Starting phenix.real_space_refine
on Wed Jul 23 17:45:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7soa_25264/07_2025/7soa_25264.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7soa_25264/07_2025/7soa_25264.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/7soa_25264/07_2025/7soa_25264.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7soa_25264/07_2025/7soa_25264.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7soa_25264/07_2025/7soa_25264.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7soa_25264/07_2025/7soa_25264.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=  -0.002 sd=   0.112
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      15      5.16       5
     C    2476      2.51       5
     N     620      2.21       5
     O     739      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3850
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "L"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 832
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 940
          Classifications: {'peptide': 121}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 1994
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 1994
          Classifications: {'peptide': 249}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 14, 'TRANS': 234}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 31
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 5.22, per 1000 atoms: 1.36
  Number of scatterers: 3850
  At special positions: 0
  Unit cell: (63.225, 85.143, 76.713, 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      15     16.00
     O     739      8.00
     N     620      7.00
     C    2476      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 164 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 289 " - pdb=" SG  CYS A 299 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG A1301 " - " ASN A  61 "
      " NAG A1302 " - " ASN A 280 "
      " NAG A1303 " - " ASN A 163 "
      " NAG A1304 " - " ASN A 232 "
      " NAG B   1 " - " ASN A 122 "
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 447.8 milliseconds
  

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  888

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 10 sheets defined
      4.2% alpha, 55.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'A' and resid 292 through 301
    Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.970A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER L  67 " --> pdb=" O   ASP L  70 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.557A  pdb=" N   LEU L  11 " --> pdb=" O   ASP L 105 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   GLN L  37 " --> pdb=" O   LEU L  46 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   LEU L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.557A  pdb=" N   LEU L  11 " --> pdb=" O   ASP L 105 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.681A  pdb=" N   MET H  34 " --> pdb=" O   PHE H  50 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   PHE H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AA7, first strand: chain 'A' and resid 27 through 31
      removed outlier: 3.826A  pdb=" N   SER A  60 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
      removed outlier: 8.688A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 267 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   TYR A 267 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ALA A 262 " --> pdb=" O   THR A  95 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   THR A  95 " --> pdb=" O   ALA A 262 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   PHE A 199 " --> pdb=" O   ASP A 226 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   ASP A 226 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   ILE A 201 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 47 through 55
      removed outlier: 7.386A  pdb=" N   THR A 272 " --> pdb=" O   ASP A 288 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   ASP A 288 " --> pdb=" O   THR A 272 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   LEU A 274 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   ALA A 286 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   LYS A 276 " --> pdb=" O   THR A 284 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 85
      removed outlier: 6.990A  pdb=" N   ARG A 235 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   PHE A 106 " --> pdb=" O   ARG A 235 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   GLN A 237 " --> pdb=" O   TRP A 104 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   TRP A 104 " --> pdb=" O   GLN A 237 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   LEU A 239 " --> pdb=" O   ARG A 102 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ARG A 102 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   VAL A 126 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   TYR A 168 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ILE A 128 " --> pdb=" O   PHE A 166 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   PHE A 166 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   VAL A 130 " --> pdb=" O   CYS A 164 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   CYS A 164 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   SER A 160 " --> pdb=" O   GLN A 134 " (cutoff:3.500A)
      removed outlier: 5.830A  pdb=" N   CYS A 136 " --> pdb=" O   TYR A 158 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   TYR A 158 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   ASP A 138 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   GLY A 156 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 84 through 85
      removed outlier: 13.614A  pdb=" N   PHE A 236 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 13.010A  pdb=" N   ASN A 137 " --> pdb=" O   PHE A 236 " (cutoff:3.500A)
      removed outlier: 10.215A  pdb=" N   THR A 238 " --> pdb=" O   ASN A 137 " (cutoff:3.500A)
      removed outlier: 4.936A  pdb=" N   LEU A 240 " --> pdb=" O   PRO A 139 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   VAL A 126 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   TYR A 168 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ILE A 128 " --> pdb=" O   PHE A 166 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   PHE A 166 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   VAL A 130 " --> pdb=" O   CYS A 164 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   CYS A 164 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   SER A 160 " --> pdb=" O   GLN A 134 " (cutoff:3.500A)
      removed outlier: 5.830A  pdb=" N   CYS A 136 " --> pdb=" O   TYR A 158 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   TYR A 158 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   ASP A 138 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   GLY A 156 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)

    151 hydrogen bonds defined for protein.
