Starting phenix.real_space_refine
on Thu Jun  5 05:31:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qbc_13886/06_2025/7qbc_13886.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qbc_13886/06_2025/7qbc_13886.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qbc_13886/06_2025/7qbc_13886.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qbc_13886/06_2025/7qbc_13886.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qbc_13886/06_2025/7qbc_13886.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qbc_13886/06_2025/7qbc_13886.cif"
  }
  resolution = 3.53
  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=   0.002 sd=   0.088
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      22      5.16       5
     C    3400      2.51       5
     N     728      2.21       5
     O     904      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5054
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2169
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2169
          Classifications: {'peptide': 298}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 8, 'TRANS': 289}
          Unresolved non-hydrogen bonds: 140
          Unresolved non-hydrogen angles: 175
          Unresolved non-hydrogen dihedrals: 113
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 3, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 69
    Chain: "I"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 120
          Classifications: {'peptide': 13}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 10}
    Chain: "K"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 120
          Classifications: {'peptide': 13}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 10}
    Chain: "B"
      Number of atoms: 2169
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2169
          Classifications: {'peptide': 298}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 8, 'TRANS': 289}
          Unresolved non-hydrogen bonds: 140
          Unresolved non-hydrogen angles: 175
          Unresolved non-hydrogen dihedrals: 113
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 3, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 69
    Chain: "A"
      Number of atoms: 238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 238
          Unusual residues: {'NAG': 2, 'Y01': 6}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          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: 238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 238
          Unusual residues: {'NAG': 2, 'Y01': 6}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 3.65, per 1000 atoms: 0.72
  Number of scatterers: 5054
  At special positions: 0
  Unit cell: (75.9, 78.1, 96.8, 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      22     16.00
     O     904      8.00
     N     728      7.00
     C    3400      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: 1.21
  Conformation dependent library (CDL) restraints added in 639.0 milliseconds
  

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1180

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 2 sheets defined
      73.0% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 13
    Processing helix  chain 'A' and resid 37 through 73
      removed outlier: 3.520A  pdb=" N   THR A  48 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE A  53 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   MET A  54 " --> pdb=" O   THR A  50 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   PHE A  55 " --> pdb=" O   GLN A  51 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   VAL A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 103
      removed outlier: 3.583A  pdb=" N   ILE A  82 " --> pdb=" O   THR A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 114
    Processing helix  chain 'A' and resid 116 through 120
    Processing helix  chain 'A' and resid 123 through 154
      removed outlier: 3.865A  pdb=" N   VAL A 136 " --> pdb=" O   ASN A 132 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   SER A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   PHE A 148 " --> pdb=" O   THR A 144 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   VAL A 152 " --> pdb=" O   PHE A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 195
      removed outlier: 3.514A  pdb=" N   GLY A 163 " --> pdb=" O   PHE A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 237
    Processing helix  chain 'A' and resid 244 through 249
      removed outlier: 4.471A  pdb=" N   LEU A 248 " --> pdb=" O   PHE A 244 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ILE A 249 " --> pdb=" O   HIS A 245 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 244 through 249'
    Processing helix  chain 'A' and resid 255 through 266
      removed outlier: 3.731A  pdb=" N   ILE A 263 " --> pdb=" O   SER A 259 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   TYR A 266 " --> pdb=" O   PHE A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 297
      removed outlier: 3.642A  pdb=" N   THR A 279 " --> pdb=" O   ASP A 275 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   THR A 282 " --> pdb=" O   THR A 278 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   LEU A 283 " --> pdb=" O   THR A 279 " (cutoff:3.500A)
