Starting phenix.real_space_refine
on Sat Oct 11 00:04:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oe4_16824/10_2025/8oe4_16824.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oe4_16824/10_2025/8oe4_16824.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8oe4_16824/10_2025/8oe4_16824.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oe4_16824/10_2025/8oe4_16824.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oe4_16824/10_2025/8oe4_16824.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oe4_16824/10_2025/8oe4_16824.cif"
  }
  resolution = 3.6
  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=   0.011
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      62      5.16       5
     C    6273      2.51       5
     N    1682      2.21       5
     O    1934      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9951
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2388
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2388
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 287}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 1116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1116
          Classifications: {'peptide': 144}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 134}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "C"
      Number of atoms: 2384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2384
          Classifications: {'peptide': 293}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 280}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "D"
      Number of atoms: 3957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 510, 3957
          Classifications: {'peptide': 510}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 39, 'TRANS': 470}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "E"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 2.29, per 1000 atoms: 0.23
  Number of scatterers: 9951
  At special positions: 0
  Unit cell: (104.039, 135.447, 162.929, 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      62     16.00
     O    1934      8.00
     N    1682      7.00
     C    6273      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=20, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 142 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 170 " - pdb=" SG  CYS A 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 199 " - pdb=" SG  CYS B  73 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 300 " - pdb=" SG  CYS A 327 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  77 " - pdb=" SG  CYS B  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  30 " - pdb=" SG  CYS C 115 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  52 " - pdb=" SG  CYS C 101 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  59 " - pdb=" SG  CYS C 105 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 133 " - pdb=" SG  CYS C 144 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 253 " - pdb=" SG  CYS C 296 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  24 " - pdb=" SG  CYS D  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  29 " - pdb=" SG  CYS D  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  52 " - pdb=" SG  CYS D  62 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  80 " - pdb=" SG  CYS D  86 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 186 " - pdb=" SG  CYS D 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 230 " - pdb=" SG  CYS D 271 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 291 " - pdb=" SG  CYS D 368 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 293 " - pdb=" SG  CYS D 383 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 413 " - pdb=" SG  CYS D 474 " 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
    ALPHA1-3
      " BMA E   3 " - " MAN E   4 "
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C 601 " - " ASN C  81 "
      " NAG C 602 " - " ASN C 141 "
      " NAG E   1 " - " ASN A 222 "
      " NAG F   1 " - " ASN C 180 "
  Time building additional restraints: 0.90
  Conformation dependent library (CDL) restraints added in 390.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2352

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 28 sheets defined
      11.0% alpha, 44.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 228 through 232
    Processing helix  chain 'B' and resid 29 through 48
      removed outlier: 3.735A  pdb=" N   HIS B  48 " --> pdb=" O   ALA B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 85
    Processing helix  chain 'B' and resid 85 through 105
      removed outlier: 4.560A  pdb=" N   CYS B  89 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG B  92 " --> pdb=" O   PHE B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 111
    Processing helix  chain 'B' and resid 119 through 136
      removed outlier: 3.888A  pdb=" N   GLN B 123 " --> pdb=" O   SER B 119 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   HIS B 125 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA B 126 " --> pdb=" O   GLY B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 187
