Starting phenix.real_space_refine
on Wed Sep 17 08:22:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hpe_52327/09_2025/9hpe_52327.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hpe_52327/09_2025/9hpe_52327.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hpe_52327/09_2025/9hpe_52327.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hpe_52327/09_2025/9hpe_52327.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hpe_52327/09_2025/9hpe_52327.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hpe_52327/09_2025/9hpe_52327.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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      35      5.16       5
     C    4515      2.51       5
     N    1222      2.21       5
     O    1312      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7084
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 3067
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 375, 3045
          Classifications: {'peptide': 375}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 363}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
      Conformer: "B"
        Number of residues, atoms: 375, 3045
          Classifications: {'peptide': 375}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 363}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
          bond proxies already assigned to first conformer: 3092
    Chain: "C"
      Number of atoms: 3959
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 491, 3948
          Classifications: {'peptide': 491}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 473}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
      Conformer: "B"
        Number of residues, atoms: 491, 3948
          Classifications: {'peptide': 491}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 473}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
          bond proxies already assigned to first conformer: 4022
    Chain: "B"
      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: "C"
      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: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N  AARG B 184 " occ=0.48
      ... (20 atoms not shown)
      pdb=" NH2BARG B 184 " occ=0.52
    residue:
      pdb=" N  AARG B 265 " occ=0.86
      ... (20 atoms not shown)
      pdb=" NH2BARG B 265 " occ=0.14
    residue:
      pdb=" N  AARG C 300 " occ=0.85
      ... (20 atoms not shown)
      pdb=" NH2BARG C 300 " occ=0.15
  Time building chain proxies: 3.16, per 1000 atoms: 0.45
  Number of scatterers: 7084
  At special positions: 0
  Unit cell: (84.252, 100.772, 113.988, 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      35     16.00
     O    1312      8.00
     N    1222      7.00
     C    4515      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  63 " - pdb=" SG  CYS B 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  63 " - pdb=" SG  CYS C 312 " 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
    NAG-ASN
      " NAG B1202 " - " ASN B 238 "
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 581.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1634

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      41.9% alpha, 15.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'B' and resid 16 through 32
    Processing helix  chain 'B' and resid 54 through 68
      removed outlier: 3.546A  pdb=" N   ARG B  68 " --> pdb=" O   SER B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 93
      removed outlier: 3.505A  pdb=" N   LEU B  85 " --> pdb=" O   SER B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 129
    Processing helix  chain 'B' and resid 143 through 157
    Processing helix  chain 'B' and resid 170 through 184
      removed outlier: 3.886A  pdb=" N   PHE B 174 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 208
    Processing helix  chain 'B' and resid 229 through 234
      removed outlier: 3.860A  pdb=" N   HIS B 234 " --> pdb=" O   GLU B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 260
    Processing helix  chain 'B' and resid 276 through 299
      removed outlier: 3.541A  pdb=" N   ALA B 280 " --> pdb=" O   LYS B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 332
    Processing helix  chain 'C' and resid 16 through 32
    Processing helix  chain 'C' and resid 54 through 69
    Processing helix  chain 'C' and resid 81 through 92
    Processing helix  chain 'C' and resid 117 through 129
    Processing helix  chain 'C' and resid 143 through 157
    Processing helix  chain 'C' and resid 170 through 184
      removed outlier: 3.811A  pdb=" N   PHE C 174 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 209
    Processing helix  chain 'C' and resid 223 through 227
      removed outlier: 3.527A  pdb=" N   ILE C 227 " --> pdb=" O   PHE C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 229 through 235
    Processing helix  chain 'C' and resid 249 through 260
    Processing helix  chain 'C' and resid 276 through 299
    Processing helix  chain 'C' and resid 322 through 332
    Processing helix  chain 'C' and resid 425 through 439
    Processing helix  chain 'C' and resid 464 through 471
    Processing helix  chain 'C' and resid 484 through 489
    Processing helix  chain 'C' and resid 746 through 760
    Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 49
      removed outlier: 9.989A  pdb=" N   ALA B  72 " --> pdb=" O   THR B   5 " (cutoff:3.500A)
      removed outlier: 7.412A  pdb=" N   SER B   7 " --> pdb=" O   ALA B  72 " (cutoff:3.500A)
