Starting phenix.real_space_refine
on Thu Jun  5 07:28:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qb9_13882/06_2025/7qb9_13882.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qb9_13882/06_2025/7qb9_13882.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qb9_13882/06_2025/7qb9_13882.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qb9_13882/06_2025/7qb9_13882.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qb9_13882/06_2025/7qb9_13882.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qb9_13882/06_2025/7qb9_13882.cif"
  }
  resolution = 3.1
  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=   0.003 sd=   0.119
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      21      5.16       5
     C    3732      2.51       5
     N     732      2.21       5
     O     934      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5419
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2295
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 8, 'TRANS': 290}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 2298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2298
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 8, 'TRANS': 290}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 13
    Chain: "A"
      Number of atoms: 413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 413
          Unusual residues: {'NAG': 2, 'Y01': 11}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
          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: 413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 413
          Unusual residues: {'NAG': 2, 'Y01': 11}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.50, per 1000 atoms: 0.83
  Number of scatterers: 5419
  At special positions: 0
  Unit cell: (81.2736, 83.8134, 100.745, 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      21     16.00
     O     934      8.00
     N     732      7.00
     C    3732      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 501 " - " ASN A  25 "
      " NAG A 502 " - " ASN A  32 "
      " NAG B 501 " - " ASN B  25 "
      " NAG B 502 " - " ASN B  32 "
  Time building additional restraints: 1.50
  Conformation dependent library (CDL) restraints added in 754.9 milliseconds
  

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1136

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 2 sheets defined
      75.3% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 14
      removed outlier: 3.506A  pdb=" N   PHE A  12 " --> pdb=" O   SER A   9 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASP A  14 " --> pdb=" O   LEU A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 73
      removed outlier: 3.638A  pdb=" N   SER A  47 " --> pdb=" O   GLY A  43 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   THR A  48 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE A  53 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   MET A  54 " --> pdb=" O   THR A  50 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   PHE A  55 " --> pdb=" O   GLN A  51 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE A  67 " --> pdb=" O   ALA A  63 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 103
      removed outlier: 3.856A  pdb=" N   LEU A  88 " --> pdb=" O   ASN A  84 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   PHE A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU A 103 " --> pdb=" O   PHE A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 114
    Processing helix  chain 'A' and resid 116 through 120
      removed outlier: 3.600A  pdb=" N   ILE A 120 " --> pdb=" O   PRO A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 154
      removed outlier: 3.806A  pdb=" N   THR A 131 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ASN A 132 " --> pdb=" O   TYR A 128 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ILE A 133 " --> pdb=" O   GLY A 129 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   VAL A 136 " --> pdb=" O   ASN A 132 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   VAL A 152 " --> pdb=" O   PHE A 148 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ILE A 153 " --> pdb=" O   GLN A 149 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   PHE A 154 " --> pdb=" O   ILE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 195
      removed outlier: 4.070A  pdb=" N   THR A 172 " --> pdb=" O   SER A 168 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LEU A 173 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLY A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   VAL A 191 " --> pdb=" O   LYS A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 236
      removed outlier: 3.705A  pdb=" N   PHE A 235 " --> pdb=" O   ARG A 231 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   LEU A 236 " --> pdb=" O   SER A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 251
    Processing helix  chain 'A' and resid 256 through 266