    369 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: 1.23

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 722
        1.33 -     1.45: 1076
        1.45 -     1.57: 2128
        1.57 -     1.70: 2
        1.70 -     1.82: 20
  Bond restraints: 3948
  Sorted by residual:
  bond pdb=" CA  SER A  31 "
       pdb=" CB  SER A  31 "
    ideal  model  delta    sigma   weight residual
    1.524  1.469  0.055 1.30e-02 5.92e+03 1.79e+01
  bond pdb=" CA  SER A 155 "
       pdb=" CB  SER A 155 "
    ideal  model  delta    sigma   weight residual
    1.529  1.475  0.054 1.55e-02 4.16e+03 1.22e+01
  bond pdb=" CB  LEU A 242 "
       pdb=" CG  LEU A 242 "
    ideal  model  delta    sigma   weight residual
    1.530  1.592 -0.062 2.00e-02 2.50e+03 9.67e+00
  bond pdb=" C5  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.472 -0.059 2.00e-02 2.50e+03 8.67e+00
  bond pdb=" C5  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.471 -0.058 2.00e-02 2.50e+03 8.38e+00
  ... (remaining 3943 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 4971
        2.21 -     4.41: 327
        4.41 -     6.62: 54
        6.62 -     8.82: 11
        8.82 -    11.03: 1
  Bond angle restraints: 5364
  Sorted by residual:
  angle pdb=" C   LEU A  24 "
        pdb=" N   PRO A  25 "
        pdb=" CA  PRO A  25 "
      ideal   model   delta    sigma   weight residual
     119.66  126.12   -6.46 7.20e-01 1.93e+00 8.05e+01
  angle pdb=" C   ASN A  81 "
        pdb=" N   PRO A  82 "
        pdb=" CA  PRO A  82 "
      ideal   model   delta    sigma   weight residual
     120.03  127.67   -7.64 9.90e-01 1.02e+00 5.96e+01
  angle pdb=" C   LEU A 214 "
        pdb=" N   PRO A 215 "
        pdb=" CA  PRO A 215 "
      ideal   model   delta    sigma   weight residual
     120.03  127.11   -7.08 9.90e-01 1.02e+00 5.11e+01
  angle pdb=" C   PRO A  25 "
        pdb=" N   PRO A  26 "
        pdb=" CA  PRO A  26 "
      ideal   model   delta    sigma   weight residual
     119.85  127.00   -7.15 1.01e+00 9.80e-01 5.01e+01
  angle pdb=" C   ALA L  43 "
        pdb=" N   PRO L  44 "
        pdb=" CA  PRO L  44 "
      ideal   model   delta    sigma   weight residual
     119.76  126.92   -7.16 1.03e+00 9.43e-01 4.83e+01
  ... (remaining 5359 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 2277
       17.19 -    34.39: 83
       34.39 -    51.58: 15
       51.58 -    68.77: 7
       68.77 -    85.96: 2
  Dihedral angle restraints: 2384
    sinusoidal: 998
      harmonic: 1386
  Sorted by residual:
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.58   45.42     1      1.00e+01 1.00e-02 2.86e+01
  dihedral pdb=" C   LYS A 185 "
           pdb=" N   LYS A 185 "
           pdb=" CA  LYS A 185 "
           pdb=" CB  LYS A 185 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.27   -8.33     0      2.50e+00 1.60e-01 1.11e+01
  dihedral pdb=" CB  GLU A 189 "
           pdb=" CG  GLU A 189 "
           pdb=" CD  GLU A 189 "
           pdb=" OE1 GLU A 189 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.96  -85.96     1      3.00e+01 1.11e-03 9.92e+00
  ... (remaining 2381 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 485
       0.095 -    0.190: 94
       0.190 -    0.285: 16
       0.285 -    0.380: 8
       0.380 -    0.475: 1
  Chirality restraints: 604
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.51    0.11 2.00e-02 2.50e+03 2.93e+01
  chirality pdb=" C1  NAG A1304 "
            pdb=" ND2 ASN A 232 "
            pdb=" C2  NAG A1304 "
            pdb=" O5  NAG A1304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.92   -0.48 2.00e-01 2.50e+01 5.65e+00
  chirality pdb=" CA  LYS A 185 "
            pdb=" N   LYS A 185 "
            pdb=" C   LYS A 185 "
            pdb=" CB  LYS A 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 3.02e+00
  ... (remaining 601 not shown)

  Planarity restraints: 680
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A1304 "   -0.242 2.00e-02 2.50e+03   2.08e-01 5.42e+02
        pdb=" C7  NAG A1304 "    0.052 2.00e-02 2.50e+03
        pdb=" C8  NAG A1304 "    0.025 2.00e-02 2.50e+03
        pdb=" N2  NAG A1304 "    0.348 2.00e-02 2.50e+03
        pdb=" O7  NAG A1304 "   -0.184 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  34 "    0.013 2.00e-02 2.50e+03   2.72e-02 7.40e+00