      Proline residue:  A 290  - end of helix
    Processing helix  chain 'B' and resid 9 through 13
    Processing helix  chain 'B' and resid 37 through 73
      removed outlier: 3.519A  pdb=" N   THR B  48 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE B  53 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   MET B  54 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   PHE B  55 " --> pdb=" O   GLN B  51 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   VAL B  68 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 103
      removed outlier: 3.583A  pdb=" N   ILE B  82 " --> pdb=" O   THR B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 114
    Processing helix  chain 'B' and resid 116 through 120
    Processing helix  chain 'B' and resid 123 through 154
      removed outlier: 3.864A  pdb=" N   VAL B 136 " --> pdb=" O   ASN B 132 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   SER B 141 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   PHE B 148 " --> pdb=" O   THR B 144 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   VAL B 152 " --> pdb=" O   PHE B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 195
      removed outlier: 3.513A  pdb=" N   GLY B 163 " --> pdb=" O   PHE B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 237
    Processing helix  chain 'B' and resid 244 through 249
      removed outlier: 4.471A  pdb=" N   LEU B 248 " --> pdb=" O   PHE B 244 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ILE B 249 " --> pdb=" O   HIS B 245 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 244 through 249'
    Processing helix  chain 'B' and resid 255 through 266
      removed outlier: 3.732A  pdb=" N   ILE B 263 " --> pdb=" O   SER B 259 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   TYR B 266 " --> pdb=" O   PHE B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 297
      removed outlier: 3.641A  pdb=" N   THR B 279 " --> pdb=" O   ASP B 275 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   THR B 282 " --> pdb=" O   THR B 278 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   LEU B 283 " --> pdb=" O   THR B 279 " (cutoff:3.500A)
      Proline residue:  B 290  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28
      removed outlier: 6.823A  pdb=" N   TYR A  26 " --> pdb=" O   GLY A  33 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   GLY A  33 " --> pdb=" O   TYR A  26 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 28
      removed outlier: 6.823A  pdb=" N   TYR B  26 " --> pdb=" O   GLY B  33 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   GLY B  33 " --> pdb=" O   TYR B  26 " (cutoff:3.500A)

    332 hydrogen bonds defined for protein.
    966 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: 1.31

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 738
        1.31 -     1.44: 1336
        1.44 -     1.56: 3062
        1.56 -     1.69: 14
        1.69 -     1.81: 40
  Bond restraints: 5190
  Sorted by residual:
  bond pdb=" C7  NAG B 501 "
       pdb=" N2  NAG B 501 "
    ideal  model  delta    sigma   weight residual
    1.346  1.454 -0.108 2.00e-02 2.50e+03 2.92e+01
  bond pdb=" C7  NAG A 501 "
       pdb=" N2  NAG A 501 "
    ideal  model  delta    sigma   weight residual
    1.346  1.454 -0.108 2.00e-02 2.50e+03 2.89e+01
  bond pdb=" C7  NAG A 502 "
       pdb=" N2  NAG A 502 "
    ideal  model  delta    sigma   weight residual
    1.346  1.452 -0.106 2.00e-02 2.50e+03 2.83e+01
  bond pdb=" C7  NAG B 502 "
       pdb=" N2  NAG B 502 "
    ideal  model  delta    sigma   weight residual
    1.346  1.451 -0.105 2.00e-02 2.50e+03 2.77e+01
  bond pdb=" C1  NAG A 502 "
       pdb=" O5  NAG A 502 "
    ideal  model  delta    sigma   weight residual
    1.406  1.504 -0.098 2.00e-02 2.50e+03 2.39e+01
  ... (remaining 5185 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 6615
        1.64 -     3.27: 418
        3.27 -     4.91: 98
        4.91 -     6.54: 30
        6.54 -     8.18: 5
  Bond angle restraints: 7166
  Sorted by residual:
  angle pdb=" N   TYR A 181 "
        pdb=" CA  TYR A 181 "
        pdb=" C   TYR A 181 "
      ideal   model   delta    sigma   weight residual
     111.28  105.83    5.45 1.09e+00 8.42e-01 2.50e+01
  angle pdb=" N   TYR B 181 "
        pdb=" CA  TYR B 181 "
        pdb=" C   TYR B 181 "
      ideal   model   delta    sigma   weight residual
     111.28  105.94    5.34 1.09e+00 8.42e-01 2.40e+01
  angle pdb=" N   MET B 294 "
        pdb=" CA  MET B 294 "
        pdb=" C   MET B 294 "
      ideal   model   delta    sigma   weight residual
     113.28  107.62    5.66 1.22e+00 6.72e-01 2.15e+01
  angle pdb=" N   MET A 294 "
        pdb=" CA  MET A 294 "
        pdb=" C   MET A 294 "
      ideal   model   delta    sigma   weight residual
     113.28  107.67    5.61 1.22e+00 6.72e-01 2.12e+01
  angle pdb=" N   MET B  69 "
        pdb=" CA  MET B  69 "
        pdb=" C   MET B  69 "
      ideal   model   delta    sigma   weight residual
     111.28  106.32    4.96 1.09e+00 8.42e-01 2.07e+01
  ... (remaining 7161 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.42: 3284