      removed outlier: 3.745A  pdb=" N   PHE A 262 " --> pdb=" O   PRO A 258 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ILE A 263 " --> pdb=" O   SER A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 272
    Processing helix  chain 'A' and resid 273 through 278
      removed outlier: 3.653A  pdb=" N   THR A 278 " --> pdb=" O   THR A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 297
      Proline residue:  A 290  - end of helix
      removed outlier: 3.714A  pdb=" N   MET A 294 " --> pdb=" O   PRO A 290 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   TRP A 295 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   THR A 297 " --> pdb=" O   SER A 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 14
      removed outlier: 3.505A  pdb=" N   PHE B  12 " --> pdb=" O   SER B   9 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASP B  14 " --> pdb=" O   LEU B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 73
      removed outlier: 3.637A  pdb=" N   SER B  47 " --> pdb=" O   GLY B  43 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   THR B  48 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE B  53 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   MET B  54 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   PHE B  55 " --> pdb=" O   GLN B  51 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE B  67 " --> pdb=" O   ALA B  63 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL B  68 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 103
      removed outlier: 3.857A  pdb=" N   LEU B  88 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   PHE B  89 " --> pdb=" O   GLN B  85 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU B 103 " --> pdb=" O   PHE B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 114
    Processing helix  chain 'B' and resid 116 through 120
      removed outlier: 3.601A  pdb=" N   ILE B 120 " --> pdb=" O   PRO B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 154
      removed outlier: 3.806A  pdb=" N   THR B 131 " --> pdb=" O   VAL B 127 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ASN B 132 " --> pdb=" O   TYR B 128 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ILE B 133 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   VAL B 136 " --> pdb=" O   ASN B 132 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   VAL B 152 " --> pdb=" O   PHE B 148 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ILE B 153 " --> pdb=" O   GLN B 149 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   PHE B 154 " --> pdb=" O   ILE B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 195
      removed outlier: 4.069A  pdb=" N   THR B 172 " --> pdb=" O   SER B 168 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LEU B 173 " --> pdb=" O   ILE B 169 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLY B 174 " --> pdb=" O   SER B 170 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   VAL B 191 " --> pdb=" O   LYS B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 236
      removed outlier: 3.668A  pdb=" N   PHE B 235 " --> pdb=" O   ARG B 231 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   LEU B 236 " --> pdb=" O   SER B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 251
    Processing helix  chain 'B' and resid 256 through 266
      removed outlier: 3.746A  pdb=" N   PHE B 262 " --> pdb=" O   PRO B 258 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ILE B 263 " --> pdb=" O   SER B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 272
    Processing helix  chain 'B' and resid 273 through 278
      removed outlier: 3.653A  pdb=" N   THR B 278 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 297
      Proline residue:  B 290  - end of helix
      removed outlier: 3.714A  pdb=" N   MET B 294 " --> pdb=" O   PRO B 290 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   TRP B 295 " --> pdb=" O   LEU B 291 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   THR B 297 " --> pdb=" O   SER B 293 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 28
      removed outlier: 6.507A  pdb=" N   SER A  28 " --> pdb=" O   ASN A  32 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   ASN A  32 " --> pdb=" O   SER A  28 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 28
      removed outlier: 6.507A  pdb=" N   SER B  28 " --> pdb=" O   ASN B  32 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   ASN B  32 " --> pdb=" O   SER B  28 " (cutoff:3.500A)

    290 hydrogen bonds defined for protein.
    852 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: 1.36

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 749
        1.31 -     1.44: 1357
        1.44 -     1.56: 3413
        1.56 -     1.68: 22
        1.68 -     1.81: 38
  Bond restraints: 5579
  Sorted by residual:
  bond pdb=" C7  NAG B 501 "
       pdb=" N2  NAG B 501 "
    ideal  model  delta    sigma   weight residual
    1.346  1.474 -0.128 2.00e-02 2.50e+03 4.10e+01
  bond pdb=" C7  NAG A 501 "
       pdb=" N2  NAG A 501 "