        pdb=" C   ARG A  34 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   ARG A  34 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLY A  35 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H 104 "   -0.031 2.00e-02 2.50e+03   1.70e-02 5.79e+00
        pdb=" CG  TYR H 104 "    0.011 2.00e-02 2.50e+03
        pdb=" CD1 TYR H 104 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR H 104 "    0.014 2.00e-02 2.50e+03
        pdb=" CE1 TYR H 104 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR H 104 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR H 104 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR H 104 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 677 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 205
        2.73 -     3.28: 3456
        3.28 -     3.82: 6166
        3.82 -     4.36: 8061
        4.36 -     4.90: 13416
  Nonbonded interactions: 31304
  Sorted by model distance:
  nonbonded pdb=" O   SER A  31 "
            pdb=" OG  SER A  31 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" N   THR A  29 "
            pdb=" O   THR A  29 "
     model   vdw
     2.551 2.496
  nonbonded pdb=" N   SER A 151 "
            pdb=" O   SER A 151 "
     model   vdw
     2.556 2.496
  nonbonded pdb=" N   GLY A 156 "
            pdb=" N   VAL A 157 "
     model   vdw
     2.588 2.560
  nonbonded pdb=" O   ASP L  92 "
            pdb=" NH1 ARG H 103 "
     model   vdw
     2.595 3.120
  ... (remaining 31299 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             7.400
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     16.270
  Find NCS groups from input model:        0.040
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
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      :  0.011   0.067   3959  Z= 0.600
  Angle     :  1.290  11.028   5392  Z= 0.862
  Chirality :  0.085   0.475    604
  Planarity :  0.010   0.208    675
  Dihedral  : 10.148  85.964   1481
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 1.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.73 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  0.99 (0.37), residues: 461
  helix:  0.55 (1.59), residues: 11
  sheet:  1.38 (0.37), residues: 184
  loop :  0.20 (0.35), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.004   TRP H  47 
 HIS   0.001   0.001   HIS A  66 
 PHE   0.018   0.003   PHE A  55 
 TYR   0.031   0.004   TYR H 104 
 ARG   0.004   0.001   ARG L  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.05265 (    5)
  link_NAG-ASN         : angle       3.19914 (   15)
  link_BETA1-4         : bond        0.05551 (    1)
  link_BETA1-4         : angle       2.62906 (    3)
  hydrogen bonds       : bond        0.17232 (  139)
  hydrogen bonds       : angle       9.28537 (  369)
  SS BOND              : bond        0.00330 (    5)
  SS BOND              : angle       3.09685 (   10)
  covalent geometry    : bond        0.01073 ( 3948)
  covalent geometry    : angle       1.27327 ( 5364)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.438 
Fit side-chains
REVERT: A  154 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7276 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1969
  time to fit residues: 19.9844
Evaluate side-chains
  57 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 23 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 194 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.133965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.104341 restraints weight = 4054.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 2.21
r_work: 0.3003 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   3959  Z= 0.201
  Angle     :  0.702  13.324   5392  Z= 0.343
  Chirality :  0.048   0.155    604
  Planarity :  0.005   0.048    675
  Dihedral  :  6.753  59.492    644
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  5.83 %
    Favored  : 92.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  1.11 (0.38), residues: 461
  helix:  2.84 (1.63), residues: 11
  sheet:  1.40 (0.36), residues: 193
  loop :  0.17 (0.38), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP H  47 
 HIS   0.003   0.001   HIS A  66 
 PHE   0.015   0.002   PHE A 133 
 TYR   0.015   0.002   TYR H  95 