      removed outlier: 4.439A  pdb=" N   LEU B 160 " --> pdb=" O   TRP B 156 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA B 171 " --> pdb=" O   ARG B 167 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   VAL B 175 " --> pdb=" O   ALA B 171 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA B 184 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ALA B 185 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 184 through 186
      No H-bonds generated for 'chain 'C' and resid 184 through 186'
    Processing helix  chain 'D' and resid 102 through 104
      No H-bonds generated for 'chain 'D' and resid 102 through 104'
    Processing helix  chain 'D' and resid 275 through 279
    Processing helix  chain 'D' and resid 426 through 430
      removed outlier: 3.583A  pdb=" N   TRP D 430 " --> pdb=" O   LEU D 427 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 442 through 447
    Processing helix  chain 'D' and resid 469 through 474
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27
      removed outlier: 7.101A  pdb=" N   VAL A  30 " --> pdb=" O   LEU A  26 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   TYR A  31 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   HIS A 105 " --> pdb=" O   TYR A  31 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   VAL A  33 " --> pdb=" O   HIS A 105 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   LYS A 107 " --> pdb=" O   VAL A  33 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   LEU A  35 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   CYS A  90 " --> pdb=" O   LEU A  97 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   HIS A  99 " --> pdb=" O   TYR A  88 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   TYR A  88 " --> pdb=" O   HIS A  99 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 27
      removed outlier: 7.101A  pdb=" N   VAL A  30 " --> pdb=" O   LEU A  26 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   TYR A  31 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   HIS A 105 " --> pdb=" O   TYR A  31 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   VAL A  33 " --> pdb=" O   HIS A 105 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   LYS A 107 " --> pdb=" O   VAL A  33 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   LEU A  35 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 49
    Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118
      removed outlier: 4.753A  pdb=" N   LEU A 145 " --> pdb=" O   LYS A 118 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 132
      removed outlier: 3.634A  pdb=" N   ASN A 184 " --> pdb=" O   ARG A 181 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   SER A 190 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   LEU A 175 " --> pdb=" O   SER A 190 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 153
    Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 160
    Processing sheet with id=AA8, first strand: chain 'A' and resid 239 through 245
      removed outlier: 5.558A  pdb=" N   ASN A 240 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   GLU A 257 " --> pdb=" O   ASN A 240 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LYS A 244 " --> pdb=" O   GLU A 253 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLU A 253 " --> pdb=" O   LYS A 244 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 279
      removed outlier: 3.758A  pdb=" N   CYS A 274 " --> pdb=" O   ARG A 309 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL A 308 " --> pdb=" O   ALA A 323 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 32 through 37
      removed outlier: 3.747A  pdb=" N   HIS C  33 " --> pdb=" O   GLN C  53 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 43
      removed outlier: 6.461A  pdb=" N   PHE C  42 " --> pdb=" O   GLY C 122 " (cutoff:3.500A)
      removed outlier: 7.121A  pdb=" N   CYS C 101 " --> pdb=" O   ILE C 114 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   GLY C 116 " --> pdb=" O   MET C  99 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   MET C  99 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   ASP C 118 " --> pdb=" O   ALA C  97 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   ALA C  97 " --> pdb=" O   ASP C 118 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   TYR C 100 " --> pdb=" O   TYR C  67 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LYS C  63 " --> pdb=" O   GLU C 104 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 179 through 182
      removed outlier: 4.014A  pdb=" N   ILE C 179 " --> pdb=" O   CYS C 144 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   ASN C 141 " --> pdb=" O   TYR C 136 " (cutoff:3.500A)
      removed outlier: 7.765A  pdb=" N   ILE C 219 " --> pdb=" O   CYS C 133 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ILE C 135 " --> pdb=" O   ILE C 219 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 170 through 175
    Processing sheet with id=AB5, first strand: chain 'C' and resid 170 through 175
    Processing sheet with id=AB6, first strand: chain 'C' and resid 223 through 231