    ideal  model  delta    sigma   weight residual
    1.346  1.474 -0.128 2.00e-02 2.50e+03 4.08e+01
  bond pdb=" C7  NAG A 502 "
       pdb=" N2  NAG A 502 "
    ideal  model  delta    sigma   weight residual
    1.346  1.462 -0.116 2.00e-02 2.50e+03 3.37e+01
  bond pdb=" C7  NAG B 502 "
       pdb=" N2  NAG B 502 "
    ideal  model  delta    sigma   weight residual
    1.346  1.462 -0.116 2.00e-02 2.50e+03 3.34e+01
  bond pdb=" C1  NAG B 502 "
       pdb=" O5  NAG B 502 "
    ideal  model  delta    sigma   weight residual
    1.406  1.510 -0.104 2.00e-02 2.50e+03 2.69e+01
  ... (remaining 5574 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 7140
        1.80 -     3.61: 472
        3.61 -     5.41: 85
        5.41 -     7.21: 16
        7.21 -     9.02: 4
  Bond angle restraints: 7717
  Sorted by residual:
  angle pdb=" N   PHE B 204 "
        pdb=" CA  PHE B 204 "
        pdb=" C   PHE B 204 "
      ideal   model   delta    sigma   weight residual
     111.54  106.03    5.51 1.36e+00 5.41e-01 1.64e+01
  angle pdb=" N   PHE A 204 "
        pdb=" CA  PHE A 204 "
        pdb=" C   PHE A 204 "
      ideal   model   delta    sigma   weight residual
     111.54  106.24    5.30 1.36e+00 5.41e-01 1.52e+01
  angle pdb=" N   PHE B 235 "
        pdb=" CA  PHE B 235 "
        pdb=" C   PHE B 235 "
      ideal   model   delta    sigma   weight residual
     111.28  107.10    4.18 1.09e+00 8.42e-01 1.47e+01
  angle pdb=" N   TYR B 106 "
        pdb=" CA  TYR B 106 "
        pdb=" C   TYR B 106 "
      ideal   model   delta    sigma   weight residual
     113.23  108.60    4.63 1.24e+00 6.50e-01 1.39e+01
  angle pdb=" N   PHE A 235 "
        pdb=" CA  PHE A 235 "
        pdb=" C   PHE A 235 "
      ideal   model   delta    sigma   weight residual
     111.28  107.23    4.05 1.09e+00 8.42e-01 1.38e+01
  ... (remaining 7712 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.26: 3918
       15.26 -    30.52: 345
       30.52 -    45.78: 83
       45.78 -    61.03: 51
       61.03 -    76.29: 4
  Dihedral angle restraints: 4401
    sinusoidal: 2643
      harmonic: 1758
  Sorted by residual:
  dihedral pdb=" CA  ILE A 263 "
           pdb=" C   ILE A 263 "
           pdb=" N   LEU A 264 "
           pdb=" CA  LEU A 264 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.44   19.56     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  ILE B 263 "
           pdb=" C   ILE B 263 "
           pdb=" N   LEU B 264 "
           pdb=" CA  LEU B 264 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.48   19.52     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" N   ASN A  25 "
           pdb=" C   ASN A  25 "
           pdb=" CA  ASN A  25 "
           pdb=" CB  ASN A  25 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  114.48    8.32     0      2.50e+00 1.60e-01 1.11e+01
  ... (remaining 4398 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 883
       0.079 -    0.157: 98
       0.157 -    0.236: 12
       0.236 -    0.314: 5
       0.314 -    0.393: 2
  Chirality restraints: 1000
  Sorted by residual:
  chirality pdb=" CBC Y01 A 513 "
            pdb=" CAR Y01 A 513 "
            pdb=" CAV Y01 A 513 "
            pdb=" OAW Y01 A 513 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.54   -2.15   -0.39 2.00e-01 2.50e+01 3.85e+00
  chirality pdb=" CBC Y01 A 509 "
            pdb=" CAR Y01 A 509 "
            pdb=" CAV Y01 A 509 "
            pdb=" OAW Y01 A 509 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.54   -2.19   -0.36 2.00e-01 2.50e+01 3.16e+00
  chirality pdb=" CA  ASN A  25 "
            pdb=" N   ASN A  25 "
            pdb=" C   ASN A  25 "
            pdb=" CB  ASN A  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.06e+00
  ... (remaining 997 not shown)

  Planarity restraints: 820
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 269 "    0.071 5.00e-02 4.00e+02   1.08e-01 1.85e+01
        pdb=" N   PRO A 270 "   -0.186 5.00e-02 4.00e+02
        pdb=" CA  PRO A 270 "    0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO A 270 "    0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 269 "    0.071 5.00e-02 4.00e+02   1.08e-01 1.85e+01
        pdb=" N   PRO B 270 "   -0.186 5.00e-02 4.00e+02
        pdb=" CA  PRO B 270 "    0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO B 270 "    0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 247 "   -0.020 2.00e-02 2.50e+03   3.92e-02 1.54e+01
        pdb=" C   LEU B 247 "    0.068 2.00e-02 2.50e+03
        pdb=" O   LEU B 247 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   LEU B 248 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 817 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1313
        2.81 -     3.33: 4887
        3.33 -     3.86: 7972
        3.86 -     4.38: 9176
        4.38 -     4.90: 16024
  Nonbonded interactions: 39372
  Sorted by model distance:
  nonbonded pdb=" O   ILE B 175 "
            pdb=" OG1 THR B 179 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   ILE A 175 "
