Starting phenix.real_space_refine
on Fri Jul 25 06:35:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d85_27247/07_2025/8d85_27247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d85_27247/07_2025/8d85_27247.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d85_27247/07_2025/8d85_27247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d85_27247/07_2025/8d85_27247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d85_27247/07_2025/8d85_27247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d85_27247/07_2025/8d85_27247.cif"
  }
  resolution = 3.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.019
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      31      5.16       5
     C    4527      2.51       5
     N    1197      2.21       5
     O    1338      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7093
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "C"
      Number of atoms: 1590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1590
          Classifications: {'peptide': 201}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 178}
    Chain: "D"
      Number of atoms: 1452
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 177, 1452
          Classifications: {'peptide': 177}
          Link IDs: {'PTRANS': 9, 'TRANS': 167}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1524
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 191, 1524
          Classifications: {'peptide': 191}
          Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 172}
    Chain: "B"
      Number of atoms: 2373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 296, 2373
          Classifications: {'peptide': 296}
          Link IDs: {'PTRANS': 16, 'TRANS': 279}
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      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: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 5.25, per 1000 atoms: 0.74
  Number of scatterers: 7093
  At special positions: 0
  Unit cell: (107.5, 104.06, 139.32, 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      31     16.00
     O    1338      8.00
     N    1197      7.00
     C    4527      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  35 " - pdb=" SG  CYS C  46 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  79 " - pdb=" SG  CYS C  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  41 " - pdb=" SG  CYS A  52 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 164 " - pdb=" SG  CYS A 208 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  28 " - pdb=" SG  CYS B  54 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  48 " - pdb=" SG  CYS B 103 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 134 " - pdb=" SG  CYS B 144 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 172 " - pdb=" SG  CYS B 182 " 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 E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG A 601 " - " ASN A  76 "
      " NAG B 701 " - " ASN B 227 "
      " NAG B 702 " - " ASN B 157 "
      " NAG B 703 " - " ASN B 131 "
      " NAG C 301 " - " ASN C 105 "
      " NAG E   1 " - " ASN A  51 "
      " NAG F   1 " - " ASN B  83 "
      " NAG G   1 " - " ASN B  43 "
  Time building additional restraints: 2.48
  Conformation dependent library (CDL) restraints added in 939.3 milliseconds
  

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1646

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 18 sheets defined
      17.8% alpha, 21.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'D' and resid 42 through 73
    Processing helix  chain 'D' and resid 93 through 100
    Processing helix  chain 'D' and resid 103 through 124
      Proline residue:  D 115  - end of helix
    Processing helix  chain 'D' and resid 130 through 158
    Processing helix  chain 'D' and resid 166 through 179
    Processing helix  chain 'D' and resid 196 through 225
    Processing helix  chain 'B' and resid 51 through 58
    Processing helix  chain 'B' and resid 247 through 251
      removed outlier: 4.305A  pdb=" N   SER B 251 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 278
      removed outlier: 3.643A  pdb=" N   ALA B 278 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 46
      removed outlier: 4.160A  pdb=" N   CYS C  46 " --> pdb=" O   CYS C  89 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   CYS C  89 " --> pdb=" O   CYS C  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78
      removed outlier: 3.649A  pdb=" N   ILE C  63 " --> pdb=" O   THR C 107 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL C 103 " --> pdb=" O   ARG C  67 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   PHE C 121 " --> pdb=" O   TYR C 102 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 136 through 138
      removed outlier: 3.686A  pdb=" N   LEU C 145 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 178 through 183
      removed outlier: 6.205A  pdb=" N   TYR C 165 " --> pdb=" O   PRO C 182 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 66
      removed outlier: 3.674A  pdb=" N   GLU A  65 " --> pdb=" O   THR A 108 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   THR A 108 " --> pdb=" O   GLU A  65 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 102 through 105
      removed outlier: 3.526A  pdb=" N   VAL A 105 " --> pdb=" O   VAL A 118 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL A 118 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 132 through 139
      removed outlier: 3.829A  pdb=" N   ARG A 132 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
      removed outlier: 5.038A  pdb=" N   HIS A 150 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   ASP A 136 " --> pdb=" O   THR A 148 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   THR A 148 " --> pdb=" O   ASP A 136 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 177 through 178
      removed outlier: 3.869A  pdb=" N   LEU A 183 " --> pdb=" O   CYS A 164 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 177 through 178
    Processing sheet with id=AB1, first strand: chain 'A' and resid 202 through 204
      removed outlier: 3.561A  pdb=" N   LEU A 224 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 38
      removed outlier: 3.957A  pdb=" N   VAL B  38 " --> pdb=" O   ILE B 121 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 47
    Processing sheet with id=AB4, first strand: chain 'B' and resid 73 through 74
      removed outlier: 4.735A  pdb=" N   TRP B  67 " --> pdb=" O   ILE B  74 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL B  66 " --> pdb=" O   ASN B 104 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ASN B 104 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLN B 113 " --> pdb=" O   ILE B 105 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 181 through 183
      removed outlier: 4.364A  pdb=" N   CYS B 182 " --> pdb=" O   CYS B 144 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   CYS B 144 " --> pdb=" O   CYS B 182 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ARG B 143 " --> pdb=" O   ILE B 135 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ASP B 147 " --> pdb=" O   ASN B 131 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   ASN B 131 " --> pdb=" O   ASP B 147 " (cutoff:3.500A)
      removed outlier: 8.563A  pdb=" N   LYS B 221 " --> pdb=" O   CYS B 134 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   VAL B 136 " --> pdb=" O   LYS B 221 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 172 through 173
      removed outlier: 3.864A  pdb=" N   LYS B 161 " --> pdb=" O   TRP B 197 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   TRP B 197 " --> pdb=" O   LYS B 161 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLU B 195 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 172 through 173
      removed outlier: 3.864A  pdb=" N   LYS B 161 " --> pdb=" O   TRP B 197 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   TRP B 197 " --> pdb=" O   LYS B 161 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLU B 195 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ILE B 194 " --> pdb=" O   PHE B 214 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   PHE B 214 " --> pdb=" O   ILE B 194 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   VAL B 196 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ILE B 212 " --> pdb=" O   VAL B 196 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 229 through 231
      removed outlier: 3.622A  pdb=" N   THR B 243 " --> pdb=" O   SER B 229 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LYS B 241 " --> pdb=" O   ILE B 231 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 270 through 271
      removed outlier: 3.987A  pdb=" N   TYR B 295 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLY B 319 " --> pdb=" O   TYR B 295 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA B 317 " --> pdb=" O   PHE B 297 " (cutoff:3.500A)