      removed outlier: 5.265A  pdb=" N   ILE C 225 " --> pdb=" O   ASP C 243 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ASP C 243 " --> pdb=" O   ILE C 225 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   SER C 280 " --> pdb=" O   ILE C 240 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   TRP C 242 " --> pdb=" O   GLN C 278 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLN C 278 " --> pdb=" O   TRP C 242 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 266 through 272
      removed outlier: 3.592A  pdb=" N   LYS C 268 " --> pdb=" O   MET C 255 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   MET C 255 " --> pdb=" O   LYS C 268 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL C 251 " --> pdb=" O   THR C 272 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 47 through 54
      removed outlier: 4.296A  pdb=" N   LEU D  50 " --> pdb=" O   SER D  63 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   SER D  63 " --> pdb=" O   LEU D  50 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   CYS D  52 " --> pdb=" O   GLU D  61 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   GLU D  61 " --> pdb=" O   CYS D  52 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   ARG D  54 " --> pdb=" O   ARG D  59 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   ARG D  59 " --> pdb=" O   ARG D  54 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 86 through 92
      removed outlier: 5.117A  pdb=" N   TYR D  88 " --> pdb=" O   CYS D  79 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   CYS D  79 " --> pdb=" O   TYR D  88 " (cutoff:3.500A)
      removed outlier: 5.656A  pdb=" N   ALA D  90 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   LEU D  77 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLY D  92 " --> pdb=" O   HIS D  75 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 86 through 92
      removed outlier: 5.117A  pdb=" N   TYR D  88 " --> pdb=" O   CYS D  79 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   CYS D  79 " --> pdb=" O   TYR D  88 " (cutoff:3.500A)
      removed outlier: 5.656A  pdb=" N   ALA D  90 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   LEU D  77 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLY D  92 " --> pdb=" O   HIS D  75 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 146 through 151
    Processing sheet with id=AC3, first strand: chain 'D' and resid 182 through 189
      removed outlier: 3.655A  pdb=" N   CYS D 186 " --> pdb=" O   VAL D 170 " (cutoff:3.500A)
      removed outlier: 7.510A  pdb=" N   VAL D 170 " --> pdb=" O   CYS D 186 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   ALA D 168 " --> pdb=" O   PRO D 188 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 242 through 245
      removed outlier: 6.200A  pdb=" N   ARG D 242 " --> pdb=" O   LYS D 259 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'D' and resid 298 through 302
    Processing sheet with id=AC6, first strand: chain 'D' and resid 298 through 302
    Processing sheet with id=AC7, first strand: chain 'D' and resid 346 through 349
    Processing sheet with id=AC8, first strand: chain 'D' and resid 382 through 389
      removed outlier: 4.217A  pdb=" N   TYR D 367 " --> pdb=" O   THR D 386 " (cutoff:3.500A)
      removed outlier: 5.501A  pdb=" N   MET D 365 " --> pdb=" O   PRO D 388 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LYS D 412 " --> pdb=" O   GLY D 440 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   ALA D 420 " --> pdb=" O   THR D 432 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   THR D 432 " --> pdb=" O   ALA D 420 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'D' and resid 450 through 458
      removed outlier: 5.874A  pdb=" N   HIS D 451 " --> pdb=" O   ALA D 467 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   ALA D 467 " --> pdb=" O   HIS D 451 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   SER D 461 " --> pdb=" O   HIS D 457 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'D' and resid 493 through 498

    399 hydrogen bonds defined for protein.
    1062 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.72

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3202
        1.34 -     1.47: 2530
        1.47 -     1.59: 4394
        1.59 -     1.71: 1
        1.71 -     1.83: 78
  Bond restraints: 10205
  Sorted by residual:
  bond pdb=" CG  PRO A 326 "
       pdb=" CD  PRO A 326 "
    ideal  model  delta    sigma   weight residual
    1.503  1.311  0.192 3.40e-02 8.65e+02 3.21e+01
  bond pdb=" CB  PRO A 326 "
       pdb=" CG  PRO A 326 "
    ideal  model  delta    sigma   weight residual
    1.492  1.671 -0.179 5.00e-02 4.00e+02 1.29e+01
  bond pdb=" N   PRO A 326 "
       pdb=" CD  PRO A 326 "
    ideal  model  delta    sigma   weight residual
    1.473  1.522 -0.049 1.40e-02 5.10e+03 1.23e+01
  bond pdb=" C1  NAG C 601 "
       pdb=" O5  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.443 -0.037 2.00e-02 2.50e+03 3.38e+00
  bond pdb=" N   PRO A 326 "
       pdb=" CA  PRO A 326 "
    ideal  model  delta    sigma   weight residual
    1.465  1.447  0.018 1.11e-02 8.12e+03 2.62e+00
  ... (remaining 10200 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.31: 13767
        3.31 -     6.62: 112
        6.62 -     9.94: 10
        9.94 -    13.25: 1
       13.25 -    16.56: 2
