Starting phenix.real_space_refine
on Thu Jul  2 06:16:55 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8d85_27247/07_2026/8d85_27247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d85_27247/07_2026/8d85_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d85_27247/07_2026/8d85_27247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d85_27247/07_2026/8d85_27247.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d85_27247/07_2026/8d85_27247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d85_27247/07_2026/8d85_27247.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8d85_27247/07_2026/8d85_27247.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8d85_27247/07_2026/8d85_27247.cif"
  }
  resolution = 3.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 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 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 chiralities: 3
  Time building chain proxies: 1.68, per 1000 atoms: 0.24
  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: 0.59
  Conformation dependent library (CDL) restraints added in 450.1 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: 0.21
  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: 0.91

  Time building geometry restraints manager: 0.82 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 -    16.41: 3951
       16.41 -    32.82: 280
       32.82 -    49.24: 50
       49.24 -    65.65: 5
       65.65 -    82.06: 11
  Dihedral angle restraints: 4297
    sinusoidal: 1764
      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=" CA  TYR B  30 "
           pdb=" C   TYR B  30 "
           pdb=" N   ILE B  31 "
           pdb=" CA  ILE B  31 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.46   15.54     0      5.00e+00 4.00e-02 9.65e+00
  ... (remaining 4294 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:             4.280
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.200
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6407
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  : 11.745  82.060   2627
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.001   0.000   ARG D 152 
 TYR   0.005   0.000   TYR B  79 
 PHE   0.005   0.000   PHE D 116 
 TRP   0.007   0.000   TRP A 115 
 HIS   0.001   0.000   HIS D 117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.13 ( 7289)
  covalent geometry    : angle       0.53136 /  0.26 ( 9941)
  SS BOND              : bond        0.00108 /  0.05 (    8)
  SS BOND              : angle       0.59197 /  0.36 (   16)
  hydrogen bonds       : bond        0.23180 / 15.14 (  196)
  hydrogen bonds       : angle       7.44029 /  5.25 (  549)
  link_BETA1-4         : bond        0.00251 /  0.12 (    3)
  link_BETA1-4         : angle       0.72290 /  0.35 (    9)
  link_NAG-ASN         : bond        0.00444 /  0.22 (    8)
  link_NAG-ASN         : angle       1.80770 /  1.14 (   24)

*********************** 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  : 0.332 
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: 0.7777 (mt)
REVERT: C  110 HIS cc_start: 0.2159 (m170) cc_final: 0.1912 (m90)
REVERT: D  144 LEU cc_start: 0.8883 (tp) cc_final: 0.8468 (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: 0.0994
  time to fit residues: 24.2335
Evaluate side-chains
  108 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  75 HIS
D 126 GLN
D 154 GLN
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  96 GLN
A 159 HIS
A 167 HIS
B 114 ASN
B 193 ASN
B 211 HIS
B 258 ASN
B 260 GLN
B 271 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.176087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.154166 restraints weight = 14976.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.157311 restraints weight = 9136.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.159597 restraints weight = 6463.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.161139 restraints weight = 5000.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.162182 restraints weight = 4143.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.4214
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4213 r_free = 0.4213    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       91 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4210 r_free = 0.4210    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.4210
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6816
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7308  Z= 0.162
  Angle     :  0.675  11.179   9990  Z= 0.320
  Chirality :  0.047   0.584   1128
  Planarity :  0.005   0.089   1256
  Dihedral  :  3.378  28.777    936
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.15 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.49 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.27), residues: 855
  helix:  1.70 (0.42), residues: 148
  sheet: -0.93 (0.34), residues: 203
  loop : -2.09 (0.24), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 105 
 TYR   0.016   0.001   TYR B  79 
 PHE   0.016   0.001   PHE C 188 
 TRP   0.023   0.002   TRP A 217 
 HIS   0.004   0.001   HIS A 167 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.16 ( 7289)
  covalent geometry    : angle       0.65656 /  0.31 ( 9941)
  SS BOND              : bond        0.00626 /  0.32 (    8)
  SS BOND              : angle       1.59515 /  0.77 (   16)
  hydrogen bonds       : bond        0.04271 /  2.84 (  196)
  hydrogen bonds       : angle       5.16786 /  3.64 (  549)
  link_BETA1-4         : bond        0.00267 /  0.13 (    3)
  link_BETA1-4         : angle       1.19626 /  0.60 (    9)
  link_NAG-ASN         : bond        0.00825 /  0.41 (    8)
  link_NAG-ASN         : angle       3.02432 /  1.95 (   24)