 ARG   0.006   0.001   ARG A  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01265 (    5)
  link_NAG-ASN         : angle       3.96633 (   15)
  link_BETA1-4         : bond        0.00274 (    1)
  link_BETA1-4         : angle       1.45096 (    3)
  hydrogen bonds       : bond        0.03972 (  139)
  hydrogen bonds       : angle       6.42803 (  369)
  SS BOND              : bond        0.00338 (    5)
  SS BOND              : angle       0.74175 (   10)
  covalent geometry    : bond        0.00477 ( 3948)
  covalent geometry    : angle       0.66969 ( 5364)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: H   17 SER cc_start: 0.8394 (p) cc_final: 0.8164 (t)
  outliers start: 8
  outliers final: 5
  residues processed: 63
  average time/residue: 0.1683
  time to fit residues: 13.3979
Evaluate side-chains
  54 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  170 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 3 optimal weight:    0.2980
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3626 r_free = 0.3626 target = 0.144150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.115520 restraints weight = 3941.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 2.05
r_work: 0.2821 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2662 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8693
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3959  Z= 0.154
  Angle     :  0.609  11.501   5392  Z= 0.301
  Chirality :  0.045   0.145    604
  Planarity :  0.004   0.040    675
  Dihedral  :  4.910  27.143    641
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  :  7.04 %
    Favored  : 90.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  1.10 (0.38), residues: 461
  helix:  3.21 (1.70), residues: 11
  sheet:  1.59 (0.37), residues: 190
  loop : -0.02 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H  47 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.013   0.002   PHE A 133 
 TYR   0.014   0.001   TYR A 168 
 ARG   0.002   0.000   ARG A  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00514 (    5)
  link_NAG-ASN         : angle       4.44497 (   15)
  link_BETA1-4         : bond        0.00335 (    1)
  link_BETA1-4         : angle       1.55068 (    3)
  hydrogen bonds       : bond        0.03698 (  139)
  hydrogen bonds       : angle       5.91073 (  369)
  SS BOND              : bond        0.00175 (    5)
  SS BOND              : angle       0.71219 (   10)
  covalent geometry    : bond        0.00369 ( 3948)
  covalent geometry    : angle       0.56107 ( 5364)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.424 
Fit side-chains
REVERT: H   17 SER cc_start: 0.8473 (p) cc_final: 0.8228 (t)
  outliers start: 9
  outliers final: 6
  residues processed: 58
  average time/residue: 0.1563
  time to fit residues: 11.5698
Evaluate side-chains
  58 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  285 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0670
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 28 optimal weight:    0.3980
   chunk 29 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.5920

-------------------------------------------------------------------------------
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 = 0.3413 r_free = 0.3413 target = 0.127642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.098462 restraints weight = 4176.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 2.12
r_work: 0.2763 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2601 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3959  Z= 0.161
  Angle     :  0.574  10.609   5392  Z= 0.290
  Chirality :  0.046   0.244    604
  Planarity :  0.004   0.036    675
  Dihedral  :  5.028  33.322    641
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  :  6.31 %
    Favored  : 90.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  1.02 (0.39), residues: 461
  helix:  2.98 (1.63), residues: 11
  sheet:  1.44 (0.36), residues: 200
  loop : -0.04 (0.39), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP H  47 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.015   0.002   PHE A 133 
 TYR   0.013   0.001   TYR H  95 
 ARG   0.002   0.000   ARG A  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00314 (    5)
  link_NAG-ASN         : angle       2.28152 (   15)