    205 hydrogen bonds defined for protein.
    549 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: 1.69

  Time building geometry restraints manager: 2.04 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2263
        1.34 -     1.46: 1724
        1.46 -     1.58: 3259
        1.58 -     1.70: 0
        1.70 -     1.82: 43
  Bond restraints: 7289
  Sorted by residual:
  bond pdb=" C   ASP D 102 "
       pdb=" N   PRO D 103 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.019 1.08e-02 8.57e+03 3.24e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.21e+00
  bond pdb=" C1  NAG G   2 "
       pdb=" O5  NAG G   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.20e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.05e+00
  bond pdb=" C1  NAG B 702 "
       pdb=" O5  NAG B 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.83e+00
  ... (remaining 7284 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 9795
        2.03 -     4.05: 129
        4.05 -     6.08: 14
        6.08 -     8.10: 2
        8.10 -    10.13: 1
  Bond angle restraints: 9941
  Sorted by residual:
  angle pdb=" CA  LEU A  68 "
        pdb=" CB  LEU A  68 "
        pdb=" CG  LEU A  68 "
      ideal   model   delta    sigma   weight residual
     116.30  126.43  -10.13 3.50e+00 8.16e-02 8.37e+00
  angle pdb=" N   SER B  32 "
        pdb=" CA  SER B  32 "
        pdb=" C   SER B  32 "
      ideal   model   delta    sigma   weight residual
     109.81  115.62   -5.81 2.21e+00 2.05e-01 6.92e+00
  angle pdb=" C   VAL C 109 "
        pdb=" N   HIS C 110 "
        pdb=" CA  HIS C 110 "
      ideal   model   delta    sigma   weight residual
     121.80  116.20    5.60 2.44e+00 1.68e-01 5.28e+00
  angle pdb=" C   LEU A 198 "
        pdb=" N   ALA A 199 "
        pdb=" CA  ALA A 199 "
      ideal   model   delta    sigma   weight residual
     122.08  125.21   -3.13 1.47e+00 4.63e-01 4.53e+00
  angle pdb=" C   ILE B  31 "
        pdb=" N   SER B  32 "
        pdb=" CA  SER B  32 "
      ideal   model   delta    sigma   weight residual
     121.80  116.99    4.81 2.44e+00 1.68e-01 3.89e+00
  ... (remaining 9936 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.69: 4205
       21.69 -    43.38: 204
       43.38 -    65.07: 46
       65.07 -    86.76: 21
       86.76 -   108.45: 52
  Dihedral angle restraints: 4528
    sinusoidal: 1995
      harmonic: 2533
  Sorted by residual:
  dihedral pdb=" CB  CYS C  35 "
           pdb=" SG  CYS C  35 "
           pdb=" SG  CYS C  46 "
           pdb=" CB  CYS C  46 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -43.34  -42.66     1      1.00e+01 1.00e-02 2.54e+01
  dihedral pdb=" CA  SER B  32 "
           pdb=" C   SER B  32 "
           pdb=" N   PRO B  33 "
           pdb=" CA  PRO B  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.58   24.42     0      5.00e+00 4.00e-02 2.39e+01
  dihedral pdb=" C1  NAG G   1 "
           pdb=" C2  NAG G   1 "
           pdb=" C3  NAG G   1 "
           pdb=" O3  NAG G   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -175.09  -66.64 -108.45     1      3.00e+01 1.11e-03 1.40e+01
  ... (remaining 4525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 891
       0.041 -    0.082: 136
       0.082 -    0.122: 92
       0.122 -    0.163: 7
       0.163 -    0.204: 2
  Chirality restraints: 1128
  Sorted by residual:
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN A  51 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" C1  NAG C 301 "
            pdb=" ND2 ASN C 105 "
            pdb=" C2  NAG C 301 "
            pdb=" O5  NAG C 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.23   -0.17 2.00e-01 2.50e+01 7.51e-01
  chirality pdb=" C1  NAG B 701 "
            pdb=" ND2 ASN B 227 "
            pdb=" C2  NAG B 701 "
            pdb=" O5  NAG B 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.24   -0.16 2.00e-01 2.50e+01 6.44e-01
  ... (remaining 1125 not shown)