      removed outlier: 8.689A  pdb=" N   PHE B  74 " --> pdb=" O   SER B   7 " (cutoff:3.500A)
      removed outlier: 6.006A  pdb=" N   GLY B   9 " --> pdb=" O   PHE B  74 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 159 through 164
      removed outlier: 6.987A  pdb=" N   PHE B 133 " --> pdb=" O   THR B 161 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   ARG B 163 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   TYR B 135 " --> pdb=" O   ARG B 163 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   LYS B 132 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
      removed outlier: 8.248A  pdb=" N   LEU B 190 " --> pdb=" O   LYS B 132 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   VAL B 134 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   ASP B 192 " --> pdb=" O   VAL B 134 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   LEU B 136 " --> pdb=" O   ASP B 192 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   TYR B 189 " --> pdb=" O   MET B 218 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   PHE B 242 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 334 through 337
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 49
      removed outlier: 10.305A  pdb=" N   ALA C  72 " --> pdb=" O   THR C   5 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   SER C   7 " --> pdb=" O   ALA C  72 " (cutoff:3.500A)
      removed outlier: 8.488A  pdb=" N   PHE C  74 " --> pdb=" O   SER C   7 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   GLY C   9 " --> pdb=" O   PHE C  74 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 159 through 164
      removed outlier: 7.005A  pdb=" N   PHE C 133 " --> pdb=" O   THR C 161 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   ARG C 163 " --> pdb=" O   PHE C 133 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   TYR C 135 " --> pdb=" O   ARG C 163 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   LYS C 132 " --> pdb=" O   ARG C 188 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   LEU C 190 " --> pdb=" O   LYS C 132 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   VAL C 134 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   ASP C 192 " --> pdb=" O   VAL C 134 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LEU C 136 " --> pdb=" O   ASP C 192 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   TYR C 189 " --> pdb=" O   MET C 218 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   PHE C 242 " --> pdb=" O   LEU C 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 335 through 337
    Processing sheet with id=AA7, first strand: chain 'C' and resid 396 through 401
    Processing sheet with id=AA8, first strand: chain 'C' and resid 409 through 410
    Processing sheet with id=AA9, first strand: chain 'C' and resid 454 through 455
      removed outlier: 3.688A  pdb=" N   ALA C 454 " --> pdb=" O   ASN C 463 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 491 through 493

    318 hydrogen bonds defined for protein.
    939 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: 1.25

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2322
        1.34 -     1.46: 1295
        1.46 -     1.57: 3564
        1.57 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 7242
  Sorted by residual:
  bond pdb=" C1  NAG B1202 "
       pdb=" O5  NAG B1202 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.85e+00
  bond pdb=" C1  NAG C1202 "
       pdb=" O5  NAG C1202 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.73e+00
  bond pdb=" C2  NAG C1202 "
       pdb=" N2  NAG C1202 "
    ideal  model  delta    sigma   weight residual
    1.439  1.464 -0.025 2.00e-02 2.50e+03 1.50e+00
  bond pdb=" C1  NAG C1201 "
       pdb=" O5  NAG C1201 "
    ideal  model  delta    sigma   weight residual
    1.406  1.429 -0.023 2.00e-02 2.50e+03 1.38e+00
  bond pdb=" C5  NAG C1201 "
       pdb=" O5  NAG C1201 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.35e+00
  ... (remaining 7237 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 9360
        0.98 -     1.95: 342
        1.95 -     2.93: 82
        2.93 -     3.90: 19
        3.90 -     4.88: 6
  Bond angle restraints: 9809
  Sorted by residual:
  angle pdb=" N   VAL B 362 "
        pdb=" CA  VAL B 362 "
        pdb=" C   VAL B 362 "
      ideal   model   delta    sigma   weight residual
     110.21  107.46    2.75 1.13e+00 7.83e-01 5.94e+00
  angle pdb=" CA  GLU B 269 "
        pdb=" CB  GLU B 269 "
        pdb=" CG  GLU B 269 "
      ideal   model   delta    sigma   weight residual
     114.10  118.76   -4.66 2.00e+00 2.50e-01 5.43e+00
  angle pdb=" N   THR C  36 "
        pdb=" CA  THR C  36 "
        pdb=" CB  THR C  36 "
      ideal   model   delta    sigma   weight residual
     113.65  110.52    3.13 1.47e+00 4.63e-01 4.55e+00
  angle pdb=" C   ARG B  14 "
        pdb=" N   ASN B  15 "
        pdb=" CA  ASN B  15 "
      ideal   model   delta    sigma   weight residual
     122.46  125.30   -2.84 1.41e+00 5.03e-01 4.06e+00
  angle pdb=" C   GLU B 375 "
        pdb=" CA  GLU B 375 "
        pdb=" CB  GLU B 375 "
      ideal   model   delta    sigma   weight residual
     110.81  114.01   -3.20 1.65e+00 3.67e-01 3.76e+00
  ... (remaining 9804 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 3933
       17.93 -    35.87: 335
       35.87 -    53.80: 52
       53.80 -    71.73: 20
       71.73 -    89.67: 5
  Dihedral angle restraints: 4345
    sinusoidal: 1803
      harmonic: 2542
  Sorted by residual:
  dihedral pdb=" CB  CYS C  63 "
           pdb=" SG  CYS C  63 "
           pdb=" SG  CYS C 312 "
           pdb=" CB  CYS C 312 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -155.57   69.57     1      1.00e+01 1.00e-02 6.25e+01
  dihedral pdb=" CB  CYS B  63 "
           pdb=" SG  CYS B  63 "
           pdb=" SG  CYS B 312 "
           pdb=" CB  CYS B 312 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -140.31   54.31     1      1.00e+01 1.00e-02 4.00e+01
  dihedral pdb=" CA  GLU B 375 "
           pdb=" C   GLU B 375 "
           pdb=" N   ARG B 376 "
           pdb=" CA  ARG B 376 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.43  -19.57     0      5.00e+00 4.00e-02 1.53e+01
  ... (remaining 4342 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 695
       0.035 -    0.070: 285
       0.070 -    0.105: 66
       0.105 -    0.140: 29
       0.140 -    0.175: 1
  Chirality restraints: 1076
  Sorted by residual:
  chirality pdb=" C2  NAG C1202 "
            pdb=" C1  NAG C1202 "
            pdb=" C3  NAG C1202 "
            pdb=" N2  NAG C1202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.32   -0.17 2.00e-01 2.50e+01 7.65e-01
  chirality pdb=" CA  VAL B 362 "
            pdb=" N   VAL B 362 "
            pdb=" C   VAL B 362 "
            pdb=" CB  VAL B 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.49e-01
  chirality pdb=" CA  ILE C 239 "
            pdb=" N   ILE C 239 "
            pdb=" C   ILE C 239 "
            pdb=" CB  ILE C 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.86e-01
  ... (remaining 1073 not shown)

  Planarity restraints: 1267
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 320 "    0.014 2.00e-02 2.50e+03   1.22e-02 3.75e+00
        pdb=" CG  TRP B 320 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 320 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 320 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 320 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 320 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 320 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 320 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 320 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 320 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  98 "   -0.026 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO B  99 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B  99 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  99 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 748 "    0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO C 749 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO C 749 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 749 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1264 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 172
        2.71 -     3.26: 6843
        3.26 -     3.81: 11353
        3.81 -     4.35: 14698
        4.35 -     4.90: 25267
  Nonbonded interactions: 58333
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 128 "
            pdb=" OE1 GLU C 359 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" OE1 GLU C 404 "
            pdb=" OH  TYR C 452 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OD2 ASP B 284 "
            pdb=" OG1 THR B 339 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OD2 ASP C 182 "
            pdb=" OH  TYR C 215 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OE2 GLU C  19 "
            pdb=" OG1 THR C 278 "
     model   vdw
     2.276 3.040
  ... (remaining 58328 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.14 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             14.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     10.240
  Find NCS groups from input model:        0.030
  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:9.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7245  Z= 0.126
  Angle     :  0.480   4.879   9816  Z= 0.267
  Chirality :  0.042   0.175   1076
  Planarity :  0.003   0.040   1266
  Dihedral  : 13.776  89.667   2705
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.00 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.29), residues: 859
  helix:  1.92 (0.28), residues: 357
  sheet: -0.94 (0.41), residues: 141
  loop : -0.58 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 141 
 TYR   0.018   0.001   TYR C  45 
 PHE   0.009   0.001   PHE B 293 
 TRP   0.033   0.002   TRP B 320 
 HIS   0.004   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 7242)
  covalent geometry    : angle       0.47786 ( 9809)
  SS BOND              : bond        0.00084 (    2)
  SS BOND              : angle       1.05826 (    4)
  hydrogen bonds       : bond        0.11261 (  318)
  hydrogen bonds       : angle       5.35801 (  939)
  link_NAG-ASN         : bond        0.00286 (    1)
  link_NAG-ASN         : angle       2.55620 (    3)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: B  359 GLU cc_start: 0.7368 (tp30) cc_final: 0.7080 (mm-30)
REVERT: C  155 GLN cc_start: 0.7685 (tt0) cc_final: 0.7421 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.7708
  time to fit residues: 72.2537
Evaluate side-chains
  69 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.0570
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
B 352 ASN
C 185 GLN
C 315 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.111790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.085702 restraints weight = 41912.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 4.19