*********************** 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
  129 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.6839 (mtm-85) cc_final: 0.6502 (mtm-85)
REVERT: D  144 LEU cc_start: 0.8916 (tp) cc_final: 0.8643 (tt)
REVERT: B  146 TRP cc_start: 0.8661 (p90) cc_final: 0.8341 (p90)
REVERT: B  239 ILE cc_start: 0.7057 (mm) cc_final: 0.6758 (pt)
REVERT: B  302 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5762 (ptt)
  outliers start: 14
  outliers final: 8
  residues processed: 125
  average time/residue: 0.0840
  time to fit residues: 13.7706
Evaluate side-chains
  105 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
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 57 optimal weight:    0.0980
   chunk 17 optimal weight:    4.9990
   chunk 84 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 80 optimal weight:    0.0020
   chunk 45 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0770
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.6148

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4341 r_free = 0.4341 target = 0.174568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.152910 restraints weight = 14824.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.156071 restraints weight = 9004.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.158353 restraints weight = 6365.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.159878 restraints weight = 4932.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.160902 restraints weight = 4100.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.4202
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4201
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4201 r_free = 0.4201    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4201 r_free = 0.4201    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (8 function evaluations)
r_final: 0.4201
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6859
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7308  Z= 0.115
  Angle     :  0.598  11.517   9990  Z= 0.280
  Chirality :  0.044   0.405   1128
  Planarity :  0.005   0.082   1256
  Dihedral  :  3.463  30.189    936
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.80 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.05 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.17 (0.28), residues: 855
  helix:  2.22 (0.42), residues: 148
  sheet: -0.70 (0.32), residues: 228
  loop : -1.88 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  67 
 TYR   0.014   0.001   TYR B 295 
 PHE   0.015   0.001   PHE C 188 
 TRP   0.014   0.001   TRP B 310 
 HIS   0.003   0.001   HIS A 150 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.11 ( 7289)
  covalent geometry    : angle       0.58057 /  0.28 ( 9941)
  SS BOND              : bond        0.00263 /  0.14 (    8)
  SS BOND              : angle       1.01089 /  0.52 (   16)
  hydrogen bonds       : bond        0.03874 /  2.61 (  196)
  hydrogen bonds       : angle       4.55819 /  3.20 (  549)
  link_BETA1-4         : bond        0.00235 /  0.12 (    3)
  link_BETA1-4         : angle       0.98443 /  0.48 (    9)
  link_NAG-ASN         : bond        0.00775 /  0.38 (    8)
  link_NAG-ASN         : angle       2.89712 /  1.97 (   24)