       15.42 -    30.84: 245
       30.84 -    46.25: 83
       46.25 -    61.67: 34
       61.67 -    77.09: 8
  Dihedral angle restraints: 3654
    sinusoidal: 1828
      harmonic: 1826
  Sorted by residual:
  dihedral pdb=" CA  PHE B  55 "
           pdb=" C   PHE B  55 "
           pdb=" N   GLY B  56 "
           pdb=" CA  GLY B  56 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.45   18.55     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  PHE A  55 "
           pdb=" C   PHE A  55 "
           pdb=" N   GLY A  56 "
           pdb=" CA  GLY A  56 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.50   18.50     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  THR B 144 "
           pdb=" C   THR B 144 "
           pdb=" N   SER B 145 "
           pdb=" CA  SER B 145 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.88   17.12     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 3651 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 650
       0.046 -    0.092: 202
       0.092 -    0.138: 50
       0.138 -    0.184: 12
       0.184 -    0.230: 2
  Chirality restraints: 916
  Sorted by residual:
  chirality pdb=" CB  VAL B 191 "
            pdb=" CA  VAL B 191 "
            pdb=" CG1 VAL B 191 "
            pdb=" CG2 VAL B 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CB  VAL A 191 "
            pdb=" CA  VAL A 191 "
            pdb=" CG1 VAL A 191 "
            pdb=" CG2 VAL A 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  VAL A 191 "
            pdb=" N   VAL A 191 "
            pdb=" C   VAL A 191 "
            pdb=" CB  VAL A 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.27    0.18 2.00e-01 2.50e+01 7.75e-01
  ... (remaining 913 not shown)

  Planarity restraints: 816
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 293 "    0.021 2.00e-02 2.50e+03   4.36e-02 1.90e+01
        pdb=" C   SER A 293 "   -0.075 2.00e-02 2.50e+03
        pdb=" O   SER A 293 "    0.029 2.00e-02 2.50e+03
        pdb=" N   MET A 294 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 293 "   -0.021 2.00e-02 2.50e+03   4.26e-02 1.81e+01
        pdb=" C   SER B 293 "    0.074 2.00e-02 2.50e+03
        pdb=" O   SER B 293 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   MET B 294 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 179 "   -0.020 2.00e-02 2.50e+03   4.11e-02 1.69e+01
        pdb=" C   THR A 179 "    0.071 2.00e-02 2.50e+03
        pdb=" O   THR A 179 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   MET A 180 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 813 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.62: 40
        2.62 -     3.19: 4851
        3.19 -     3.76: 7546
        3.76 -     4.33: 10065
        4.33 -     4.90: 16455
  Nonbonded interactions: 38957
  Sorted by model distance:
  nonbonded pdb=" O   LYS B 100 "
            pdb=" OG  SER B 104 "
     model   vdw
     2.055 3.040
  nonbonded pdb=" O   LYS A 100 "
            pdb=" OG  SER A 104 "
     model   vdw
     2.056 3.040
  nonbonded pdb=" O   LEU B 102 "
            pdb=" OG  SER B 107 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" O   LEU A 102 "
            pdb=" OG  SER A 107 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   ILE A 142 "
            pdb=" OG  SER A 145 "
     model   vdw
     2.210 3.040
  ... (remaining 38952 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'I'
  selection = chain 'K'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.930
  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:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.710
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
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   0.108   5194  Z= 0.394
  Angle     :  0.975   8.181   7178  Z= 0.532
  Chirality :  0.049   0.230    916
  Planarity :  0.007   0.047    812
  Dihedral  : 13.182  77.087   2474
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  0.43 %
    Favored  : 99.15 %
  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: -2.40 (0.31), residues: 614
  helix: -1.04 (0.24), residues: 414
  sheet: -3.35 (1.02), residues: 24
  loop : -2.33 (0.40), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.004   TRP A  70 
 HIS   0.002   0.001   HIS B 126 
 PHE   0.034   0.002   PHE A 262 
 TYR   0.025   0.002   TYR B 193 
 ARG   0.002   0.000   ARG A  58 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00059 (    4)
  link_NAG-ASN         : angle       0.98719 (   12)
  hydrogen bonds       : bond        0.14335 (  332)
  hydrogen bonds       : angle       6.98824 (  966)
  covalent geometry    : bond        0.00790 ( 5190)
  covalent geometry    : angle       0.97480 ( 7166)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 0.485 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1386
  time to fit residues: 20.5694
Evaluate side-chains
  87 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 15 optimal weight:   20.0000
   chunk 30 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 54 optimal weight:    8.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 205 ASN