  Bond angle restraints: 13892
  Sorted by residual:
  angle pdb=" CA  PRO A 326 "
        pdb=" N   PRO A 326 "
        pdb=" CD  PRO A 326 "
      ideal   model   delta    sigma   weight residual
     112.00   95.44   16.56 1.40e+00 5.10e-01 1.40e+02
  angle pdb=" N   PRO A 326 "
        pdb=" CD  PRO A 326 "
        pdb=" CG  PRO A 326 "
      ideal   model   delta    sigma   weight residual
     103.20   91.36   11.84 1.50e+00 4.44e-01 6.23e+01
  angle pdb=" CA  PRO A 326 "
        pdb=" CB  PRO A 326 "
        pdb=" CG  PRO A 326 "
      ideal   model   delta    sigma   weight residual
     104.50   95.89    8.61 1.90e+00 2.77e-01 2.06e+01
  angle pdb=" N   PRO A 326 "
        pdb=" CA  PRO A 326 "
        pdb=" C   PRO A 326 "
      ideal   model   delta    sigma   weight residual
     112.01  120.10   -8.09 1.84e+00 2.95e-01 1.93e+01
  angle pdb=" C   ASN C  81 "
        pdb=" CA  ASN C  81 "
        pdb=" CB  ASN C  81 "
      ideal   model   delta    sigma   weight residual
     110.43  116.93   -6.50 1.68e+00 3.54e-01 1.50e+01
  ... (remaining 13887 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.28: 5789
       21.28 -    42.55: 385
       42.55 -    63.83: 49
       63.83 -    85.10: 15
       85.10 -   106.38: 9
  Dihedral angle restraints: 6247
    sinusoidal: 2605
      harmonic: 3642
  Sorted by residual:
  dihedral pdb=" CB  CYS D  24 "
           pdb=" SG  CYS D  24 "
           pdb=" SG  CYS D  30 "
           pdb=" CB  CYS D  30 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.18  -60.18     1      1.00e+01 1.00e-02 4.83e+01
  dihedral pdb=" CA  ASN C 141 "
           pdb=" C   ASN C 141 "
           pdb=" N   MET C 142 "
           pdb=" CA  MET C 142 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.52   27.48     0      5.00e+00 4.00e-02 3.02e+01
  dihedral pdb=" CB  CYS C  59 "
           pdb=" SG  CYS C  59 "
           pdb=" SG  CYS C 105 "
           pdb=" CB  CYS C 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -129.31   43.31     1      1.00e+01 1.00e-02 2.61e+01
  ... (remaining 6244 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1261
       0.062 -    0.124: 253
       0.124 -    0.186: 22
       0.186 -    0.248: 5
       0.248 -    0.310: 1
  Chirality restraints: 1542
  Sorted by residual:
  chirality pdb=" CA  PRO A 326 "
            pdb=" N   PRO A 326 "
            pdb=" C   PRO A 326 "
            pdb=" CB  PRO A 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.41    0.31 2.00e-01 2.50e+01 2.40e+00
  chirality pdb=" C5  BMA E   3 "
            pdb=" C4  BMA E   3 "
            pdb=" C6  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.52    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN A 222 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.62    0.22 2.00e-01 2.50e+01 1.19e+00
  ... (remaining 1539 not shown)

  Planarity restraints: 1781
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C  81 "    0.033 2.00e-02 2.50e+03   3.11e-02 1.21e+01
        pdb=" CG  ASN C  81 "   -0.046 2.00e-02 2.50e+03
        pdb=" OD1 ASN C  81 "    0.009 2.00e-02 2.50e+03
        pdb=" ND2 ASN C  81 "   -0.026 2.00e-02 2.50e+03
        pdb=" C1  NAG C 601 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 325 "   -0.056 5.00e-02 4.00e+02   7.56e-02 9.15e+00
        pdb=" N   PRO A 326 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO A 326 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 326 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 222 "   -0.027 2.00e-02 2.50e+03   2.53e-02 7.98e+00
        pdb=" CG  ASN A 222 "    0.034 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 222 "   -0.006 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 222 "    0.024 2.00e-02 2.50e+03
        pdb=" C1  NAG E   1 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 1778 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 664
        2.74 -     3.28: 8931
        3.28 -     3.82: 15796
        3.82 -     4.36: 18796
        4.36 -     4.90: 32359
  Nonbonded interactions: 76546
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 135 "
            pdb=" OG  SER A 137 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   ASP A  84 "
            pdb=" OH  TYR A  88 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OH  TYR B 100 "
            pdb=" OG  SER B 168 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OG  SER A 158 "
            pdb=" O   GLU A 209 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OE2 GLU B 101 "
            pdb=" OG  SER B 132 "
     model   vdw
     2.285 3.040
  ... (remaining 76541 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.230
  Find NCS groups from input model:        0.050
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
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      :  0.005   0.192  10233  Z= 0.239
  Angle     :  0.863  16.562  13956  Z= 0.471
  Chirality :  0.049   0.310   1542
  Planarity :  0.006   0.098   1777
  Dihedral  : 14.527 106.377   3835
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 12.74 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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 aren not related in a simple way.