*********************** 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
  132 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.6890 (mtm-85) cc_final: 0.6558 (mtm-85)
REVERT: D  144 LEU cc_start: 0.8920 (tp) cc_final: 0.8602 (tt)
REVERT: B  146 TRP cc_start: 0.8667 (p90) cc_final: 0.8338 (p90)
REVERT: B  239 ILE cc_start: 0.7126 (mm) cc_final: 0.6811 (pt)
  outliers start: 21
  outliers final: 14
  residues processed: 124
  average time/residue: 0.0869
  time to fit residues: 14.3279
Evaluate side-chains
  112 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   36 ARG
Chi-restraints excluded: chain C residue   75 HIS
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   90 VAL
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain A residue   99 MET
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  114 ASN
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  301 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.6384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  77 ASN
D 150 HIS
D 154 GLN
A  71 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.162126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.140473 restraints weight = 15029.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.143436 restraints weight = 9277.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.145600 restraints weight = 6641.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.146863 restraints weight = 5180.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.147999 restraints weight = 4393.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.4306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   7308  Z= 0.200
  Angle     :  0.727  11.336   9990  Z= 0.354
  Chirality :  0.049   0.405   1128
  Planarity :  0.006   0.092   1256
  Dihedral  :  4.351  32.166    936
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.20 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 18.55 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.28), residues: 855
  helix:  2.21 (0.42), residues: 148
  sheet: -0.73 (0.31), residues: 237
  loop : -1.85 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 141 
 TYR   0.020   0.002   TYR B  79 
 PHE   0.019   0.002   PHE C 188 
 TRP   0.012   0.002   TRP A 217 
 HIS   0.005   0.001   HIS D  52 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00465 /  0.20 ( 7289)
  covalent geometry    : angle       0.70732 /  0.35 ( 9941)
  SS BOND              : bond        0.00453 /  0.24 (    8)
  SS BOND              : angle       1.88698 /  1.01 (   16)
  hydrogen bonds       : bond        0.05362 /  3.61 (  196)
  hydrogen bonds       : angle       4.74718 /  3.35 (  549)
  link_BETA1-4         : bond        0.00118 /  0.06 (    3)
  link_BETA1-4         : angle       1.22886 /  0.58 (    9)
  link_NAG-ASN         : bond        0.00703 /  0.35 (    8)
  link_NAG-ASN         : angle       3.10389 /  2.02 (   24)

*********************** 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
  135 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.7037 (mtm-85) cc_final: 0.6690 (mtm-85)
REVERT: D   64 GLN cc_start: 0.7823 (tp40) cc_final: 0.7463 (tp40)
REVERT: B   76 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.6995 (tttp)
REVERT: B  146 TRP cc_start: 0.8845 (p90) cc_final: 0.8390 (p90)
  outliers start: 24
  outliers final: 16
  residues processed: 129
  average time/residue: 0.0701
  time to fit residues: 12.1856
Evaluate side-chains
  108 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
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  140 LEU
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 A residue  120 VAL
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 20 optimal weight:    0.0020
   chunk 53 optimal weight:    2.9990
   chunk 76 optimal weight:    0.3980
   chunk 59 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0970
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.4786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 154 GLN
B 271 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.167843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.146830 restraints weight = 15395.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.150046 restraints weight = 9378.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.152275 restraints weight = 6579.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.153758 restraints weight = 5071.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.154762 restraints weight = 4195.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
moved from start:          0.4369

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= 0.112
  Angle     :  0.630  11.774   9990  Z= 0.292
  Chirality :  0.045   0.390   1128
  Planarity :  0.005   0.089   1256
  Dihedral  :  3.996  33.768    936
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.61 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.10 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.28), residues: 855
  helix:  2.45 (0.42), residues: 148
  sheet: -0.67 (0.30), residues: 247
  loop : -1.76 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 298 
 TYR   0.017   0.001   TYR D 204 
 PHE   0.019   0.001   PHE B  72 
 TRP   0.022   0.001   TRP A  89 
 HIS   0.004   0.001   HIS D 117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.11 ( 7289)
  covalent geometry    : angle       0.61094 /  0.29 ( 9941)
  SS BOND              : bond        0.00348 /  0.18 (    8)
  SS BOND              : angle       1.61272 /  0.87 (   16)
  hydrogen bonds       : bond        0.04389 /  2.97 (  196)
  hydrogen bonds       : angle       4.41333 /  3.11 (  549)
  link_BETA1-4         : bond        0.00260 /  0.13 (    3)
  link_BETA1-4         : angle       0.99291 /  0.47 (    9)
  link_NAG-ASN         : bond        0.00662 /  0.33 (    8)
  link_NAG-ASN         : angle       2.91267 /  1.99 (   24)

*********************** 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
  116 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.6998 (mtm-85) cc_final: 0.6659 (mtm-85)
REVERT: D   64 GLN cc_start: 0.7774 (tp40) cc_final: 0.7395 (tp40)
REVERT: D  132 MET cc_start: 0.7435 (ppp) cc_final: 0.7145 (ppp)
REVERT: A  115 TRP cc_start: 0.5828 (p90) cc_final: 0.5608 (p90)
REVERT: B   76 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7026 (tttp)
REVERT: B  146 TRP cc_start: 0.8775 (p90) cc_final: 0.8341 (p90)
  outliers start: 23
  outliers final: 15
  residues processed: 108
  average time/residue: 0.0726
  time to fit residues: 10.6346
Evaluate side-chains
  104 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
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   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   90 VAL
Chi-restraints excluded: chain D residue  102 ASP
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   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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 69 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 15 optimal weight:    0.4980
   chunk 6 optimal weight:    0.0770
   overall best weight:    1.5144