r_work: 0.2647 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2668
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2668 r_free = 0.2668    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2668 r_free = 0.2668    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2668
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.0845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7245  Z= 0.148
  Angle     :  0.505   9.673   9816  Z= 0.270
  Chirality :  0.043   0.248   1076
  Planarity :  0.004   0.039   1266
  Dihedral  :  5.062  54.483   1050
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  7.16 %
    Favored  : 91.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.29), residues: 859
  helix:  2.02 (0.27), residues: 360
  sheet: -0.94 (0.41), residues: 141
  loop : -0.58 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 231 
 TYR   0.019   0.001   TYR C 295 
 PHE   0.011   0.001   PHE B  23 
 TRP   0.029   0.002   TRP B 320 
 HIS   0.007   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7242)
  covalent geometry    : angle       0.50295 ( 9809)
  SS BOND              : bond        0.00015 (    2)
  SS BOND              : angle       0.96703 (    4)
  hydrogen bonds       : bond        0.03843 (  318)
  hydrogen bonds       : angle       4.46289 (  939)
  link_NAG-ASN         : bond        0.00390 (    1)
  link_NAG-ASN         : angle       2.47799 (    3)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.8038 (t0) cc_final: 0.7792 (t0)
REVERT: C  155 GLN cc_start: 0.8020 (tt0) cc_final: 0.7767 (mt0)
  outliers start: 7
  outliers final: 3
  residues processed: 75
  average time/residue: 0.7105
  time to fit residues: 55.7979
Evaluate side-chains
  71 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain C residue   48 ASP
Chi-restraints excluded: chain C residue  251 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 43 optimal weight:    0.3980
   chunk 38 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
C  15 ASN
C 315 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.108849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.082831 restraints weight = 42723.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.2826 rms_B_bonded: 4.25
r_work: 0.2628 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2629
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2629 r_free = 0.2629    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2629 r_free = 0.2629    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2629
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8781
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7245  Z= 0.176
  Angle     :  0.509   9.644   9816  Z= 0.272
  Chirality :  0.044   0.244   1076
  Planarity :  0.004   0.038   1266
  Dihedral  :  4.814  54.741   1050
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  9.02 %
    Favored  : 89.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.29), residues: 859
  helix:  1.95 (0.27), residues: 361
  sheet: -1.01 (0.41), residues: 141
  loop : -0.62 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 265 
 TYR   0.016   0.002   TYR C  77 
 PHE   0.012   0.002   PHE B 293 
 TRP   0.020   0.002   TRP B 320 
 HIS   0.007   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 7242)
  covalent geometry    : angle       0.50635 ( 9809)
  SS BOND              : bond        0.00059 (    2)
  SS BOND              : angle       0.89700 (    4)
  hydrogen bonds       : bond        0.04010 (  318)
  hydrogen bonds       : angle       4.39681 (  939)
  link_NAG-ASN         : bond        0.00433 (    1)
  link_NAG-ASN         : angle       2.63789 (    3)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.8092 (t0) cc_final: 0.7831 (t0)
REVERT: B  359 GLU cc_start: 0.7261 (mm-30) cc_final: 0.7012 (mm-30)
REVERT: C  155 GLN cc_start: 0.7962 (tt0) cc_final: 0.7706 (mt0)
  outliers start: 9
  outliers final: 5
  residues processed: 73
  average time/residue: 0.7029
  time to fit residues: 53.7364
Evaluate side-chains
  74 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  226 ASP
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  257 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0870
   chunk 56 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 82 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0170
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
C 315 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.112102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.086141 restraints weight = 42981.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 4.23
r_work: 0.2655 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2652
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2652 r_free = 0.2652    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2652 r_free = 0.2652    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2652
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.1110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7245  Z= 0.121
  Angle     :  0.468   9.623   9816  Z= 0.251
  Chirality :  0.042   0.242   1076
  Planarity :  0.004   0.039   1266
  Dihedral  :  4.500  55.339   1050
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  9.28 %
    Favored  : 89.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.29), residues: 859
  helix:  2.13 (0.27), residues: 361
  sheet: -1.01 (0.41), residues: 141
  loop : -0.58 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 265 
 TYR   0.015   0.001   TYR C 295 