B 205 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.192040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.162259 restraints weight = 6540.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.166105 restraints weight = 3809.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.168235 restraints weight = 2787.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5194  Z= 0.159
  Angle     :  0.656   7.019   7178  Z= 0.321
  Chirality :  0.042   0.128    916
  Planarity :  0.005   0.061    812
  Dihedral  :  9.377  59.482   1592
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  8.94 %
    Favored  : 89.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.31 (0.34), residues: 614
  helix:  0.72 (0.26), residues: 408
  sheet: -3.05 (1.19), residues: 20
  loop : -1.88 (0.40), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 295 
 HIS   0.001   0.001   HIS A 126 
 PHE   0.029   0.002   PHE B 244 
 TYR   0.014   0.002   TYR B  17 
 ARG   0.001   0.000   ARG A  76 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00185 (    4)
  link_NAG-ASN         : angle       1.56892 (   12)
  hydrogen bonds       : bond        0.04226 (  332)
  hydrogen bonds       : angle       4.48973 (  966)
  covalent geometry    : bond        0.00370 ( 5190)
  covalent geometry    : angle       0.65330 ( 7166)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.554 
Fit side-chains
REVERT: A  111 TYR cc_start: 0.8609 (t80) cc_final: 0.8196 (t80)
REVERT: B  205 ASN cc_start: 0.7556 (OUTLIER) cc_final: 0.7277 (t0)
  outliers start: 6
  outliers final: 3
  residues processed: 110
  average time/residue: 0.1401
  time to fit residues: 20.7846
Evaluate side-chains
  107 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain B residue  149 GLN
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  205 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 35 optimal weight:    0.4980
   chunk 28 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
A 149 GLN
A 205 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.182031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.150875 restraints weight = 6648.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.154302 restraints weight = 4183.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.156476 restraints weight = 3205.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5194  Z= 0.185
  Angle     :  0.646   6.274   7178  Z= 0.320
  Chirality :  0.042   0.123    916
  Planarity :  0.005   0.076    812
  Dihedral  :  9.374  56.071   1592
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 11.28 %
    Favored  : 86.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.34 (0.34), residues: 614
  helix:  1.25 (0.26), residues: 412
  sheet: -2.80 (1.23), residues: 20
  loop : -1.79 (0.42), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 295 
 HIS   0.001   0.000   HIS A  94 
 PHE   0.019   0.001   PHE B  55 
 TYR   0.012   0.002   TYR B  98 
 ARG   0.002   0.000   ARG A  76 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00086 (    4)
  link_NAG-ASN         : angle       1.72323 (   12)
  hydrogen bonds       : bond        0.03906 (  332)
  hydrogen bonds       : angle       4.03769 (  966)
  covalent geometry    : bond        0.00437 ( 5190)
  covalent geometry    : angle       0.64294 ( 7166)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.489 
Fit side-chains
REVERT: A   69 MET cc_start: 0.7767 (mmm) cc_final: 0.7467 (mmm)
REVERT: B   69 MET cc_start: 0.7816 (mmm) cc_final: 0.7411 (mmm)
  outliers start: 11
  outliers final: 6
  residues processed: 115
  average time/residue: 0.1502
  time to fit residues: 22.7359
Evaluate side-chains
  104 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  149 GLN
Chi-restraints excluded: chain B residue  150 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 15 optimal weight:   20.0000
   chunk 17 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 29 optimal weight:    0.4980
   chunk 16 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 149 GLN
A 205 ASN
B  51 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.179718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.147644 restraints weight = 6683.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.151536 restraints weight = 3819.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.153938 restraints weight = 2793.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5194  Z= 0.154
  Angle     :  0.615   7.303   7178  Z= 0.301
  Chirality :  0.041   0.124    916
  Planarity :  0.005   0.076    812
  Dihedral  :  9.436  58.783   1592
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 15.53 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.76 (0.35), residues: 614
  helix:  1.57 (0.26), residues: 412
  sheet: -2.98 (1.11), residues: 20
  loop : -1.57 (0.45), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 295 
 HIS   0.001   0.000   HIS A 126 
 PHE   0.017   0.001   PHE A  55 
 TYR   0.013   0.001   TYR B  98 
 ARG   0.002   0.000   ARG B  76 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00095 (    4)
  link_NAG-ASN         : angle       1.56183 (   12)
  hydrogen bonds       : bond        0.03526 (  332)
  hydrogen bonds       : angle       3.85838 (  966)