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4213 r_free = 0.4213 target = 0.160589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.139842 restraints weight = 15484.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.142756 restraints weight = 9596.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.144796 restraints weight = 6863.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.146128 restraints weight = 5403.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.146950 restraints weight = 4566.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.4058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.5237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   7308  Z= 0.189
  Angle     :  0.742  15.950   9990  Z= 0.353
  Chirality :  0.049   0.399   1128
  Planarity :  0.006   0.099   1256
  Dihedral  :  4.688  36.431    936
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.02 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 21.14 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.28), residues: 855
  helix:  2.32 (0.42), residues: 148
  sheet: -0.69 (0.31), residues: 228
  loop : -1.86 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 105 
 TYR   0.020   0.002   TYR B  79 
 PHE   0.021   0.002   PHE B  72 
 TRP   0.017   0.002   TRP A  89 
 HIS   0.005   0.001   HIS D  52 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00437 /  0.19 ( 7289)
  covalent geometry    : angle       0.72361 /  0.35 ( 9941)
  SS BOND              : bond        0.00577 /  0.30 (    8)
  SS BOND              : angle       2.19386 /  1.16 (   16)
  hydrogen bonds       : bond        0.05622 /  3.74 (  196)
  hydrogen bonds       : angle       4.71400 /  3.30 (  549)
  link_BETA1-4         : bond        0.00297 /  0.14 (    3)
  link_BETA1-4         : angle       1.25082 /  0.53 (    9)
  link_NAG-ASN         : bond        0.00645 /  0.32 (    8)
  link_NAG-ASN         : angle       2.93172 /  1.90 (   24)

*********************** 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
  123 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   45 ASP cc_start: 0.7019 (t0) cc_final: 0.6762 (m-30)
REVERT: C  150 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7710 (mm-30)
REVERT: C  198 ARG cc_start: 0.7134 (mtm-85) cc_final: 0.6756 (mtm-85)
REVERT: D   64 GLN cc_start: 0.7864 (tp40) cc_final: 0.7574 (tp40)
REVERT: D   95 GLN cc_start: 0.8573 (mm110) cc_final: 0.8284 (mm-40)
REVERT: D  132 MET cc_start: 0.7513 (ppp) cc_final: 0.7290 (ppp)
REVERT: D  140 MET cc_start: 0.8491 (tmm) cc_final: 0.8219 (tmm)
REVERT: A  182 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6437 (mm-30)
REVERT: B   76 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7167 (tttp)
REVERT: B  146 TRP cc_start: 0.8823 (p90) cc_final: 0.8311 (p90)
REVERT: B  260 GLN cc_start: 0.7122 (mt0) cc_final: 0.6834 (mt0)
  outliers start: 24
  outliers final: 16
  residues processed: 116
  average time/residue: 0.0741
  time to fit residues: 11.4831
Evaluate side-chains
  107 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
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  140 LEU
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   90 VAL
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  200 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  164 TRP
Chi-restraints excluded: chain B residue  196 VAL
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 29 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 41 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 82 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0370
   chunk 21 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    1.9464