  Planarity restraints: 1264
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 102 "   -0.026 5.00e-02 4.00e+02   3.92e-02 2.46e+00
        pdb=" N   PRO D 103 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C  40 "    0.023 5.00e-02 4.00e+02   3.53e-02 1.99e+00
        pdb=" N   PRO C  41 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO C  41 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C  41 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 272 "   -0.021 5.00e-02 4.00e+02   3.25e-02 1.69e+00
        pdb=" N   PRO B 273 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 273 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 273 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1261 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 2379
        2.87 -     3.37: 6114
        3.37 -     3.88: 10679
        3.88 -     4.39: 10827
        4.39 -     4.90: 19504
  Nonbonded interactions: 49503
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN C  81 "
            pdb=" O   SER C  86 "
     model   vdw
     2.357 3.120
  nonbonded pdb=" NH2 ARG C 168 "
            pdb=" OE1 GLN C 202 "
     model   vdw
     2.367 3.120
  nonbonded pdb=" NE1 TRP C 166 "
            pdb=" OE1 GLN C 206 "
     model   vdw
     2.372 3.120
  nonbonded pdb=" OE1 GLU B  34 "
            pdb=" OG  SER B  35 "
     model   vdw
     2.374 3.040
  nonbonded pdb=" ND2 ASN B 246 "
            pdb=" OG  SER B 282 "
     model   vdw
     2.381 3.120
  ... (remaining 49498 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.99
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:             3.140
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     20.110
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6271
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7308  Z= 0.127
  Angle     :  0.538  10.127   9990  Z= 0.262
  Chirality :  0.040   0.204   1128
  Planarity :  0.003   0.039   1256
  Dihedral  : 19.549 108.448   2858
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.09 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    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: -2.45 (0.25), residues: 855
  helix:  0.17 (0.39), residues: 154
  sheet: -0.72 (0.39), residues: 174
  loop : -2.67 (0.22), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.000   TRP A 115 
 HIS   0.001   0.000   HIS D 117 
 PHE   0.005   0.000   PHE D 116 
 TYR   0.005   0.000   TYR B  79 
 ARG   0.001   0.000   ARG D 152 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00444 (    8)
  link_NAG-ASN         : angle       1.80770 (   24)
  link_BETA1-4         : bond        0.00251 (    3)
  link_BETA1-4         : angle       0.72290 (    9)
  hydrogen bonds       : bond        0.23180 (  196)
  hydrogen bonds       : angle       7.44029 (  549)
  SS BOND              : bond        0.00108 (    8)
  SS BOND              : angle       0.59197 (   16)
  covalent geometry    : bond        0.00255 ( 7289)
  covalent geometry    : angle       0.53136 ( 9941)

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

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   30 LEU cc_start: 0.8169 (pt) cc_final: 0.7776 (mt)
REVERT: C  110 HIS cc_start: 0.2159 (m170) cc_final: 0.1914 (m90)
REVERT: D  144 LEU cc_start: 0.8883 (tp) cc_final: 0.8462 (tt)
REVERT: B  146 TRP cc_start: 0.8176 (p90) cc_final: 0.7824 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.2441
  time to fit residues: 58.4981
Evaluate side-chains
  109 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 34 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
C  75 HIS
D 126 GLN
D 150 HIS
** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  96 GLN
A 159 HIS
A 167 HIS
** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 193 ASN
B 211 HIS
B 258 ASN
B 260 GLN
B 271 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.174904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.153365 restraints weight = 14875.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.156664 restraints weight = 8954.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.158897 restraints weight = 6220.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4171 r_free = 0.4171    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       91 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4168 r_free = 0.4168    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
r_final: 0.4168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6749
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7308  Z= 0.179
  Angle     :  0.753  10.772   9990  Z= 0.343
  Chirality :  0.053   0.704   1128
  Planarity :  0.005   0.090   1256
  Dihedral  : 17.458  87.802   1167
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.03 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 14.27 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    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: -1.61 (0.27), residues: 855
  helix:  1.71 (0.42), residues: 148
  sheet: -0.99 (0.34), residues: 203
  loop : -2.08 (0.25), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 217 
 HIS   0.005   0.001   HIS B 211 
 PHE   0.018   0.002   PHE C 188 
 TYR   0.016   0.002   TYR B  79 
 ARG   0.007   0.001   ARG D 105 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00799 (    8)
  link_NAG-ASN         : angle       3.03256 (   24)
  link_BETA1-4         : bond        0.00543 (    3)
  link_BETA1-4         : angle       2.41357 (    9)
  hydrogen bonds       : bond        0.04103 (  196)
  hydrogen bonds       : angle       5.06540 (  549)
  SS BOND              : bond        0.01954 (    8)
  SS BOND              : angle       1.63088 (   16)
  covalent geometry    : bond        0.00395 ( 7289)
  covalent geometry    : angle       0.73321 ( 9941)