  link_BETA1-4         : bond        0.00223 (    1)
  link_BETA1-4         : angle       1.55643 (    3)
  hydrogen bonds       : bond        0.03440 (  139)
  hydrogen bonds       : angle       5.69016 (  369)
  SS BOND              : bond        0.00202 (    5)
  SS BOND              : angle       0.52635 (   10)
  covalent geometry    : bond        0.00391 ( 3948)
  covalent geometry    : angle       0.56118 ( 5364)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A  170 SER cc_start: 0.8105 (OUTLIER) cc_final: 0.7564 (p)
REVERT: A  229 ILE cc_start: 0.8610 (mt) cc_final: 0.8202 (pt)
  outliers start: 12
  outliers final: 10
  residues processed: 64
  average time/residue: 0.1398
  time to fit residues: 11.6855
Evaluate side-chains
  64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  285 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 26 optimal weight:    0.2980
   chunk 32 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 23 optimal weight:    0.1980
   chunk 9 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0770
   chunk 35 optimal weight:    0.9980
   chunk 42 optimal weight:    0.5980
   chunk 0 optimal weight:    0.5980
   overall best weight:    0.3538

-------------------------------------------------------------------------------
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 = 0.3454 r_free = 0.3454 target = 0.130572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.102089 restraints weight = 4192.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 2.06
r_work: 0.2795 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2638 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8706
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3959  Z= 0.118
  Angle     :  0.593  12.892   5392  Z= 0.284
  Chirality :  0.045   0.185    604
  Planarity :  0.004   0.035    675
  Dihedral  :  4.635  23.677    641
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  :  6.80 %
    Favored  : 90.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  1.10 (0.40), residues: 461
  helix:  3.04 (1.65), residues: 11
  sheet:  1.50 (0.37), residues: 200
  loop :  0.01 (0.39), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  47 
 HIS   0.003   0.001   HIS A 205 
 PHE   0.013   0.001   PHE A 133 
 TYR   0.015   0.001   TYR A 168 
 ARG   0.002   0.000   ARG A  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00351 (    5)
  link_NAG-ASN         : angle       4.94274 (   15)
  link_BETA1-4         : bond        0.00263 (    1)
  link_BETA1-4         : angle       1.45348 (    3)
  hydrogen bonds       : bond        0.03160 (  139)
  hydrogen bonds       : angle       5.54086 (  369)
  SS BOND              : bond        0.00170 (    5)
  SS BOND              : angle       0.38905 (   10)
  covalent geometry    : bond        0.00279 ( 3948)
  covalent geometry    : angle       0.53223 ( 5364)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.451 
Fit side-chains
REVERT: A  170 SER cc_start: 0.8160 (OUTLIER) cc_final: 0.7607 (p)
REVERT: A  229 ILE cc_start: 0.8603 (mt) cc_final: 0.8187 (pt)
  outliers start: 12
  outliers final: 10
  residues processed: 62
  average time/residue: 0.1531
  time to fit residues: 12.2305
Evaluate side-chains
  66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  285 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 4 optimal weight:    0.1980
   chunk 1 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0970
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.129751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.101448 restraints weight = 4143.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.2951 rms_B_bonded: 2.03
r_work: 0.2793 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2634 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.3523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3959  Z= 0.141
  Angle     :  0.617  16.684   5392  Z= 0.294
  Chirality :  0.047   0.363    604
  Planarity :  0.004   0.035    675
  Dihedral  :  4.959  39.567    641
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  :  5.83 %
    Favored  : 90.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  1.01 (0.39), residues: 461
  helix:  2.98 (1.64), residues: 11
  sheet:  1.52 (0.38), residues: 191