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 126 GLN
** 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 = 0.4189 r_free = 0.4189 target = 0.158835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.137481 restraints weight = 15131.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.140204 restraints weight = 9759.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.142079 restraints weight = 7170.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.143214 restraints weight = 5773.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.144246 restraints weight = 4972.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.5968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   7308  Z= 0.220
  Angle     :  0.779  11.274   9990  Z= 0.378
  Chirality :  0.050   0.402   1128
  Planarity :  0.007   0.097   1256
  Dihedral  :  5.205  44.457    936
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.25 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 21.14 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.28), residues: 855
  helix:  2.45 (0.42), residues: 141
  sheet: -0.82 (0.31), residues: 230
  loop : -2.03 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 105 
 TYR   0.020   0.002   TYR B 257 
 PHE   0.019   0.002   PHE B  72 
 TRP   0.024   0.002   TRP A 217 
 HIS   0.006   0.001   HIS D  52 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00507 /  0.22 ( 7289)
  covalent geometry    : angle       0.75790 /  0.37 ( 9941)
  SS BOND              : bond        0.00756 /  0.39 (    8)
  SS BOND              : angle       2.61371 /  1.39 (   16)
  hydrogen bonds       : bond        0.06201 /  4.10 (  196)
  hydrogen bonds       : angle       4.87184 /  3.43 (  549)
  link_BETA1-4         : bond        0.00241 /  0.12 (    3)
  link_BETA1-4         : angle       1.31369 /  0.62 (    9)
  link_NAG-ASN         : bond        0.00601 /  0.30 (    8)
  link_NAG-ASN         : angle       3.10270 /  2.04 (   24)

*********************** 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
  128 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 95
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.7124 (mtm-85) cc_final: 0.6755 (mtm-85)
REVERT: D   64 GLN cc_start: 0.7976 (tp40) cc_final: 0.7729 (tp40)
REVERT: D  132 MET cc_start: 0.7559 (ppp) cc_final: 0.6851 (ppp)
REVERT: D  140 MET cc_start: 0.8461 (tmm) cc_final: 0.8173 (tmm)
REVERT: A  182 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6358 (mm-30)
REVERT: A  194 GLN cc_start: 0.7180 (pm20) cc_final: 0.6870 (pm20)
REVERT: A  196 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7571 (pp)
REVERT: B   74 ILE cc_start: 0.9098 (mm) cc_final: 0.8893 (mt)
REVERT: B   76 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7014 (tttp)
REVERT: B  146 TRP cc_start: 0.8854 (p90) cc_final: 0.8384 (p90)
  outliers start: 33
  outliers final: 23
  residues processed: 119
  average time/residue: 0.0790
  time to fit residues: 12.7180
Evaluate side-chains
  117 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 91
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
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  107 THR
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  209 THR
Chi-restraints excluded: chain C residue  211 TYR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain D residue  195 VAL
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  200 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  164 TRP
Chi-restraints excluded: chain B residue  181 SER
Chi-restraints excluded: chain B residue  182 CYS
Chi-restraints excluded: chain B residue  191 PHE
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  265 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 80 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 50 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 61 optimal weight:    0.2980
   chunk 74 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 126 GLN
** 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 = 0.4241 r_free = 0.4241 target = 0.162532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.141374 restraints weight = 15261.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.144417 restraints weight = 9322.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.146540 restraints weight = 6626.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.147981 restraints weight = 5181.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.148983 restraints weight = 4330.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.5948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7308  Z= 0.129
  Angle     :  0.704  12.018   9990  Z= 0.332
  Chirality :  0.046   0.381   1128
  Planarity :  0.006   0.099   1256
  Dihedral  :  4.738  37.925    936
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.55 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 22.83 %
    Favored  : 73.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.28), residues: 855
  helix:  2.70 (0.43), residues: 142
  sheet: -0.69 (0.32), residues: 228
  loop : -1.87 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 134 
 TYR   0.028   0.001   TYR B 295 
 PHE   0.024   0.001   PHE B  72 
 TRP   0.025   0.002   TRP A  89 
 HIS   0.004   0.001   HIS D 117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.13 ( 7289)
  covalent geometry    : angle       0.68353 /  0.33 ( 9941)
  SS BOND              : bond        0.00511 /  0.26 (    8)
  SS BOND              : angle       2.15378 /  1.14 (   16)
  hydrogen bonds       : bond        0.05241 /  3.51 (  196)
  hydrogen bonds       : angle       4.62343 /  3.27 (  549)
  link_BETA1-4         : bond        0.00305 /  0.15 (    3)
  link_BETA1-4         : angle       1.23722 /  0.64 (    9)
  link_NAG-ASN         : bond        0.00675 /  0.33 (    8)
  link_NAG-ASN         : angle       2.97070 /  2.01 (   24)