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

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  110 HIS cc_start: 0.2958 (m170) cc_final: 0.2577 (m90)
REVERT: C  198 ARG cc_start: 0.6912 (mtm-85) cc_final: 0.6568 (mtm-85)
REVERT: D  144 LEU cc_start: 0.8933 (tp) cc_final: 0.8659 (tt)
REVERT: B  146 TRP cc_start: 0.8716 (p90) cc_final: 0.8395 (p90)
REVERT: B  239 ILE cc_start: 0.7125 (mm) cc_final: 0.6868 (pt)
REVERT: B  302 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.5866 (ptt)
  outliers start: 13
  outliers final: 8
  residues processed: 127
  average time/residue: 0.2136
  time to fit residues: 35.4270
Evaluate side-chains
  107 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain A residue   99 MET
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue  223 ASN
Chi-restraints excluded: chain B residue  301 CYS
Chi-restraints excluded: chain B residue  302 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0970
   chunk 31 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  79 GLN
B 114 ASN
B 258 ASN
B 260 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.172886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.151142 restraints weight = 14885.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.154373 restraints weight = 8917.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.156675 restraints weight = 6256.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4137
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4137 r_free = 0.4137    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4137 r_free = 0.4137    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
r_final: 0.4137
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6785
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7308  Z= 0.124
  Angle     :  0.670  10.592   9990  Z= 0.300
  Chirality :  0.047   0.476   1128
  Planarity :  0.005   0.084   1256
  Dihedral  : 13.449  78.287   1167
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.03 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.95 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    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: -1.22 (0.28), residues: 855
  helix:  2.25 (0.42), residues: 148
  sheet: -0.81 (0.32), residues: 230
  loop : -1.89 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 310 
 HIS   0.002   0.001   HIS D 117 
 PHE   0.015   0.001   PHE C 188 
 TYR   0.016   0.001   TYR B 295 
 ARG   0.004   0.000   ARG D 105 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00890 (    8)
  link_NAG-ASN         : angle       2.89305 (   24)
  link_BETA1-4         : bond        0.00342 (    3)
  link_BETA1-4         : angle       1.89739 (    9)
  hydrogen bonds       : bond        0.04093 (  196)
  hydrogen bonds       : angle       4.51461 (  549)
  SS BOND              : bond        0.00288 (    8)
  SS BOND              : angle       1.21403 (   16)
  covalent geometry    : bond        0.00288 ( 7289)
  covalent geometry    : angle       0.65172 ( 9941)

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

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.6932 (mtm-85) cc_final: 0.6583 (mtm-85)
REVERT: D  144 LEU cc_start: 0.8939 (tp) cc_final: 0.8619 (tt)
REVERT: B   76 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6806 (tttp)
REVERT: B  146 TRP cc_start: 0.8715 (p90) cc_final: 0.8352 (p90)
REVERT: B  239 ILE cc_start: 0.7026 (mm) cc_final: 0.6731 (pt)
  outliers start: 21
  outliers final: 10
  residues processed: 127
  average time/residue: 0.2004
  time to fit residues: 33.7157
Evaluate side-chains
  106 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  230 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 55 optimal weight:    0.3980
   chunk 73 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 57 optimal weight:    0.1980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
D  77 ASN
A  71 GLN
B 114 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.169814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.148073 restraints weight = 14878.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.151343 restraints weight = 8895.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.153609 restraints weight = 6194.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4102
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4102 r_free = 0.4102    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4102 r_free = 0.4102    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
r_final: 0.4102
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
moved from start:          0.3818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7308  Z= 0.121
  Angle     :  0.683  13.169   9990  Z= 0.302
  Chirality :  0.047   0.395   1128
  Planarity :  0.005   0.073   1256
  Dihedral  : 11.087  65.917   1167
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.15 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.03 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    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 (0.28), residues: 855
  helix:  2.55 (0.42), residues: 148
  sheet: -0.71 (0.31), residues: 245
  loop : -1.78 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 115 
 HIS   0.003   0.001   HIS D 117 
 PHE   0.017   0.001   PHE B  72 
 TYR   0.013   0.001   TYR B  79 
 ARG   0.003   0.000   ARG B 298 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00687 (    8)
  link_NAG-ASN         : angle       2.97709 (   24)
  link_BETA1-4         : bond        0.00315 (    3)
  link_BETA1-4         : angle       2.19445 (    9)
  hydrogen bonds       : bond        0.03851 (  196)
  hydrogen bonds       : angle       4.33513 (  549)
  SS BOND              : bond        0.00302 (    8)
  SS BOND              : angle       1.25712 (   16)
  covalent geometry    : bond        0.00280 ( 7289)
  covalent geometry    : angle       0.66382 ( 9941)