 PHE   0.010   0.001   PHE B  23 
 TRP   0.017   0.001   TRP B 259 
 HIS   0.004   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7242)
  covalent geometry    : angle       0.46584 ( 9809)
  SS BOND              : bond        0.00027 (    2)
  SS BOND              : angle       0.82705 (    4)
  hydrogen bonds       : bond        0.03489 (  318)
  hydrogen bonds       : angle       4.20817 (  939)
  link_NAG-ASN         : bond        0.00206 (    1)
  link_NAG-ASN         : angle       2.48900 (    3)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.7958 (t0) cc_final: 0.7700 (t0)
REVERT: B  359 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6937 (mm-30)
REVERT: C  155 GLN cc_start: 0.7913 (tt0) cc_final: 0.7700 (mt0)
  outliers start: 11
  outliers final: 3
  residues processed: 79
  average time/residue: 0.6686
  time to fit residues: 55.2498
Evaluate side-chains
  74 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  226 ASP
Chi-restraints excluded: chain C residue   48 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 45 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0770
   chunk 5 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0870
   overall best weight:    0.5116

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
B 253 GLN
C  15 ASN
C 283 HIS
C 315 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.110442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.084236 restraints weight = 48845.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.2885 rms_B_bonded: 4.56
r_work: 0.2678 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2676
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2676
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8768
moved from start:          0.1156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7245  Z= 0.127
  Angle     :  0.468   9.635   9816  Z= 0.251
  Chirality :  0.042   0.247   1076
  Planarity :  0.004   0.041   1266
  Dihedral  :  4.446  55.341   1050
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  9.95 %
    Favored  : 88.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.29), residues: 859
  helix:  2.20 (0.27), residues: 361
  sheet: -1.03 (0.42), residues: 140
  loop : -0.54 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 231 
 TYR   0.012   0.001   TYR C  77 
 PHE   0.011   0.001   PHE B  23 
 TRP   0.017   0.001   TRP B 320 
 HIS   0.005   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7242)
  covalent geometry    : angle       0.46588 ( 9809)
  SS BOND              : bond        0.00037 (    2)
  SS BOND              : angle       0.73237 (    4)
  hydrogen bonds       : bond        0.03523 (  318)
  hydrogen bonds       : angle       4.16703 (  939)
  link_NAG-ASN         : bond        0.00269 (    1)
  link_NAG-ASN         : angle       2.44406 (    3)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.8040 (t0) cc_final: 0.7763 (t0)
REVERT: B  359 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6948 (mm-30)
  outliers start: 7
  outliers final: 4
  residues processed: 78
  average time/residue: 0.6790
  time to fit residues: 55.4448
Evaluate side-chains
  74 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  226 ASP
Chi-restraints excluded: chain C residue   48 ASP
Chi-restraints excluded: chain C residue  229 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 50 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0870
   chunk 29 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0980
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
B 253 GLN
C 315 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.111344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.085578 restraints weight = 34174.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.2908 rms_B_bonded: 3.86
r_work: 0.2722 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2720
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2720
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.1203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7245  Z= 0.112
  Angle     :  0.454   9.626   9816  Z= 0.244
  Chirality :  0.042   0.246   1076
  Planarity :  0.003   0.041   1266
  Dihedral  :  4.372  55.525   1050
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 10.34 %
    Favored  : 88.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.29), residues: 859
  helix:  2.28 (0.27), residues: 362
  sheet: -0.93 (0.42), residues: 141
  loop : -0.53 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 231 
 TYR   0.011   0.001   TYR C  45 
 PHE   0.010   0.001   PHE B  23 
 TRP   0.016   0.001   TRP B 259 
 HIS   0.004   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7242)
  covalent geometry    : angle       0.45250 ( 9809)
  SS BOND              : bond        0.00030 (    2)
  SS BOND              : angle       0.70922 (    4)
  hydrogen bonds       : bond        0.03348 (  318)
  hydrogen bonds       : angle       4.07595 (  939)
  link_NAG-ASN         : bond        0.00180 (    1)
  link_NAG-ASN         : angle       2.36922 (    3)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.8016 (t0) cc_final: 0.7721 (t0)
REVERT: B  230 GLU cc_start: 0.8370 (tp30) cc_final: 0.7924 (mp0)
REVERT: B  359 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6908 (mm-30)
  outliers start: 10
  outliers final: 5
  residues processed: 79
  average time/residue: 0.6769
  time to fit residues: 56.0965
Evaluate side-chains
  75 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  226 ASP