  covalent geometry    : bond        0.00364 ( 5190)
  covalent geometry    : angle       0.61260 ( 7166)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.463 
Fit side-chains
REVERT: A  205 ASN cc_start: 0.7725 (OUTLIER) cc_final: 0.7402 (m-40)
REVERT: A  295 TRP cc_start: 0.7831 (t-100) cc_final: 0.7491 (t-100)
  outliers start: 15
  outliers final: 7
  residues processed: 117
  average time/residue: 0.1370
  time to fit residues: 21.5139
Evaluate side-chains
  107 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  149 GLN
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  205 ASN
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  149 GLN
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  173 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 1 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0980
   chunk 7 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 149 GLN
A 205 ASN
B 205 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.180201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.148609 restraints weight = 6629.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.152305 restraints weight = 3921.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.154701 restraints weight = 2915.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5194  Z= 0.136
  Angle     :  0.600   7.324   7178  Z= 0.295
  Chirality :  0.040   0.123    916
  Planarity :  0.005   0.073    812
  Dihedral  :  9.430  59.485   1592
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 18.94 %
    Favored  : 79.15 %
  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:  0.94 (0.35), residues: 614
  helix:  1.71 (0.26), residues: 414
  sheet: -3.01 (1.09), residues: 20
  loop : -1.54 (0.45), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K   3 
 HIS   0.001   0.000   HIS B  94 
 PHE   0.017   0.001   PHE B 262 
 TYR   0.012   0.001   TYR B  98 
 ARG   0.002   0.000   ARG A  76 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00096 (    4)
  link_NAG-ASN         : angle       1.53273 (   12)
  hydrogen bonds       : bond        0.03345 (  332)
  hydrogen bonds       : angle       3.75826 (  966)
  covalent geometry    : bond        0.00324 ( 5190)
  covalent geometry    : angle       0.59680 ( 7166)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.470 
Fit side-chains
REVERT: A  295 TRP cc_start: 0.7787 (t-100) cc_final: 0.7525 (t-100)
REVERT: B  295 TRP cc_start: 0.7829 (t-100) cc_final: 0.7434 (t-100)
  outliers start: 9
  outliers final: 5
  residues processed: 112
  average time/residue: 0.1444
  time to fit residues: 21.5066
Evaluate side-chains
  102 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  149 GLN
Chi-restraints excluded: chain B residue  173 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0040
   chunk 20 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
A 205 ASN
B 205 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.179606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.147087 restraints weight = 6679.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.150932 restraints weight = 3866.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.153321 restraints weight = 2862.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.3380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5194  Z= 0.133
  Angle     :  0.585   7.650   7178  Z= 0.289
  Chirality :  0.039   0.122    916
  Planarity :  0.005   0.070    812
  Dihedral  :  9.408  71.534   1592
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 20.43 %
    Favored  : 77.45 %
  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:  1.16 (0.35), residues: 614
  helix:  1.85 (0.26), residues: 414
  sheet: -3.00 (1.03), residues: 20
  loop : -1.36 (0.47), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  70 
 HIS   0.001   0.000   HIS B  94 
 PHE   0.015   0.001   PHE B 262 
 TYR   0.014   0.001   TYR B  98 
 ARG   0.002   0.000   ARG B  76 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00100 (    4)
  link_NAG-ASN         : angle       1.49034 (   12)
  hydrogen bonds       : bond        0.03260 (  332)
  hydrogen bonds       : angle       3.71328 (  966)
  covalent geometry    : bond        0.00317 ( 5190)
  covalent geometry    : angle       0.58194 ( 7166)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.514 
Fit side-chains
REVERT: A  280 VAL cc_start: 0.8460 (t) cc_final: 0.8163 (t)
REVERT: B   85 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7546 (tt0)
REVERT: B  205 ASN cc_start: 0.7745 (OUTLIER) cc_final: 0.7503 (t0)
REVERT: B  295 TRP cc_start: 0.7800 (t-100) cc_final: 0.7517 (t-100)
  outliers start: 10
  outliers final: 5
  residues processed: 113
  average time/residue: 0.1495
  time to fit residues: 22.6874
Evaluate side-chains
  105 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  149 GLN
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  205 ASN
Chi-restraints excluded: chain B residue  279 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0980
   chunk 39 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0970
   chunk 55 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
A 205 ASN