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

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.7006 (mtm-85) cc_final: 0.6644 (mtm-85)
REVERT: D   64 GLN cc_start: 0.7639 (tp40) cc_final: 0.7268 (tp40)
REVERT: D  132 MET cc_start: 0.7419 (ppp) cc_final: 0.7057 (ppp)
REVERT: A  200 THR cc_start: 0.8332 (m) cc_final: 0.7696 (p)
REVERT: B   76 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6884 (tttp)
REVERT: B  146 TRP cc_start: 0.8783 (p90) cc_final: 0.8421 (p90)
  outliers start: 19
  outliers final: 14
  residues processed: 119
  average time/residue: 0.1941
  time to fit residues: 30.7805
Evaluate side-chains
  109 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain D residue   77 ASN
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  114 ASN
Chi-restraints excluded: chain B residue  230 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 53 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0970
   chunk 57 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
D 154 GLN
** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 GLN ** 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 = 0.4287 r_free = 0.4287 target = 0.167963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.146650 restraints weight = 14776.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.149852 restraints weight = 9038.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.152032 restraints weight = 6351.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.4093
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4090
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4090 r_free = 0.4090    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4090 r_free = 0.4090    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
r_final: 0.4090
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.4242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7308  Z= 0.151
  Angle     :  0.686  10.399   9990  Z= 0.312
  Chirality :  0.047   0.504   1128
  Planarity :  0.005   0.087   1256
  Dihedral  : 10.002  56.197   1167
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.85 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.20 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    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: -0.97 (0.28), residues: 855
  helix:  2.51 (0.42), residues: 148
  sheet: -0.69 (0.31), residues: 241
  loop : -1.74 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 310 
 HIS   0.003   0.001   HIS D  52 
 PHE   0.019   0.001   PHE B  72 
 TYR   0.015   0.001   TYR B  79 
 ARG   0.006   0.000   ARG D 105 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00884 (    8)
  link_NAG-ASN         : angle       2.85360 (   24)
  link_BETA1-4         : bond        0.00326 (    3)
  link_BETA1-4         : angle       2.30833 (    9)
  hydrogen bonds       : bond        0.04383 (  196)
  hydrogen bonds       : angle       4.37272 (  549)
  SS BOND              : bond        0.00367 (    8)
  SS BOND              : angle       1.50639 (   16)
  covalent geometry    : bond        0.00348 ( 7289)
  covalent geometry    : angle       0.66661 ( 9941)

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

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.7068 (mtm-85) cc_final: 0.6680 (mtm-85)
REVERT: D   64 GLN cc_start: 0.7747 (tp40) cc_final: 0.7400 (tp40)
REVERT: D  144 LEU cc_start: 0.8926 (tp) cc_final: 0.8608 (tt)
REVERT: B   76 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7011 (tttp)
REVERT: B  146 TRP cc_start: 0.8762 (p90) cc_final: 0.8375 (p90)
  outliers start: 25
  outliers final: 17
  residues processed: 119
  average time/residue: 0.1780
  time to fit residues: 28.8694
Evaluate side-chains
  111 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  230 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 20 optimal weight:    0.3980
   chunk 26 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0570
   chunk 81 optimal weight:    7.9990
   chunk 34 optimal weight:    7.9990
   chunk 58 optimal weight:    1.9990
   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 260 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 = 0.4291 r_free = 0.4291 target = 0.168578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.147648 restraints weight = 15429.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.150891 restraints weight = 9342.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.153085 restraints weight = 6548.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.4104
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4096
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4096 r_free = 0.4096    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4096 r_free = 0.4096    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
r_final: 0.4096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.4422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7308  Z= 0.116
  Angle     :  0.665  12.922   9990  Z= 0.297
  Chirality :  0.045   0.419   1128
  Planarity :  0.005   0.080   1256
  Dihedral  :  8.716  55.266   1167
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.50 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 20.49 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    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: -0.77 (0.28), residues: 855
  helix:  2.69 (0.42), residues: 148
  sheet: -0.48 (0.31), residues: 239
  loop : -1.66 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A  89 
 HIS   0.004   0.001   HIS D 117 
 PHE   0.019   0.001   PHE B  72 
 TYR   0.014   0.001   TYR B 261 
 ARG   0.004   0.000   ARG D  67 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00774 (    8)
  link_NAG-ASN         : angle       2.96967 (   24)
  link_BETA1-4         : bond        0.00247 (    3)
  link_BETA1-4         : angle       2.47585 (    9)
  hydrogen bonds       : bond        0.04000 (  196)
  hydrogen bonds       : angle       4.24104 (  549)
  SS BOND              : bond        0.00372 (    8)
  SS BOND              : angle       1.62986 (   16)
  covalent geometry    : bond        0.00268 ( 7289)
  covalent geometry    : angle       0.64252 ( 9941)