Chi-restraints excluded: chain C residue   48 ASP
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  251 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 64 optimal weight:    0.3980
   chunk 52 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0970
   chunk 51 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
B 253 GLN
C  15 ASN
C 315 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.110673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.084590 restraints weight = 45622.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.2890 rms_B_bonded: 4.45
r_work: 0.2688 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2685
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2685
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.1237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7245  Z= 0.130
  Angle     :  0.473   9.636   9816  Z= 0.252
  Chirality :  0.042   0.249   1076
  Planarity :  0.004   0.042   1266
  Dihedral  :  4.399  55.346   1050
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 10.61 %
    Favored  : 88.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.29), residues: 859
  helix:  2.25 (0.27), residues: 362
  sheet: -0.95 (0.41), residues: 141
  loop : -0.57 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 231 
 TYR   0.017   0.001   TYR C 432 
 PHE   0.011   0.001   PHE B  23 
 TRP   0.016   0.001   TRP B 259 
 HIS   0.005   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7242)
  covalent geometry    : angle       0.47067 ( 9809)
  SS BOND              : bond        0.00047 (    2)
  SS BOND              : angle       0.68179 (    4)
  hydrogen bonds       : bond        0.03500 (  318)
  hydrogen bonds       : angle       4.08994 (  939)
  link_NAG-ASN         : bond        0.00274 (    1)
  link_NAG-ASN         : angle       2.43711 (    3)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.8043 (t0) cc_final: 0.7730 (t0)
REVERT: B  359 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6973 (mm-30)
REVERT: C   38 GLU cc_start: 0.8051 (pm20) cc_final: 0.7812 (pm20)
  outliers start: 9
  outliers final: 7
  residues processed: 79
  average time/residue: 0.6888
  time to fit residues: 57.0135
Evaluate side-chains
  79 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  226 ASP
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain C residue   48 ASP
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  251 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 66 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
B 253 GLN
C 315 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.109874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.083815 restraints weight = 42630.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 4.21
r_work: 0.2704 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2683
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2683
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8768
moved from start:          0.1280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7245  Z= 0.146
  Angle     :  0.493   9.649   9816  Z= 0.262
  Chirality :  0.043   0.252   1076
  Planarity :  0.004   0.042   1266
  Dihedral  :  4.489  55.310   1050
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 10.74 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.29), residues: 859
  helix:  2.22 (0.27), residues: 362
  sheet: -1.01 (0.41), residues: 140
  loop : -0.55 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 231 
 TYR   0.016   0.001   TYR C 432 
 PHE   0.011   0.001   PHE B 293 
 TRP   0.017   0.001   TRP B 320 
 HIS   0.006   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 7242)
  covalent geometry    : angle       0.49065 ( 9809)
  SS BOND              : bond        0.00056 (    2)
  SS BOND              : angle       0.69447 (    4)
  hydrogen bonds       : bond        0.03629 (  318)
  hydrogen bonds       : angle       4.12798 (  939)
  link_NAG-ASN         : bond        0.00241 (    1)
  link_NAG-ASN         : angle       2.49484 (    3)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.8041 (t0) cc_final: 0.7743 (t0)
REVERT: C   38 GLU cc_start: 0.8015 (pm20) cc_final: 0.7797 (pm20)
  outliers start: 11
  outliers final: 5
  residues processed: 78
  average time/residue: 0.6963
  time to fit residues: 56.8637
Evaluate side-chains
  75 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  226 ASP
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  257 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 81 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
B 253 GLN
C  15 ASN
C 315 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.109160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.083073 restraints weight = 46473.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 4.48
r_work: 0.2664 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2623
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2623 r_free = 0.2623    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2623 r_free = 0.2623    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2623
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8779
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7245  Z= 0.163
  Angle     :  0.519  12.980   9816  Z= 0.273
  Chirality :  0.043   0.256   1076
  Planarity :  0.004   0.043   1266
  Dihedral  :  4.572  55.242   1050
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 11.27 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.29), residues: 859