B 205 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.181064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.148605 restraints weight = 6656.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.152485 restraints weight = 3846.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.155018 restraints weight = 2837.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.3482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5194  Z= 0.124
  Angle     :  0.576   6.973   7178  Z= 0.288
  Chirality :  0.040   0.129    916
  Planarity :  0.005   0.068    812
  Dihedral  :  9.538  75.656   1592
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 20.64 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.35), residues: 614
  helix:  1.91 (0.26), residues: 414
  sheet: -2.88 (1.02), residues: 20
  loop : -1.17 (0.48), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 295 
 HIS   0.001   0.000   HIS K   2 
 PHE   0.016   0.001   PHE B 262 
 TYR   0.014   0.001   TYR B  98 
 ARG   0.001   0.000   ARG B  76 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00107 (    4)
  link_NAG-ASN         : angle       1.42104 (   12)
  hydrogen bonds       : bond        0.03185 (  332)
  hydrogen bonds       : angle       3.66917 (  966)
  covalent geometry    : bond        0.00292 ( 5190)
  covalent geometry    : angle       0.57360 ( 7166)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.458 
Fit side-chains
REVERT: A   85 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7533 (tt0)
REVERT: A  205 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7428 (t0)
REVERT: B   85 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7506 (tt0)
REVERT: B  165 MET cc_start: 0.7386 (ttt) cc_final: 0.7082 (ttp)
REVERT: B  295 TRP cc_start: 0.7759 (t-100) cc_final: 0.7541 (t-100)
  outliers start: 11
  outliers final: 6
  residues processed: 108
  average time/residue: 0.1436
  time to fit residues: 20.6054
Evaluate side-chains
  105 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  205 ASN
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  149 GLN
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  205 ASN
Chi-restraints excluded: chain B residue  279 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 59 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 9 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 149 GLN
A 205 ASN
B  51 GLN
B 205 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.184362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.151772 restraints weight = 6656.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.155531 restraints weight = 3990.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.157698 restraints weight = 2993.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.3577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5194  Z= 0.138
  Angle     :  0.594   8.505   7178  Z= 0.295
  Chirality :  0.040   0.124    916
  Planarity :  0.005   0.068    812
  Dihedral  :  9.444  77.208   1592
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 21.28 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.35), residues: 614
  helix:  1.90 (0.25), residues: 414
  sheet: -2.85 (1.02), residues: 20
  loop : -1.08 (0.48), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 295 
 HIS   0.001   0.000   HIS I   2 
 PHE   0.015   0.001   PHE B 262 
 TYR   0.013   0.001   TYR B  98 
 ARG   0.001   0.000   ARG B  76 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00086 (    4)
  link_NAG-ASN         : angle       1.43560 (   12)
  hydrogen bonds       : bond        0.03198 (  332)
  hydrogen bonds       : angle       3.69803 (  966)
  covalent geometry    : bond        0.00334 ( 5190)
  covalent geometry    : angle       0.59131 ( 7166)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.519 
Fit side-chains
REVERT: A   85 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7641 (tt0)
REVERT: B   85 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7635 (tt0)
REVERT: B  165 MET cc_start: 0.7354 (ttt) cc_final: 0.7051 (ttp)
REVERT: B  295 TRP cc_start: 0.7792 (t-100) cc_final: 0.7565 (t-100)
  outliers start: 13
  outliers final: 8
  residues processed: 112
  average time/residue: 0.1543
  time to fit residues: 22.8189
Evaluate side-chains
  109 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  149 GLN
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  279 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 4 optimal weight:    0.2980
   chunk 15 optimal weight:    8.9990
   chunk 32 optimal weight:    3.9990
   chunk 23 optimal weight:    0.4980
   chunk 38 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 54 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 149 GLN
A 205 ASN
B 205 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.180852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.149797 restraints weight = 6628.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.153330 restraints weight = 3992.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.155708 restraints weight = 3003.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.3715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5194  Z= 0.129
  Angle     :  0.587   8.109   7178  Z= 0.292
  Chirality :  0.040   0.132    916