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

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.6994 (mtm-85) cc_final: 0.6658 (mtm-85)
REVERT: D   64 GLN cc_start: 0.7727 (tp40) cc_final: 0.7388 (tp40)
REVERT: D  132 MET cc_start: 0.7478 (ppp) cc_final: 0.7201 (ppp)
REVERT: D  140 MET cc_start: 0.8473 (tmm) cc_final: 0.8197 (tmm)
REVERT: D  144 LEU cc_start: 0.8917 (tp) cc_final: 0.8580 (tt)
REVERT: A  217 TRP cc_start: 0.7814 (m100) cc_final: 0.6604 (m100)
REVERT: B   76 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7039 (tttp)
REVERT: B  146 TRP cc_start: 0.8735 (p90) cc_final: 0.8382 (p90)
  outliers start: 21
  outliers final: 15
  residues processed: 113
  average time/residue: 0.1890
  time to fit residues: 28.9608
Evaluate side-chains
  107 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  265 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 76 optimal weight:    0.8980
   chunk 37 optimal weight:    0.4980
   chunk 45 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0870
   chunk 64 optimal weight:    0.0870
   chunk 42 optimal weight:    0.0000
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.2540

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

Flipped N/Q/H residues before XYZ refinement:
** B 260 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 = 0.4319 r_free = 0.4319 target = 0.171004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.150190 restraints weight = 15394.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.153374 restraints weight = 9270.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.155640 restraints weight = 6509.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.4149
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4149
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4149 r_free = 0.4149    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4149 r_free = 0.4149    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
r_final: 0.4149
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6904
moved from start:          0.4440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   7308  Z= 0.104
  Angle     :  0.645  11.238   9990  Z= 0.291
  Chirality :  0.044   0.390   1128
  Planarity :  0.005   0.079   1256
  Dihedral  :  7.544  54.098   1167
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.03 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 21.27 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    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: -0.63 (0.29), residues: 855
  helix:  2.83 (0.42), residues: 148
  sheet: -0.43 (0.31), residues: 245
  loop : -1.57 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A  89 
 HIS   0.004   0.001   HIS D 117 
 PHE   0.020   0.001   PHE B  72 
 TYR   0.013   0.001   TYR C 200 
 ARG   0.005   0.000   ARG D  67 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00748 (    8)
  link_NAG-ASN         : angle       2.88117 (   24)
  link_BETA1-4         : bond        0.00445 (    3)
  link_BETA1-4         : angle       2.47583 (    9)
  hydrogen bonds       : bond        0.03437 (  196)
  hydrogen bonds       : angle       4.03680 (  549)
  SS BOND              : bond        0.00321 (    8)
  SS BOND              : angle       1.34476 (   16)
  covalent geometry    : bond        0.00243 ( 7289)
  covalent geometry    : angle       0.62378 ( 9941)

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

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.6971 (mtm-85) cc_final: 0.6647 (mtm-85)
REVERT: D   64 GLN cc_start: 0.7574 (tp40) cc_final: 0.7239 (tp40)
REVERT: D   95 GLN cc_start: 0.8471 (mm110) cc_final: 0.8190 (mm-40)
REVERT: D  132 MET cc_start: 0.7340 (ppp) cc_final: 0.7024 (ppp)
REVERT: D  134 ARG cc_start: 0.8312 (mtt-85) cc_final: 0.8046 (mtt-85)
REVERT: D  140 MET cc_start: 0.8442 (tmm) cc_final: 0.8143 (tmm)
REVERT: D  144 LEU cc_start: 0.8885 (tp) cc_final: 0.8528 (tt)
REVERT: A  217 TRP cc_start: 0.7826 (m100) cc_final: 0.6643 (m100)
REVERT: B  146 TRP cc_start: 0.8690 (p90) cc_final: 0.8347 (p90)
REVERT: B  302 MET cc_start: 0.6466 (ptt) cc_final: 0.6218 (ptm)
  outliers start: 19
  outliers final: 15
  residues processed: 112
  average time/residue: 0.1946
  time to fit residues: 28.8818
Evaluate side-chains
  108 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  211 TYR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain A residue   52 CYS
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   96 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 74 optimal weight:    7.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
D 126 GLN
D 154 GLN
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 287 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.164112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.144506 restraints weight = 14971.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.147030 restraints weight = 9735.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.148813 restraints weight = 7216.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4119
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4119 r_free = 0.4119    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4119 r_free = 0.4119    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
r_final: 0.4119
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.5726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063   7308  Z= 0.265
  Angle     :  0.890  13.173   9990  Z= 0.429
  Chirality :  0.054   0.447   1128
  Planarity :  0.006   0.095   1256
  Dihedral  :  8.035  57.112   1167
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.84 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 21.66 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    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: -1.24 (0.28), residues: 855
  helix:  2.09 (0.41), residues: 147
  sheet: -0.84 (0.31), residues: 240
  loop : -1.84 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A 156 
 HIS   0.006   0.002   HIS B 211 
 PHE   0.021   0.003   PHE B  72 
 TYR   0.024   0.002   TYR B  79 
 ARG   0.016   0.001   ARG C 143 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00742 (    8)
  link_NAG-ASN         : angle       3.86027 (   24)
  link_BETA1-4         : bond        0.00412 (    3)
  link_BETA1-4         : angle       2.71775 (    9)
  hydrogen bonds       : bond        0.06632 (  196)
  hydrogen bonds       : angle       4.91257 (  549)
  SS BOND              : bond        0.00610 (    8)
  SS BOND              : angle       2.61871 (   16)
  covalent geometry    : bond        0.00615 ( 7289)
  covalent geometry    : angle       0.86201 ( 9941)