            pdb=" OG1 THR A 179 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   ALA B  61 "
            pdb=" OG1 THR B  65 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   ALA A  61 "
            pdb=" OG1 THR A  65 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   ASN A  46 "
            pdb=" OG1 THR A  50 "
     model   vdw
     2.340 3.040
  ... (remaining 39367 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 5 through 249 or (resid 250 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 251 through 303 or resid 501 through 513))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.410
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.510
  Find NCS groups from input model:        0.180
  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:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.128   5583  Z= 0.430
  Angle     :  1.018   9.016   7729  Z= 0.546
  Chirality :  0.056   0.393   1000
  Planarity :  0.010   0.108    816
  Dihedral  : 12.615  76.292   3265
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  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: -2.92 (0.29), residues: 594
  helix: -1.69 (0.22), residues: 416
  sheet:  None (None), residues: 0
  loop : -2.11 (0.37), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  70 
 HIS   0.004   0.002   HIS B  94 
 PHE   0.042   0.003   PHE A 262 
 TYR   0.025   0.002   TYR B 266 
 ARG   0.003   0.000   ARG A  58 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01418 (    4)
  link_NAG-ASN         : angle       2.92721 (   12)
  hydrogen bonds       : bond        0.13577 (  290)
  hydrogen bonds       : angle       5.42656 (  852)
  covalent geometry    : bond        0.00811 ( 5579)
  covalent geometry    : angle       1.01256 ( 7717)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.582 
Fit side-chains
REVERT: A  218 MET cc_start: 0.8242 (tpt) cc_final: 0.7568 (tpt)
REVERT: B  180 MET cc_start: 0.7601 (tpt) cc_final: 0.7273 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.1925
  time to fit residues: 12.5861
Evaluate side-chains
  42 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 43 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 29 optimal weight:    8.9990
   chunk 23 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.180192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.123916 restraints weight = 5729.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.43
r_work: 0.3276 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.1025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5583  Z= 0.130
  Angle     :  0.553   5.937   7729  Z= 0.275
  Chirality :  0.039   0.281   1000
  Planarity :  0.005   0.065    816
  Dihedral  :  9.668  59.434   2284
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  6.41 %
    Favored  : 92.62 %
  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: -0.52 (0.33), residues: 594
  helix:  0.32 (0.25), residues: 416
  sheet:  None (None), residues: 0
  loop : -1.83 (0.39), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  70 
 HIS   0.004   0.001   HIS B  94 
 PHE   0.024   0.002   PHE B 244 
 TYR   0.019   0.001   TYR B 266 
 ARG   0.003   0.000   ARG B  58 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00548 (    4)
  link_NAG-ASN         : angle       2.44796 (   12)
  hydrogen bonds       : bond        0.06042 (  290)
  hydrogen bonds       : angle       4.01910 (  852)
  covalent geometry    : bond        0.00279 ( 5579)
  covalent geometry    : angle       0.54544 ( 7717)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 2
  residues processed: 50
  average time/residue: 0.1618
  time to fit residues: 11.6647
Evaluate side-chains
  42 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain B residue  190 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.177803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.120109 restraints weight = 5686.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 2.42
r_work: 0.3219 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.1538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5583  Z= 0.129
  Angle     :  0.524   5.433   7729  Z= 0.255
  Chirality :  0.038   0.194   1000
  Planarity :  0.004   0.053    816
  Dihedral  :  9.386  59.663   2284
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  7.96 %
    Favored  : 90.29 %
  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:  0.71 (0.35), residues: 594
  helix:  1.34 (0.27), residues: 408
  sheet:  None (None), residues: 0
  loop : -1.51 (0.41), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  70 
 HIS   0.004   0.001   HIS B  94 
 PHE   0.015   0.002   PHE B  55 
 TYR   0.019   0.001   TYR A 266 
 ARG   0.003   0.000   ARG B  58 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00712 (    4)
  link_NAG-ASN         : angle       1.93469 (   12)
  hydrogen bonds       : bond        0.05808 (  290)
  hydrogen bonds       : angle       3.68429 (  852)
  covalent geometry    : bond        0.00283 ( 5579)