  whole: -0.38 (0.23), residues: 1231
  helix: -0.14 (0.49), residues: 99
  sheet:  0.21 (0.22), residues: 520
  loop : -0.61 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG D 536 
 TYR   0.035   0.003   TYR D 357 
 PHE   0.026   0.002   PHE D 208 
 TRP   0.025   0.002   TRP D 466 
 HIS   0.018   0.001   HIS D 438 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 (10205)
  covalent geometry    : angle       0.84765 (13892)
  SS BOND              : bond        0.00368 (   20)
  SS BOND              : angle       1.47407 (   40)
  hydrogen bonds       : bond        0.23150 (  353)
  hydrogen bonds       : angle       8.59682 ( 1062)
  link_ALPHA1-3        : bond        0.00275 (    1)
  link_ALPHA1-3        : angle       1.94039 (    3)
  link_BETA1-4         : bond        0.00605 (    3)
  link_BETA1-4         : angle       2.04791 (    9)
  link_NAG-ASN         : bond        0.00348 (    4)
  link_NAG-ASN         : angle       4.70232 (   12)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8972 (tpp) cc_final: 0.8174 (tpp)
REVERT: B  107 ASP cc_start: 0.9073 (p0) cc_final: 0.8549 (t0)
REVERT: C   99 MET cc_start: 0.8464 (mmm) cc_final: 0.7499 (mmt)
REVERT: C  184 ASP cc_start: 0.9244 (m-30) cc_final: 0.8527 (t0)
REVERT: D  136 SER cc_start: 0.8247 (m) cc_final: 0.7954 (t)
REVERT: D  143 LEU cc_start: 0.8429 (mt) cc_final: 0.8063 (pp)
REVERT: D  408 MET cc_start: 0.6375 (mtt) cc_final: 0.2816 (tmm)
  outliers start: 8
  outliers final: 3
  residues processed: 121
  average time/residue: 0.1143
  time to fit residues: 18.6825
Evaluate side-chains
  60 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain D residue  474 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 123 optimal weight:    0.8980
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:   10.0000
   overall best weight:    3.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  91 HIS
A 216 HIS
D  75 HIS
D 121 ASN
D 171 GLN
D 247 GLN
D 287 HIS
D 330 GLN
D 339 HIS
D 438 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.102064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.065031 restraints weight = 47999.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.066832 restraints weight = 23750.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.066490 restraints weight = 13705.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.066723 restraints weight = 13198.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.066783 restraints weight = 11762.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.2283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  10233  Z= 0.283
  Angle     :  0.760  10.606  13956  Z= 0.383
  Chirality :  0.048   0.164   1542
  Planarity :  0.005   0.065   1777
  Dihedral  :  7.914  68.311   1513
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 16.22 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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 aren not related in a simple way.