  loop : -0.07 (0.38), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP H  47 
 HIS   0.004   0.001   HIS A 205 
 PHE   0.013   0.002   PHE A 133 
 TYR   0.012   0.001   TYR H  95 
 ARG   0.002   0.000   ARG H  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00634 (    5)
  link_NAG-ASN         : angle       5.49324 (   15)
  link_BETA1-4         : bond        0.00202 (    1)
  link_BETA1-4         : angle       1.46469 (    3)
  hydrogen bonds       : bond        0.03181 (  139)
  hydrogen bonds       : angle       5.42123 (  369)
  SS BOND              : bond        0.00160 (    5)
  SS BOND              : angle       0.46149 (   10)
  covalent geometry    : bond        0.00341 ( 3948)
  covalent geometry    : angle       0.54425 ( 5364)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.462 
Fit side-chains
REVERT: A  170 SER cc_start: 0.8144 (OUTLIER) cc_final: 0.7616 (p)
REVERT: A  229 ILE cc_start: 0.8626 (mt) cc_final: 0.8191 (pt)
REVERT: A  302 LYS cc_start: 0.8524 (mmtp) cc_final: 0.7622 (mmmt)
  outliers start: 14
  outliers final: 12
  residues processed: 64
  average time/residue: 0.1317
  time to fit residues: 11.1681
Evaluate side-chains
  67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  285 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.120733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.092074 restraints weight = 4192.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 2.04
r_work: 0.2730 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2572 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3959  Z= 0.206
  Angle     :  0.660  15.512   5392  Z= 0.317
  Chirality :  0.049   0.354    604
  Planarity :  0.004   0.035    675
  Dihedral  :  4.853  20.687    641
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  :  6.80 %
    Favored  : 89.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  0.90 (0.39), residues: 461
  helix:  2.93 (1.64), residues: 11
  sheet:  1.48 (0.38), residues: 191
  loop : -0.19 (0.38), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP H  47 
 HIS   0.005   0.001   HIS A 205 
 PHE   0.016   0.002   PHE A 133 
 TYR   0.016   0.002   TYR A 168 
 ARG   0.002   0.000   ARG A  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00619 (    5)
  link_NAG-ASN         : angle       5.12448 (   15)
  link_BETA1-4         : bond        0.00115 (    1)
  link_BETA1-4         : angle       1.63478 (    3)
  hydrogen bonds       : bond        0.03651 (  139)
  hydrogen bonds       : angle       5.59272 (  369)
  SS BOND              : bond        0.00204 (    5)
  SS BOND              : angle       0.62999 (   10)
  covalent geometry    : bond        0.00511 ( 3948)
  covalent geometry    : angle       0.60214 ( 5364)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.502 
Fit side-chains
REVERT: A  170 SER cc_start: 0.8178 (OUTLIER) cc_final: 0.7631 (p)
REVERT: A  229 ILE cc_start: 0.8584 (mt) cc_final: 0.8160 (pt)
REVERT: A  302 LYS cc_start: 0.8545 (mmtp) cc_final: 0.7654 (mmmt)
  outliers start: 14
  outliers final: 12
  residues processed: 63
  average time/residue: 0.1729
  time to fit residues: 14.3479
Evaluate side-chains
  66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  285 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 28 optimal weight:    0.2980
   chunk 27 optimal weight:    0.8980
   chunk 34 optimal weight:    0.4980
   chunk 17 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0570
   chunk 40 optimal weight:    0.9990
   chunk 0 optimal weight:    0.5980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.140377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.112468 restraints weight = 3981.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 1.98
r_work: 0.2764 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2608 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8741
moved from start:          0.3773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3959  Z= 0.135
  Angle     :  0.585  11.850   5392  Z= 0.286
  Chirality :  0.048   0.427    604
  Planarity :  0.004   0.035    675
  Dihedral  :  4.602  20.818    641
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  :  7.52 %
    Favored  : 89.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  0.95 (0.40), residues: 461
  helix:  3.03 (1.66), residues: 11
