), residues: 297
  loop : -1.21 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 304 
 HIS   0.001   0.000   HIS C 130 
 PHE   0.021   0.001   PHE A 219 
 TYR   0.019   0.002   TYR C 267 
 ARG   0.002   0.000   ARG C 188 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00301 (   12)
  link_NAG-ASN         : angle       2.10024 (   36)
  link_BETA1-4         : bond        0.00448 (    3)
  link_BETA1-4         : angle       1.40756 (    9)
  hydrogen bonds       : bond        0.03306 (  354)
  hydrogen bonds       : angle       4.79054 ( 1035)
  SS BOND              : bond        0.00077 (    3)
  SS BOND              : angle       0.62058 (    6)
  covalent geometry    : bond        0.00311 ( 6735)
  covalent geometry    : angle       0.63711 ( 9195)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 151
  time to evaluate  : 0.736 
Fit side-chains
REVERT: A   94 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7180 (tm-30)
REVERT: A  152 GLN cc_start: 0.6752 (mp10) cc_final: 0.6492 (tm-30)
REVERT: A  250 GLU cc_start: 0.6275 (OUTLIER) cc_final: 0.5854 (pt0)
REVERT: A  309 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7109 (tp)
REVERT: A  318 PHE cc_start: 0.6827 (m-10) cc_final: 0.6587 (m-10)
REVERT: B  165 VAL cc_start: 0.7257 (OUTLIER) cc_final: 0.6952 (m)
REVERT: B  188 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7840 (ttm-80)
REVERT: B  309 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7258 (tp)
REVERT: B  318 PHE cc_start: 0.6894 (m-10) cc_final: 0.6605 (m-10)
REVERT: C   94 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7366 (tm-30)
REVERT: C  152 GLN cc_start: 0.7053 (tm-30) cc_final: 0.6615 (mp10)
REVERT: C  172 GLN cc_start: 0.8238 (tp-100) cc_final: 0.7908 (tp-100)
REVERT: C  259 ARG cc_start: 0.7808 (mtp85) cc_final: 0.7465 (mtt90)
  outliers start: 26
  outliers final: 19
  residues processed: 170
  average time/residue: 0.2334
  time to fit residues: 49.8146
Evaluate side-chains
  172 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 149
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  250 GLU
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue  149 CYS
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  245 VAL
Chi-restraints excluded: chain C residue  310 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 55 optimal weight:   20.0000
   chunk 10 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
B 266 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.156610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.134276 restraints weight = 9276.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.134374 restraints weight = 8674.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.134986 restraints weight = 8519.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3444
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3444
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.6404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068   6753  Z= 0.299
  Angle     :  0.814  12.581   9246  Z= 0.401
  Chirality :  0.049   0.262   1107
  Planarity :  0.005   0.039   1152
  Dihedral  :  7.043  53.995   1233
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 16.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 29.71 %
    Favored  : 65.11 %
  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: -1.38 (0.28), residues: 855
  helix:  1.62 (0.27), residues: 297
  sheet: -2.74 (0.27), residues: 273
  loop : -1.56 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 304 
 HIS   0.003   0.001   HIS B  98 
 PHE   0.037   0.003   PHE B 232 
 TYR   0.022   0.003   TYR C 111 
 ARG   0.005   0.001   ARG A 216 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01695 (   12)
  link_NAG-ASN         : angle       2.21833 (   36)
  link_BETA1-4         : bond        0.00692 (    3)
  link_BETA1-4         : angle       1.36048 (    9)
  hydrogen bonds       : bond        0.03808 (  354)
  hydrogen bonds       : angle       5.30623 ( 1035)
  SS BOND              : bond        0.00349 (    3)
  SS BOND              : angle       1.18591 (    6)
  covalent geometry    : bond        0.00683 ( 6735)
  covalent geometry    : angle       0.80316 ( 9195)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2794.86 seconds
wall clock time: 49 minutes 36.95 seconds (2976.95 seconds total)