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

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.7038 (mtm-85) cc_final: 0.6696 (mtm-85)
REVERT: D   64 GLN cc_start: 0.8019 (tp40) cc_final: 0.7700 (tp-100)
REVERT: D   95 GLN cc_start: 0.8570 (mm110) cc_final: 0.8303 (mm-40)
REVERT: D  132 MET cc_start: 0.7484 (ppp) cc_final: 0.7252 (ppp)
REVERT: D  140 MET cc_start: 0.8425 (tmm) cc_final: 0.8178 (tmm)
REVERT: A  217 TRP cc_start: 0.8166 (m100) cc_final: 0.6836 (m100)
REVERT: B   74 ILE cc_start: 0.9131 (mm) cc_final: 0.8928 (mt)
REVERT: B   76 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7434 (tttp)
REVERT: B  146 TRP cc_start: 0.8717 (p90) cc_final: 0.8294 (p90)
REVERT: B  287 GLN cc_start: 0.3598 (OUTLIER) cc_final: 0.3310 (mp10)
  outliers start: 28
  outliers final: 18
  residues processed: 121
  average time/residue: 0.1767
  time to fit residues: 29.1761
Evaluate side-chains
  112 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  211 TYR
Chi-restraints excluded: chain D residue   61 VAL
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  265 ASP
Chi-restraints excluded: chain B residue  287 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 24 optimal weight:    0.4980
   chunk 12 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
D 126 GLN
D 154 GLN
** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.167311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.147408 restraints weight = 15022.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.150050 restraints weight = 9566.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.151929 restraints weight = 7019.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.4186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4175 r_free = 0.4175    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4175 r_free = 0.4175    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
r_final: 0.4175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.5659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   7308  Z= 0.140
  Angle     :  0.732  11.305   9990  Z= 0.344
  Chirality :  0.047   0.508   1128
  Planarity :  0.006   0.089   1256
  Dihedral  :  7.760  59.829   1167
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.26 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 23.87 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    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: -0.97 (0.28), residues: 855
  helix:  2.80 (0.42), residues: 142
  sheet: -0.75 (0.32), residues: 231
  loop : -1.73 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 115 
 HIS   0.004   0.001   HIS D 117 
 PHE   0.023   0.001   PHE B  72 
 TYR   0.019   0.001   TYR B 261 
 ARG   0.007   0.000   ARG D 105 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00962 (    8)
  link_NAG-ASN         : angle       3.36806 (   24)
  link_BETA1-4         : bond        0.00342 (    3)
  link_BETA1-4         : angle       2.34096 (    9)
  hydrogen bonds       : bond        0.05263 (  196)
  hydrogen bonds       : angle       4.49108 (  549)
  SS BOND              : bond        0.00629 (    8)
  SS BOND              : angle       2.19687 (   16)
  covalent geometry    : bond        0.00318 ( 7289)
  covalent geometry    : angle       0.70558 ( 9941)