  sheet:  1.49 (0.38), residues: 196
  loop : -0.15 (0.39), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP H  47 
 HIS   0.003   0.001   HIS A 205 
 PHE   0.014   0.002   PHE A 133 
 TYR   0.011   0.001   TYR H  95 
 ARG   0.002   0.000   ARG A 188 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00802 (    5)
  link_NAG-ASN         : angle       4.40591 (   15)
  link_BETA1-4         : bond        0.00224 (    1)
  link_BETA1-4         : angle       1.44720 (    3)
  hydrogen bonds       : bond        0.03171 (  139)
  hydrogen bonds       : angle       5.48989 (  369)
  SS BOND              : bond        0.00140 (    5)
  SS BOND              : angle       0.49676 (   10)
  covalent geometry    : bond        0.00323 ( 3948)
  covalent geometry    : angle       0.53713 ( 5364)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A  170 SER cc_start: 0.8194 (OUTLIER) cc_final: 0.7681 (p)
REVERT: A  229 ILE cc_start: 0.8563 (mt) cc_final: 0.8202 (pt)
REVERT: A  302 LYS cc_start: 0.8545 (mmtp) cc_final: 0.7683 (mmmt)
  outliers start: 14
  outliers final: 12
  residues processed: 64
  average time/residue: 0.1526
  time to fit residues: 12.8163
Evaluate side-chains
  67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  285 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 27 optimal weight:    0.3980
   chunk 45 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0470
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.4478

-------------------------------------------------------------------------------
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 = 0.3584 r_free = 0.3584 target = 0.140668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.112631 restraints weight = 4015.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 1.98
r_work: 0.2795 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2638 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8721
moved from start:          0.3817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3959  Z= 0.133
  Angle     :  0.586  11.283   5392  Z= 0.288
  Chirality :  0.050   0.518    604
  Planarity :  0.004   0.034    675
  Dihedral  :  4.523  20.403    641
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  :  7.52 %
    Favored  : 89.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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 (0.40), residues: 461
  helix:  2.91 (1.63), residues: 11
  sheet:  1.47 (0.38), residues: 196
  loop : -0.16 (0.39), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP H  47 
 HIS   0.004   0.001   HIS A 205 
 PHE   0.014   0.001   PHE A 133 
 TYR   0.019   0.001   TYR A 168 
 ARG   0.002   0.000   ARG A 188 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00684 (    5)
  link_NAG-ASN         : angle       4.41619 (   15)
  link_BETA1-4         : bond        0.00292 (    1)
  link_BETA1-4         : angle       1.41331 (    3)
  hydrogen bonds       : bond        0.03147 (  139)
  hydrogen bonds       : angle       5.48491 (  369)
  SS BOND              : bond        0.00228 (    5)
  SS BOND              : angle       0.54979 (   10)
  covalent geometry    : bond        0.00319 ( 3948)
  covalent geometry    : angle       0.53736 ( 5364)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
REVERT: L    3 TRP cc_start: 0.8129 (t60) cc_final: 0.7683 (t60)
REVERT: A  170 SER cc_start: 0.8159 (OUTLIER) cc_final: 0.7625 (p)
REVERT: A  229 ILE cc_start: 0.8570 (mt) cc_final: 0.8201 (pt)
REVERT: A  302 LYS cc_start: 0.8522 (mmtp) cc_final: 0.7651 (mmmt)
  outliers start: 14
  outliers final: 13
  residues processed: 61
  average time/residue: 0.1420
  time to fit residues: 11.2923
Evaluate side-chains
  68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  163 ASN
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  285 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 29 optimal weight:    0.1980
   chunk 15 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0770
   chunk 44 optimal weight:    0.2980
   overall best weight:    0.4138

-------------------------------------------------------------------------------
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 = 0.3592 r_free = 0.3592 target = 0.141247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.113063 restraints weight = 4007.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 2.00