  whole: -0.38 (0.23), residues: 1231
  helix:  0.43 (0.48), residues: 104
  sheet:  0.18 (0.21), residues: 528
  loop : -0.71 (0.25), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 301 
 TYR   0.022   0.002   TYR C 136 
 PHE   0.017   0.002   PHE C  75 
 TRP   0.024   0.002   TRP B  45 
 HIS   0.008   0.002   HIS A 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00643 (10205)
  covalent geometry    : angle       0.74513 (13892)
  SS BOND              : bond        0.00299 (   20)
  SS BOND              : angle       1.43120 (   40)
  hydrogen bonds       : bond        0.05570 (  353)
  hydrogen bonds       : angle       6.51456 ( 1062)
  link_ALPHA1-3        : bond        0.00003 (    1)
  link_ALPHA1-3        : angle       3.17816 (    3)
  link_BETA1-4         : bond        0.00579 (    3)
  link_BETA1-4         : angle       3.24211 (    9)
  link_NAG-ASN         : bond        0.00741 (    4)
  link_NAG-ASN         : angle       3.38006 (   12)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 62
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8305 (tpp) cc_final: 0.8027 (tpp)
REVERT: A   51 ASP cc_start: 0.8600 (t0) cc_final: 0.8182 (t70)
REVERT: A  270 SER cc_start: 0.9402 (OUTLIER) cc_final: 0.8910 (p)
REVERT: B  107 ASP cc_start: 0.8970 (p0) cc_final: 0.8404 (t0)
REVERT: C   41 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7644 (tp)
REVERT: C   99 MET cc_start: 0.9006 (mmm) cc_final: 0.7988 (mmt)
REVERT: C  126 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8439 (p0)
REVERT: C  184 ASP cc_start: 0.9358 (m-30) cc_final: 0.8862 (t0)
REVERT: C  255 MET cc_start: 0.7708 (pmm) cc_final: 0.7484 (pmm)
REVERT: D  136 SER cc_start: 0.8709 (m) cc_final: 0.8293 (t)
REVERT: D  143 LEU cc_start: 0.8727 (mt) cc_final: 0.8225 (pp)
REVERT: D  356 MET cc_start: 0.8163 (mtm) cc_final: 0.7961 (mtm)
REVERT: D  408 MET cc_start: 0.3047 (mtt) cc_final: 0.0708 (tmm)
REVERT: D  524 THR cc_start: 0.5665 (OUTLIER) cc_final: 0.5460 (t)
  outliers start: 32
  outliers final: 19
  residues processed: 88
  average time/residue: 0.0889
  time to fit residues: 11.2462
Evaluate side-chains
  74 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 51
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  270 SER
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain B residue   41 CYS
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain C residue   26 THR
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  147 LYS
Chi-restraints excluded: chain D residue  171 GLN
Chi-restraints excluded: chain D residue  229 VAL
Chi-restraints excluded: chain D residue  257 THR
Chi-restraints excluded: chain D residue  474 CYS
Chi-restraints excluded: chain D residue  524 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 101 optimal weight:    9.9990
   chunk 2 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 35 optimal weight:    0.8980
   chunk 54 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 113 optimal weight:    6.9990
   chunk 91 optimal weight:   20.0000
   chunk 32 optimal weight:    0.0050
   chunk 61 optimal weight:    6.9990
   overall best weight:    2.1598

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

Flipped N/Q/H residues before XYZ refinement:
C 161 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.102219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.066244 restraints weight = 48523.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.067565 restraints weight = 23784.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.067519 restraints weight = 15182.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.067748 restraints weight = 12923.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.067769 restraints weight = 11913.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10233  Z= 0.182
  Angle     :  0.657   9.380  13956  Z= 0.330
  Chirality :  0.044   0.156   1542
  Planarity :  0.004   0.050   1777
  Dihedral  :  6.600  59.913   1510
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 16.87 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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 aren not related in a simple way.
  whole: -0.21 (0.24), residues: 1231
  helix:  0.85 (0.51), residues: 104
  sheet:  0.16 (0.21), residues: 536
  loop : -0.51 (0.27), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  74 
 TYR   0.017   0.002   TYR C 173 
 PHE   0.012   0.002   PHE A 140 
 TRP   0.018   0.002   TRP D 466 
 HIS   0.005   0.001   HIS C  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (10205)
  covalent geometry    : angle       0.64542 (13892)
  SS BOND              : bond        0.00279 (   20)
  SS BOND              : angle       1.11492 (   40)
  hydrogen bonds       : bond        0.04773 (  353)