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

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.7078 (mtm-85) cc_final: 0.6698 (mtm-85)
REVERT: D   64 GLN cc_start: 0.7841 (tp40) cc_final: 0.7579 (tp40)
REVERT: D  132 MET cc_start: 0.7560 (ppp) cc_final: 0.6799 (ppp)
REVERT: D  140 MET cc_start: 0.8448 (tmm) cc_final: 0.8128 (tmm)
REVERT: A  182 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6324 (mm-30)
REVERT: A  217 TRP cc_start: 0.8074 (m100) cc_final: 0.6685 (m100)
REVERT: B   74 ILE cc_start: 0.9032 (mm) cc_final: 0.8797 (mt)
REVERT: B  146 TRP cc_start: 0.8760 (p90) cc_final: 0.8360 (p90)
REVERT: B  250 LYS cc_start: 0.8273 (pttm) cc_final: 0.7048 (tttt)
  outliers start: 17
  outliers final: 13
  residues processed: 106
  average time/residue: 0.1986
  time to fit residues: 28.2918
Evaluate side-chains
  100 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  211 TYR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  265 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0970
   chunk 57 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
** B 271 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 = 0.4322 r_free = 0.4322 target = 0.168120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.148497 restraints weight = 15373.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.151166 restraints weight = 9740.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.153032 restraints weight = 7065.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.4141
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4141
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4141 r_free = 0.4141    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4141 r_free = 0.4141    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
r_final: 0.4141
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
moved from start:          0.5694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   7308  Z= 0.134
  Angle     :  0.728  11.737   9990  Z= 0.343
  Chirality :  0.047   0.478   1128
  Planarity :  0.006   0.086   1256
  Dihedral  :  7.409  58.505   1167
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.55 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 23.99 %
    Favored  : 73.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    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 (0.28), residues: 855
  helix:  2.82 (0.43), residues: 142
  sheet: -0.67 (0.31), residues: 232
  loop : -1.70 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 115 
 HIS   0.004   0.001   HIS D 117 
 PHE   0.023   0.001   PHE B  72 
 TYR   0.028   0.002   TYR B 295 
 ARG   0.004   0.000   ARG B 300 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00882 (    8)
  link_NAG-ASN         : angle       3.33853 (   24)
  link_BETA1-4         : bond        0.00370 (    3)
  link_BETA1-4         : angle       2.39380 (    9)
  hydrogen bonds       : bond        0.04858 (  196)
  hydrogen bonds       : angle       4.47540 (  549)
  SS BOND              : bond        0.00472 (    8)
  SS BOND              : angle       1.97704 (   16)
  covalent geometry    : bond        0.00308 ( 7289)
  covalent geometry    : angle       0.70270 ( 9941)

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

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.7029 (mtm-85) cc_final: 0.6773 (mtm-85)
REVERT: D   64 GLN cc_start: 0.7873 (tp40) cc_final: 0.7607 (tp40)
REVERT: D  140 MET cc_start: 0.8370 (tmm) cc_final: 0.8117 (tmm)
REVERT: A  182 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6323 (mm-30)
REVERT: A  217 TRP cc_start: 0.8077 (m100) cc_final: 0.6834 (m100)
REVERT: B   74 ILE cc_start: 0.9051 (mm) cc_final: 0.8823 (mt)
REVERT: B  146 TRP cc_start: 0.8696 (p90) cc_final: 0.8316 (p90)
  outliers start: 18
  outliers final: 16
  residues processed: 109
  average time/residue: 0.2059
  time to fit residues: 30.0253
Evaluate side-chains
  106 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  211 TYR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  265 ASP
Chi-restraints excluded: chain B residue  293 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 42 optimal weight:    0.0470
   chunk 12 optimal weight:    0.4980
   chunk 78 optimal weight:    9.9990
   chunk 15 optimal weight:    0.5980
   chunk 69 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0170
   chunk 17 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.3916

-------------------------------------------------------------------------------
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 = 0.4390 r_free = 0.4390 target = 0.172938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.154001 restraints weight = 14883.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.156781 restraints weight = 9279.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.158636 restraints weight = 6618.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.4207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4207 r_free = 0.4207    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4207 r_free = 0.4207    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
r_final: 0.4207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
moved from start:          0.5645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7308  Z= 0.116
  Angle     :  0.703  12.105   9990  Z= 0.328
  Chirality :  0.046   0.453   1128
  Planarity :  0.005   0.085   1256
  Dihedral  :  7.070  56.182   1167
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.08 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 23.74 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    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: -0.80 (0.28), residues: 855
  helix:  2.86 (0.42), residues: 142
  sheet: -0.60 (0.32), residues: 230
  loop : -1.62 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 115 
 HIS   0.004   0.001   HIS D 117 
 PHE   0.023   0.001   PHE B  72 
 TYR   0.016   0.001   TYR B 295 
 ARG   0.004   0.000   ARG D 134 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00883 (    8)
  link_NAG-ASN         : angle       3.29769 (   24)
  link_BETA1-4         : bond        0.00394 (    3)
  link_BETA1-4         : angle       2.14886 (    9)
  hydrogen bonds       : bond        0.04047 (  196)
  hydrogen bonds       : angle       4.25126 (  549)
  SS BOND              : bond        0.00391 (    8)
  SS BOND              : angle       1.60966 (   16)
  covalent geometry    : bond        0.00266 ( 7289)
  covalent geometry    : angle       0.67982 ( 9941)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2732.29 seconds
wall clock time: 47 minutes 56.25 seconds (2876.25 seconds total)