r_work: 0.2776 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2619 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8711
moved from start:          0.3887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3959  Z= 0.127
  Angle     :  0.572  11.213   5392  Z= 0.283
  Chirality :  0.050   0.552    604
  Planarity :  0.004   0.034    675
  Dihedral  :  4.415  20.499    641
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  :  7.77 %
    Favored  : 88.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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 (0.40), residues: 461
  helix:  2.94 (1.64), residues: 11
  sheet:  1.49 (0.38), residues: 196
  loop : -0.16 (0.39), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP H  47 
 HIS   0.004   0.001   HIS A 205 
 PHE   0.016   0.002   PHE A 133 
 TYR   0.011   0.001   TYR H  95 
 ARG   0.002   0.000   ARG A 188 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00841 (    5)
  link_NAG-ASN         : angle       4.19523 (   15)
  link_BETA1-4         : bond        0.00197 (    1)
  link_BETA1-4         : angle       1.32925 (    3)
  hydrogen bonds       : bond        0.03091 (  139)
  hydrogen bonds       : angle       5.43730 (  369)
  SS BOND              : bond        0.00198 (    5)
  SS BOND              : angle       0.51480 (   10)
  covalent geometry    : bond        0.00300 ( 3948)
  covalent geometry    : angle       0.52755 ( 5364)

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

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

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  922 Ramachandran restraints generated.
    461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
REVERT: L    3 TRP cc_start: 0.8142 (t60) cc_final: 0.7694 (t60)
REVERT: A  170 SER cc_start: 0.8146 (OUTLIER) cc_final: 0.7658 (p)
REVERT: A  229 ILE cc_start: 0.8560 (mt) cc_final: 0.8188 (pt)
REVERT: A  302 LYS cc_start: 0.8510 (mmtp) cc_final: 0.7643 (mmmt)
  outliers start: 14
  outliers final: 13
  residues processed: 60
  average time/residue: 0.1527
  time to fit residues: 12.0916
Evaluate side-chains
  69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  163 ASN
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  285 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 3 optimal weight:    0.2980
   chunk 9 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0170
   chunk 31 optimal weight:    0.0980
   chunk 24 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0030
   overall best weight:    0.2028

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.130932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.102624 restraints weight = 4063.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 2.00
r_work: 0.3028 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.3934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3959  Z= 0.094
  Angle     :  0.524  10.978   5392  Z= 0.264
  Chirality :  0.047   0.432    604
  Planarity :  0.004   0.034    675
  Dihedral  :  4.177  19.675    641
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  :  9.22 %
    Favored  : 88.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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:  1.03 (0.40), residues: 461
  helix:  2.70 (1.65), residues: 11
  sheet:  1.52 (0.38), residues: 196
  loop : -0.07 (0.40), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.003   0.001   HIS A 205 
 PHE   0.015   0.001   PHE A 133 
 TYR   0.020   0.001   TYR A 168 
 ARG   0.002   0.000   ARG A 188 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00738 (    5)
  link_NAG-ASN         : angle       3.89444 (   15)
  link_BETA1-4         : bond        0.00318 (    1)
  link_BETA1-4         : angle       1.20894 (    3)
  hydrogen bonds       : bond        0.02784 (  139)
  hydrogen bonds       : angle       5.28589 (  369)
  SS BOND              : bond        0.00199 (    5)
  SS BOND              : angle       0.48294 (   10)
  covalent geometry    : bond        0.00206 ( 3948)
  covalent geometry    : angle       0.48225 ( 5364)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2940.84 seconds
wall clock time: 51 minutes 58.57 seconds (3118.57 seconds total)