  hydrogen bonds       : angle       6.02955 ( 1062)
  link_ALPHA1-3        : bond        0.01020 (    1)
  link_ALPHA1-3        : angle       2.18326 (    3)
  link_BETA1-4         : bond        0.00289 (    3)
  link_BETA1-4         : angle       2.59832 (    9)
  link_NAG-ASN         : bond        0.00589 (    4)
  link_NAG-ASN         : angle       2.99738 (   12)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 54
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8344 (tpp) cc_final: 0.8097 (tpp)
REVERT: A  125 ASN cc_start: 0.8624 (t0) cc_final: 0.8315 (m-40)
REVERT: A  270 SER cc_start: 0.9436 (OUTLIER) cc_final: 0.8957 (p)
REVERT: B   39 LYS cc_start: 0.8646 (tttp) cc_final: 0.8372 (mtmm)
REVERT: B  107 ASP cc_start: 0.8987 (p0) cc_final: 0.8645 (t0)
REVERT: C   34 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7747 (pt)
REVERT: C   44 MET cc_start: 0.8351 (mmm) cc_final: 0.7814 (mmm)
REVERT: C   99 MET cc_start: 0.9022 (mmm) cc_final: 0.8056 (mmt)
REVERT: C  184 ASP cc_start: 0.9343 (m-30) cc_final: 0.8892 (t0)
REVERT: C  255 MET cc_start: 0.7773 (pmm) cc_final: 0.7531 (pmm)
REVERT: D  136 SER cc_start: 0.8691 (m) cc_final: 0.8266 (t)
REVERT: D  143 LEU cc_start: 0.8721 (mt) cc_final: 0.8226 (pp)
REVERT: D  256 LEU cc_start: 0.9154 (tt) cc_final: 0.8917 (pp)
REVERT: D  408 MET cc_start: 0.2892 (mtt) cc_final: 0.0717 (tmm)
  outliers start: 38
  outliers final: 26
  residues processed: 86
  average time/residue: 0.0953
  time to fit residues: 12.0769
Evaluate side-chains
  81 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 53
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  270 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue  135 LEU
Chi-restraints excluded: chain C residue   26 THR
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain D residue  229 VAL
Chi-restraints excluded: chain D residue  257 THR
Chi-restraints excluded: chain D residue  419 PHE
Chi-restraints excluded: chain D residue  450 HIS
Chi-restraints excluded: chain D residue  474 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 112 optimal weight:   20.0000
   chunk 21 optimal weight:    0.3980
   chunk 72 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 91 optimal weight:   20.0000
   chunk 111 optimal weight:   20.0000
   chunk 86 optimal weight:    9.9990
   chunk 87 optimal weight:    8.9990
   chunk 52 optimal weight:    9.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    3.6788

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

Flipped N/Q/H residues before XYZ refinement:
** B 170 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 = 0.4178 r_free = 0.4178 target = 0.100546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.065952 restraints weight = 49636.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.066408 restraints weight = 25737.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.066091 restraints weight = 20147.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.066375 restraints weight = 17757.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.066506 restraints weight = 16172.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  10233  Z= 0.277
  Angle     :  0.722  10.945  13956  Z= 0.363
  Chirality :  0.046   0.181   1542
  Planarity :  0.005   0.043   1777
  Dihedral  :  6.219  55.703   1510
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 16.13 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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 aren not related in a simple way.
  whole: -0.41 (0.24), residues: 1231
  helix:  0.58 (0.52), residues: 101
  sheet:  0.04 (0.22), residues: 545
  loop : -0.63 (0.27), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  86 
 TYR   0.024   0.002   TYR D  36 
 PHE   0.013   0.002   PHE A 273 
 TRP   0.032   0.002   TRP D 466 
 HIS   0.006   0.001   HIS C  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00625 (10205)
  covalent geometry    : angle       0.70913 (13892)
  SS BOND              : bond        0.00366 (   20)
  SS BOND              : angle       1.08372 (   40)
  hydrogen bonds       : bond        0.04937 (  353)
  hydrogen bonds       : angle       6.07441 ( 1062)
  link_ALPHA1-3        : bond        0.00315 (    1)
  link_ALPHA1-3        : angle       3.01145 (    3)
  link_BETA1-4         : bond        0.00786 (    3)
  link_BETA1-4         : angle       3.18083 (    9)
  link_NAG-ASN         : bond        0.00795 (    4)
  link_NAG-ASN         : angle       3.19284 (   12)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 52
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7907 (mt-10)
REVERT: A   45 MET cc_start: 0.8294 (tpp) cc_final: 0.8056 (tpp)
REVERT: A  125 ASN cc_start: 0.8769 (t0) cc_final: 0.8357 (m-40)
REVERT: A  209 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7890 (mm-30)