  covalent geometry    : angle       0.51833 ( 7717)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  244 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.5942 (m-80)
  outliers start: 9
  outliers final: 5
  residues processed: 56
  average time/residue: 0.1694
  time to fit residues: 13.0587
Evaluate side-chains
  50 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  244 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.4020 r_free = 0.4020 target = 0.174526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.119949 restraints weight = 5705.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.35
r_work: 0.3188 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5583  Z= 0.127
  Angle     :  0.514   5.062   7729  Z= 0.248
  Chirality :  0.038   0.189   1000
  Planarity :  0.004   0.049    816
  Dihedral  :  9.236  59.876   2284
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  8.93 %
    Favored  : 88.93 %
  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:  1.14 (0.35), residues: 594
  helix:  1.61 (0.27), residues: 416
  sheet:  None (None), residues: 0
  loop : -1.32 (0.43), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  70 
 HIS   0.004   0.001   HIS B  94 
 PHE   0.015   0.001   PHE A  55 
 TYR   0.013   0.001   TYR A 266 
 ARG   0.003   0.000   ARG B  58 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00716 (    4)
  link_NAG-ASN         : angle       2.17786 (   12)
  hydrogen bonds       : bond        0.05730 (  290)
  hydrogen bonds       : angle       3.60097 (  852)
  covalent geometry    : bond        0.00281 ( 5579)
  covalent geometry    : angle       0.50688 ( 7717)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6793 (OUTLIER) cc_final: 0.6041 (m-80)
REVERT: B  228 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6991 (tt)
  outliers start: 11
  outliers final: 6
  residues processed: 56
  average time/residue: 0.1741
  time to fit residues: 13.4421
Evaluate side-chains
  54 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  228 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 50 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0030
   chunk 5 optimal weight:    0.5980
   chunk 48 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.6790

-------------------------------------------------------------------------------
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 = 0.4053 r_free = 0.4053 target = 0.178517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.120325 restraints weight = 5638.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.47
r_work: 0.3193 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5583  Z= 0.109
  Angle     :  0.482   4.981   7729  Z= 0.232
  Chirality :  0.037   0.214   1000
  Planarity :  0.003   0.045    816
  Dihedral  :  8.990  58.184   2284
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 10.29 %
    Favored  : 87.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.36), residues: 594
  helix:  1.93 (0.27), residues: 416
  sheet:  None (None), residues: 0
  loop : -1.25 (0.44), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  70 
 HIS   0.004   0.001   HIS A  94 
 PHE   0.012   0.001   PHE B 244 
 TYR   0.013   0.001   TYR A 266 
 ARG   0.002   0.000   ARG B  58 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00766 (    4)
  link_NAG-ASN         : angle       2.39697 (   12)
  hydrogen bonds       : bond        0.05084 (  290)
  hydrogen bonds       : angle       3.44942 (  852)
  covalent geometry    : bond        0.00228 ( 5579)
  covalent geometry    : angle       0.47333 ( 7717)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6840 (OUTLIER) cc_final: 0.6132 (m-80)
REVERT: B  228 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7041 (tt)
REVERT: B  244 PHE cc_start: 0.6843 (OUTLIER) cc_final: 0.6074 (m-80)
  outliers start: 11
  outliers final: 7
  residues processed: 53
  average time/residue: 0.1464
  time to fit residues: 10.8332
Evaluate side-chains
  55 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  244 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0770
   chunk 36 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.6338

-------------------------------------------------------------------------------
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 = 0.4025 r_free = 0.4025 target = 0.175388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.121030 restraints weight = 5508.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.32
r_work: 0.3239 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5583  Z= 0.105
  Angle     :  0.474   4.950   7729  Z= 0.226
  Chirality :  0.037   0.204   1000
  Planarity :  0.003   0.044    816
  Dihedral  :  8.830  59.855   2284
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  :  9.51 %
    Favored  : 87.77 %
  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:  1.88 (0.36), residues: 594
  helix:  2.22 (0.26), residues: 416
  sheet:  None (None), residues: 0