  helix:  2.15 (0.27), residues: 362
  sheet: -1.06 (0.41), residues: 140
  loop : -0.58 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 231 
 TYR   0.017   0.001   TYR C 432 
 PHE   0.012   0.001   PHE B 293 
 TRP   0.018   0.002   TRP B 320 
 HIS   0.006   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 7242)
  covalent geometry    : angle       0.51660 ( 9809)
  SS BOND              : bond        0.00076 (    2)
  SS BOND              : angle       0.72650 (    4)
  hydrogen bonds       : bond        0.03784 (  318)
  hydrogen bonds       : angle       4.17910 (  939)
  link_NAG-ASN         : bond        0.00338 (    1)
  link_NAG-ASN         : angle       2.56659 (    3)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.8077 (t0) cc_final: 0.7775 (t0)
  outliers start: 6
  outliers final: 5
  residues processed: 75
  average time/residue: 0.7223
  time to fit residues: 56.6590
Evaluate side-chains
  75 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  226 ASP
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  257 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 66 optimal weight:    0.0040
   chunk 52 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 81 optimal weight:    0.0570
   chunk 78 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0980
   chunk 2 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 76 optimal weight:    0.5980
   overall best weight:    0.3110

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

Flipped N/Q/H residues before XYZ refinement:
B  42 HIS
B 157 ASN
B 253 GLN
C 315 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.111851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.086060 restraints weight = 45216.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 4.35
r_work: 0.2742 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2720
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2720
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8734
moved from start:          0.1326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7245  Z= 0.104
  Angle     :  0.487  12.780   9816  Z= 0.257
  Chirality :  0.042   0.247   1076
  Planarity :  0.004   0.041   1266
  Dihedral  :  4.394  55.675   1050
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 11.80 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.29), residues: 859
  helix:  2.33 (0.27), residues: 362
  sheet: -0.92 (0.41), residues: 141
  loop : -0.53 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 231 
 TYR   0.016   0.001   TYR C 432 
 PHE   0.009   0.001   PHE B 293 
 TRP   0.017   0.001   TRP B 259 
 HIS   0.003   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 7242)
  covalent geometry    : angle       0.48560 ( 9809)
  SS BOND              : bond        0.00019 (    2)
  SS BOND              : angle       0.67571 (    4)
  hydrogen bonds       : bond        0.03217 (  318)
  hydrogen bonds       : angle       4.01816 (  939)
  link_NAG-ASN         : bond        0.00101 (    1)
  link_NAG-ASN         : angle       2.33487 (    3)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.8002 (t0) cc_final: 0.7702 (t0)
REVERT: B  230 GLU cc_start: 0.8433 (tp30) cc_final: 0.7940 (mp0)
  outliers start: 3
  outliers final: 1
  residues processed: 76
  average time/residue: 0.6788
  time to fit residues: 53.9585
Evaluate side-chains
  72 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  232 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0670
   chunk 10 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 85 optimal weight:    0.1980
   chunk 33 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0040
   overall best weight:    0.3530

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
B 253 GLN
C 315 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.111868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.086454 restraints weight = 36747.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.2920 rms_B_bonded: 3.87
r_work: 0.2733 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2713
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2713 r_free = 0.2713    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2713 r_free = 0.2713    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2713
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8738
moved from start:          0.1333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7245  Z= 0.108
  Angle     :  0.485  12.937   9816  Z= 0.255
  Chirality :  0.042   0.250   1076
  Planarity :  0.004   0.045   1266
  Dihedral  :  4.330  55.492   1050
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 11.94 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.29), residues: 859
  helix:  2.37 (0.27), residues: 362
  sheet: -0.92 (0.41), residues: 141
  loop : -0.51 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 231 
 TYR   0.013   0.001   TYR C  45 
 PHE   0.009   0.001   PHE B  23 
 TRP   0.017   0.001   TRP B 259 
 HIS   0.004   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 7242)
  covalent geometry    : angle       0.48305 ( 9809)
  SS BOND              : bond        0.00031 (    2)
  SS BOND              : angle       0.64962 (    4)
  hydrogen bonds       : bond        0.03253 (  318)
  hydrogen bonds       : angle       3.98148 (  939)
  link_NAG-ASN         : bond        0.00190 (    1)
  link_NAG-ASN         : angle       2.33337 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2706.20 seconds
wall clock time: 46 minutes 57.90 seconds (2817.90 seconds total)