*********************** 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
  120 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   80 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7105 (mm)
REVERT: D   64 GLN cc_start: 0.7874 (tp40) cc_final: 0.7631 (tp40)
REVERT: D  135 MET cc_start: 0.7737 (ptp) cc_final: 0.7522 (pmm)
REVERT: D  140 MET cc_start: 0.8439 (tmm) cc_final: 0.8151 (tmm)
REVERT: A  182 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6227 (mm-30)
REVERT: A  194 GLN cc_start: 0.7052 (pm20) cc_final: 0.6813 (pm20)
REVERT: B   76 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7118 (tttp)
REVERT: B  146 TRP cc_start: 0.8767 (p90) cc_final: 0.8343 (p90)
  outliers start: 26
  outliers final: 18
  residues processed: 114
  average time/residue: 0.0725
  time to fit residues: 11.2485
Evaluate side-chains
  107 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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   80 LEU
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  155 THR
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  189 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  119 THR
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  182 CYS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  265 ASP
Chi-restraints excluded: chain B residue  293 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.9580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4238 r_free = 0.4238 target = 0.162156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.141316 restraints weight = 15163.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.144282 restraints weight = 9286.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.146369 restraints weight = 6623.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.147826 restraints weight = 5168.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.148708 restraints weight = 4328.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.4116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.6005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7308  Z= 0.142
  Angle     :  0.699  11.492   9990  Z= 0.333
  Chirality :  0.047   0.380   1128
  Planarity :  0.006   0.098   1256
  Dihedral  :  4.723  41.276    936
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.55 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 21.79 %
    Favored  : 74.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.28), residues: 855
  helix:  2.76 (0.43), residues: 142
  sheet: -0.70 (0.32), residues: 225
  loop : -1.81 (0.26), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 298 
 TYR   0.016   0.001   TYR B  79 
 PHE   0.023   0.001   PHE B  72 
 TRP   0.017   0.002   TRP B 244 
 HIS   0.004   0.001   HIS D 117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.14 ( 7289)
  covalent geometry    : angle       0.68110 /  0.33 ( 9941)
  SS BOND              : bond        0.00537 /  0.28 (    8)
  SS BOND              : angle       2.09368 /  1.11 (   16)
  hydrogen bonds       : bond        0.05019 /  3.35 (  196)
  hydrogen bonds       : angle       4.58674 /  3.24 (  549)
  link_BETA1-4         : bond        0.00280 /  0.14 (    3)
  link_BETA1-4         : angle       1.18621 /  0.60 (    9)
  link_NAG-ASN         : bond        0.00563 /  0.28 (    8)
  link_NAG-ASN         : angle       2.79772 /  1.88 (   24)

*********************** 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
  119 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   80 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7287 (mm)
REVERT: D   64 GLN cc_start: 0.7922 (tp40) cc_final: 0.7630 (tp40)
REVERT: D  135 MET cc_start: 0.7709 (ptp) cc_final: 0.7384 (pmm)
REVERT: D  140 MET cc_start: 0.8399 (tmm) cc_final: 0.8121 (tmm)
REVERT: A  182 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6358 (mm-30)
REVERT: A  194 GLN cc_start: 0.7156 (pm20) cc_final: 0.6924 (pm20)
REVERT: B   76 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7166 (tttp)
REVERT: B  146 TRP cc_start: 0.8780 (p90) cc_final: 0.8343 (p90)
  outliers start: 29
  outliers final: 22
  residues processed: 113
  average time/residue: 0.0717
  time to fit residues: 11.3550
Evaluate side-chains
  110 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
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   80 LEU
Chi-restraints excluded: chain C residue  180 VAL
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  155 THR
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  208 CYS
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  100 GLN
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  182 CYS
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  230 VAL
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 16 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0270
   chunk 58 optimal weight:    6.9990
   chunk 78 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    1.0042

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4241 r_free = 0.4241 target = 0.162183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.141472 restraints weight = 15097.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.144475 restraints weight = 9265.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.146516 restraints weight = 6588.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.147910 restraints weight = 5170.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.148707 restraints weight = 4335.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.4131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.6075