  Planarity :  0.005   0.064    812
  Dihedral  :  9.200  81.260   1592
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 22.55 %
    Favored  : 75.53 %
  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:  1.37 (0.35), residues: 614
  helix:  1.92 (0.25), residues: 416
  sheet: -2.76 (1.02), residues: 20
  loop : -1.08 (0.49), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 295 
 HIS   0.001   0.000   HIS I   2 
 PHE   0.017   0.001   PHE B  55 
 TYR   0.013   0.001   TYR A  98 
 ARG   0.001   0.000   ARG B  76 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00102 (    4)
  link_NAG-ASN         : angle       1.36807 (   12)
  hydrogen bonds       : bond        0.03165 (  332)
  hydrogen bonds       : angle       3.65952 (  966)
  covalent geometry    : bond        0.00311 ( 5190)
  covalent geometry    : angle       0.58506 ( 7166)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.427 
Fit side-chains
REVERT: B  111 TYR cc_start: 0.8913 (t80) cc_final: 0.8696 (t80)
REVERT: B  165 MET cc_start: 0.7273 (ttt) cc_final: 0.6986 (ttp)
  outliers start: 9
  outliers final: 9
  residues processed: 118
  average time/residue: 0.1438
  time to fit residues: 22.6266
Evaluate side-chains
  113 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  149 GLN
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  205 ASN
Chi-restraints excluded: chain B residue  279 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0570
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
B  51 GLN
** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.184879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.153509 restraints weight = 6639.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.157485 restraints weight = 3734.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.160036 restraints weight = 2712.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.3756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5194  Z= 0.139
  Angle     :  0.609   8.087   7178  Z= 0.301
  Chirality :  0.041   0.129    916
  Planarity :  0.005   0.069    812
  Dihedral  :  9.208  82.396   1592
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 23.19 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.35), residues: 614
  helix:  1.89 (0.25), residues: 416
  sheet: -2.69 (1.03), residues: 20
  loop : -1.07 (0.49), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP B 295 
 HIS   0.001   0.000   HIS K   2 
 PHE   0.016   0.001   PHE B  55 
 TYR   0.013   0.001   TYR B  98 
 ARG   0.001   0.000   ARG B  76 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00077 (    4)
  link_NAG-ASN         : angle       1.38600 (   12)
  hydrogen bonds       : bond        0.03202 (  332)
  hydrogen bonds       : angle       3.69256 (  966)
  covalent geometry    : bond        0.00337 ( 5190)
  covalent geometry    : angle       0.60646 ( 7166)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.500 
Fit side-chains
REVERT: A  104 SER cc_start: 0.8979 (m) cc_final: 0.8720 (p)
REVERT: B   85 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7591 (tt0)
REVERT: B  111 TYR cc_start: 0.8969 (t80) cc_final: 0.8757 (t80)
REVERT: B  165 MET cc_start: 0.7433 (ttt) cc_final: 0.7140 (ttp)
  outliers start: 9
  outliers final: 8
  residues processed: 119
  average time/residue: 0.1527
  time to fit residues: 24.2116
Evaluate side-chains
  116 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  149 GLN
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  279 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 57 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   chunk 39 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 205 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.180431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.148111 restraints weight = 6732.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.152097 restraints weight = 3830.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.154331 restraints weight = 2804.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.3848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5194  Z= 0.142
  Angle     :  0.614   7.896   7178  Z= 0.303
  Chirality :  0.041   0.144    916
  Planarity :  0.005   0.066    812
  Dihedral  :  9.241  82.298   1592
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 23.62 %
    Favored  : 74.26 %
  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:  1.42 (0.35), residues: 614
  helix:  1.94 (0.25), residues: 416
  sheet: -2.71 (1.05), residues: 20
  loop : -1.02 (0.49), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 295 
 HIS   0.000   0.000   HIS A  94 
 PHE   0.018   0.001   PHE B  55 
 TYR   0.020   0.002   TYR B  17 
 ARG   0.001   0.000   ARG A  76 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00127 (    4)
  link_NAG-ASN         : angle       1.37631 (   12)
  hydrogen bonds       : bond        0.03254 (  332)
  hydrogen bonds       : angle       3.65611 (  966)
  covalent geometry    : bond        0.00344 ( 5190)
  covalent geometry    : angle       0.61163 ( 7166)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1753.87 seconds
wall clock time: 31 minutes 26.78 seconds (1886.78 seconds total)