  loop : -1.19 (0.44), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  70 
 HIS   0.004   0.001   HIS B  94 
 PHE   0.011   0.001   PHE A  55 
 TYR   0.014   0.001   TYR B 266 
 ARG   0.002   0.000   ARG B  58 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00608 (    4)
  link_NAG-ASN         : angle       2.33960 (   12)
  hydrogen bonds       : bond        0.04903 (  290)
  hydrogen bonds       : angle       3.36917 (  852)
  covalent geometry    : bond        0.00218 ( 5579)
  covalent geometry    : angle       0.46551 ( 7717)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6796 (OUTLIER) cc_final: 0.6143 (m-80)
REVERT: B  228 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6914 (tt)
REVERT: B  244 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.6064 (m-80)
  outliers start: 14
  outliers final: 6
  residues processed: 56
  average time/residue: 0.1556
  time to fit residues: 12.1686
Evaluate side-chains
  53 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  244 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0020
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.6190

-------------------------------------------------------------------------------
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 = 0.4052 r_free = 0.4052 target = 0.178629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.120534 restraints weight = 5624.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 2.45
r_work: 0.3232 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5583  Z= 0.105
  Angle     :  0.472   5.154   7729  Z= 0.226
  Chirality :  0.037   0.218   1000
  Planarity :  0.003   0.043    816
  Dihedral  :  8.755  58.669   2284
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 11.26 %
    Favored  : 86.41 %
  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:  2.05 (0.36), residues: 594
  helix:  2.38 (0.26), residues: 416
  sheet:  None (None), residues: 0
  loop : -1.22 (0.44), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  70 
 HIS   0.003   0.001   HIS B  94 
 PHE   0.011   0.001   PHE B 244 
 TYR   0.014   0.001   TYR A 266 
 ARG   0.002   0.000   ARG B  58 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00675 (    4)
  link_NAG-ASN         : angle       2.42093 (   12)
  hydrogen bonds       : bond        0.04852 (  290)
  hydrogen bonds       : angle       3.32472 (  852)
  covalent geometry    : bond        0.00217 ( 5579)
  covalent geometry    : angle       0.46291 ( 7717)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6161 (m-80)
REVERT: B  228 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6921 (tt)
REVERT: B  244 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.6139 (m-80)
  outliers start: 12
  outliers final: 9
  residues processed: 55
  average time/residue: 0.1437
  time to fit residues: 11.1153
Evaluate side-chains
  58 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  244 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0370
   chunk 18 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.6462

-------------------------------------------------------------------------------
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 = 0.4047 r_free = 0.4047 target = 0.178017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.119810 restraints weight = 5657.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 2.46
r_work: 0.3227 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5583  Z= 0.105
  Angle     :  0.471   5.228   7729  Z= 0.225
  Chirality :  0.037   0.190   1000
  Planarity :  0.003   0.043    816
  Dihedral  :  8.670  56.964   2284
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 11.46 %
    Favored  : 86.21 %
  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:  2.19 (0.36), residues: 594
  helix:  2.49 (0.26), residues: 416
  sheet:  None (None), residues: 0
  loop : -1.19 (0.44), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  70 
 HIS   0.003   0.001   HIS B  94 
 PHE   0.011   0.001   PHE B 244 
 TYR   0.015   0.001   TYR A 266 
 ARG   0.001   0.000   ARG A  58 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00632 (    4)
  link_NAG-ASN         : angle       2.47612 (   12)
  hydrogen bonds       : bond        0.04875 (  290)
  hydrogen bonds       : angle       3.31863 (  852)
  covalent geometry    : bond        0.00218 ( 5579)
  covalent geometry    : angle       0.46135 ( 7717)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.6212 (m-80)
REVERT: B  228 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6912 (tt)
REVERT: B  244 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.6159 (m-80)
  outliers start: 12
  outliers final: 9
  residues processed: 54
  average time/residue: 0.1482
  time to fit residues: 11.1724
Evaluate side-chains
  55 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  244 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 15 optimal weight:    0.0970
   chunk 34 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0670