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= 0.145
  Angle     :  0.709  11.217   9990  Z= 0.339
  Chirality :  0.048   0.519   1128
  Planarity :  0.006   0.096   1256
  Dihedral  :  4.723  40.406    936
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.67 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 21.79 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.28), residues: 855
  helix:  2.73 (0.43), residues: 142
  sheet: -0.68 (0.32), residues: 224
  loop : -1.83 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 298 
 TYR   0.016   0.001   TYR B  79 
 PHE   0.024   0.001   PHE B  72 
 TRP   0.020   0.002   TRP A 217 
 HIS   0.004   0.001   HIS D 117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.14 ( 7289)
  covalent geometry    : angle       0.69047 /  0.33 ( 9941)
  SS BOND              : bond        0.00519 /  0.27 (    8)
  SS BOND              : angle       2.04320 /  1.08 (   16)
  hydrogen bonds       : bond        0.04944 /  3.28 (  196)
  hydrogen bonds       : angle       4.58170 /  3.24 (  549)
  link_BETA1-4         : bond        0.00281 /  0.14 (    3)
  link_BETA1-4         : angle       1.12734 /  0.57 (    9)
  link_NAG-ASN         : bond        0.00850 /  0.43 (    8)
  link_NAG-ASN         : angle       2.89389 /  1.92 (   24)

********************** 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
  112 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 84
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   80 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7266 (mm)
REVERT: C  184 GLU cc_start: 0.8032 (tt0) cc_final: 0.7806 (tt0)
REVERT: D   64 GLN cc_start: 0.7869 (tp40) cc_final: 0.7562 (tp40)
REVERT: D  135 MET cc_start: 0.7914 (ptp) cc_final: 0.7452 (pmm)
REVERT: D  140 MET cc_start: 0.8458 (tmm) cc_final: 0.8152 (tmm)
REVERT: A  182 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6393 (mm-30)
REVERT: A  194 GLN cc_start: 0.7280 (pm20) cc_final: 0.6951 (pm20)
REVERT: B   76 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7137 (tttp)
REVERT: B  146 TRP cc_start: 0.8831 (p90) cc_final: 0.8379 (p90)
  outliers start: 28
  outliers final: 24
  residues processed: 106
  average time/residue: 0.0814
  time to fit residues: 12.0090
Evaluate side-chains
  111 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 84
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   45 ASP
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  180 VAL
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  120 VAL
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  208 CYS
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  182 CYS
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  230 VAL
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 9 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 81 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4282 r_free = 0.4282 target = 0.164475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.144913 restraints weight = 15118.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.147796 restraints weight = 9281.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.149720 restraints weight = 6598.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.150976 restraints weight = 5193.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.151570 restraints weight = 4364.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.6145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7308  Z= 0.137
  Angle     :  0.697  11.036   9990  Z= 0.332
  Chirality :  0.046   0.430   1128
  Planarity :  0.006   0.096   1256
  Dihedral  :  4.679  41.487    936
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.67 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 21.79 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.28), residues: 855
  helix:  2.76 (0.43), residues: 142
  sheet: -0.71 (0.32), residues: 225
  loop : -1.82 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 209 
 TYR   0.015   0.001   TYR B  79 
 PHE   0.023   0.001   PHE B  72 
 TRP   0.017   0.002   TRP A  89 
 HIS   0.004   0.001   HIS D 117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.14 ( 7289)
  covalent geometry    : angle       0.67687 /  0.33 ( 9941)
  SS BOND              : bond        0.00493 /  0.25 (    8)
  SS BOND              : angle       1.95155 /  1.02 (   16)
  hydrogen bonds       : bond        0.04696 /  3.12 (  196)
  hydrogen bonds       : angle       4.48735 /  3.17 (  549)
  link_BETA1-4         : bond        0.00355 /  0.17 (    3)
  link_BETA1-4         : angle       1.07517 /  0.54 (    9)
  link_NAG-ASN         : bond        0.00796 /  0.40 (    8)
  link_NAG-ASN         : angle       3.06445 /  2.05 (   24)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1290.52 seconds
wall clock time: 22 minutes 53.29 seconds (1373.29 seconds total)