   chunk 19 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.7518

-------------------------------------------------------------------------------
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 = 0.4025 r_free = 0.4025 target = 0.175029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.120660 restraints weight = 5570.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.31
r_work: 0.3218 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5583  Z= 0.113
  Angle     :  0.482   5.209   7729  Z= 0.230
  Chirality :  0.038   0.218   1000
  Planarity :  0.003   0.043    816
  Dihedral  :  8.669  56.346   2284
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 11.46 %
    Favored  : 86.21 %
  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:  2.23 (0.36), residues: 594
  helix:  2.52 (0.26), residues: 416
  sheet:  None (None), residues: 0
  loop : -1.15 (0.44), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  70 
 HIS   0.004   0.001   HIS B  94 
 PHE   0.013   0.001   PHE B 244 
 TYR   0.014   0.001   TYR A 266 
 ARG   0.002   0.000   ARG B  58 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00547 (    4)
  link_NAG-ASN         : angle       1.87890 (   12)
  hydrogen bonds       : bond        0.05186 (  290)
  hydrogen bonds       : angle       3.37117 (  852)
  covalent geometry    : bond        0.00240 ( 5579)
  covalent geometry    : angle       0.47697 ( 7717)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6248 (m-80)
REVERT: B  228 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6912 (tt)
REVERT: B  244 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6033 (m-80)
  outliers start: 12
  outliers final: 9
  residues processed: 56
  average time/residue: 0.1452
  time to fit residues: 11.5508
Evaluate side-chains
  60 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  244 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 47 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4017 r_free = 0.4017 target = 0.174295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.119915 restraints weight = 5635.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.32
r_work: 0.3208 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5583  Z= 0.116
  Angle     :  0.488   5.170   7729  Z= 0.232
  Chirality :  0.038   0.193   1000
  Planarity :  0.003   0.043    816
  Dihedral  :  8.671  56.139   2284
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 11.26 %
    Favored  : 86.41 %
  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:  2.25 (0.36), residues: 594
  helix:  2.51 (0.26), residues: 416
  sheet:  None (None), residues: 0
  loop : -1.09 (0.45), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  70 
 HIS   0.004   0.001   HIS B  94 
 PHE   0.014   0.001   PHE B 244 
 TYR   0.014   0.001   TYR A 266 
 ARG   0.002   0.000   ARG B  58 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00527 (    4)
  link_NAG-ASN         : angle       1.94762 (   12)
  hydrogen bonds       : bond        0.05326 (  290)
  hydrogen bonds       : angle       3.39291 (  852)
  covalent geometry    : bond        0.00254 ( 5579)
  covalent geometry    : angle       0.48180 ( 7717)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.6260 (m-80)
REVERT: B  228 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6889 (tt)
REVERT: B  244 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6151 (m-80)
  outliers start: 12
  outliers final: 9
  residues processed: 56
  average time/residue: 0.1406
  time to fit residues: 11.0887
Evaluate side-chains
  59 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  244 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4025 r_free = 0.4025 target = 0.175559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.117584 restraints weight = 5737.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.47
r_work: 0.3177 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5583  Z= 0.120
  Angle     :  0.496   5.172   7729  Z= 0.235
  Chirality :  0.038   0.197   1000
  Planarity :  0.003   0.043    816
  Dihedral  :  8.707  55.939   2284
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 11.26 %
    Favored  : 86.21 %
  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:  2.22 (0.36), residues: 594
  helix:  2.49 (0.26), residues: 416
  sheet:  None (None), residues: 0
  loop : -1.11 (0.45), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  70 
 HIS   0.004   0.001   HIS B  94 
 PHE   0.013   0.001   PHE A  55 
 TYR   0.015   0.001   TYR A 266 
 ARG   0.002   0.000   ARG B  58 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00484 (    4)
  link_NAG-ASN         : angle       1.84577 (   12)
  hydrogen bonds       : bond        0.05491 (  290)
  hydrogen bonds       : angle       3.43335 (  852)
  covalent geometry    : bond        0.00262 ( 5579)
  covalent geometry    : angle       0.49110 ( 7717)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2762.69 seconds
wall clock time: 49 minutes 21.57 seconds (2961.57 seconds total)