REVERT: A  270 SER cc_start: 0.9302 (OUTLIER) cc_final: 0.8854 (p)
REVERT: B   39 LYS cc_start: 0.8605 (tttp) cc_final: 0.8391 (mtmm)
REVERT: B  107 ASP cc_start: 0.8875 (p0) cc_final: 0.8568 (t0)
REVERT: B  135 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8725 (mm)
REVERT: C   34 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8144 (pt)
REVERT: C   65 HIS cc_start: 0.7248 (OUTLIER) cc_final: 0.6642 (t-90)
REVERT: C   99 MET cc_start: 0.8904 (mmm) cc_final: 0.7925 (mmt)
REVERT: C  142 MET cc_start: 0.8890 (mmt) cc_final: 0.8141 (mmp)
REVERT: C  184 ASP cc_start: 0.9305 (m-30) cc_final: 0.8811 (t0)
REVERT: D  136 SER cc_start: 0.8757 (m) cc_final: 0.8344 (t)
REVERT: D  169 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7095 (pm20)
REVERT: D  256 LEU cc_start: 0.9083 (tt) cc_final: 0.8844 (pp)
REVERT: D  356 MET cc_start: 0.8030 (mtm) cc_final: 0.7760 (mmm)
REVERT: D  408 MET cc_start: 0.2425 (mtt) cc_final: 0.0276 (tmm)
REVERT: D  419 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8479 (m-80)
  outliers start: 52
  outliers final: 33
  residues processed: 100
  average time/residue: 0.0972
  time to fit residues: 14.3792
Evaluate side-chains
  90 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 49
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  270 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain B residue   41 CYS
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue  135 LEU
Chi-restraints excluded: chain C residue   26 THR
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue   65 HIS
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  161 HIS
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain D residue  164 ASN
Chi-restraints excluded: chain D residue  169 GLU
Chi-restraints excluded: chain D residue  257 THR
Chi-restraints excluded: chain D residue  300 THR
Chi-restraints excluded: chain D residue  419 PHE
Chi-restraints excluded: chain D residue  450 HIS
Chi-restraints excluded: chain D residue  474 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 55 optimal weight:    0.4980
   chunk 95 optimal weight:    9.9990
   chunk 66 optimal weight:    0.3980
   chunk 85 optimal weight:    0.0570
   chunk 86 optimal weight:    0.7980
   chunk 115 optimal weight:   10.0000
   chunk 82 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
** C 211 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 = 0.102541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.069230 restraints weight = 48719.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.069273 restraints weight = 24443.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.069069 restraints weight = 16807.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.069235 restraints weight = 15796.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.069361 restraints weight = 14771.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.3318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10233  Z= 0.105
  Angle     :  0.604  11.082  13956  Z= 0.298
  Chirality :  0.043   0.152   1542
  Planarity :  0.004   0.048   1777
  Dihedral  :  5.583  58.073   1510
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 19.71 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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 aren not related in a simple way.
  whole: -0.11 (0.24), residues: 1231
  helix:  1.08 (0.51), residues: 111
  sheet:  0.22 (0.22), residues: 519
  loop : -0.48 (0.26), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 227 
 TYR   0.021   0.001   TYR D 357 
 PHE   0.015   0.001   PHE A 140 
 TRP   0.034   0.001   TRP D 466 
 HIS   0.003   0.001   HIS A 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (10205)
  covalent geometry    : angle       0.59616 (13892)
  SS BOND              : bond        0.00266 (   20)
  SS BOND              : angle       1.02959 (   40)
  hydrogen bonds       : bond        0.03885 (  353)
  hydrogen bonds       : angle       5.63013 ( 1062)
  link_ALPHA1-3        : bond        0.01108 (    1)
  link_ALPHA1-3        : angle       1.07767 (    3)
  link_BETA1-4         : bond        0.00322 (    3)
  link_BETA1-4         : angle       1.55012 (    9)
  link_NAG-ASN         : bond        0.00245 (    4)
  link_NAG-ASN         : angle       2.56570 (   12)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 62
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8273 (tpp) cc_final: 0.8004 (tpp)
REVERT: A  120 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7342 (mt0)
REVERT: A  125 ASN cc_start: 0.8688 (t0) cc_final: 0.8366 (m-40)
REVERT: A  209 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7872 (mm-30)
REVERT: A  270 SER cc_start: 0.9411 (m) cc_final: 0.8998 (p)
REVERT: B   39 LYS cc_start: 0.8616 (tttp) cc_final: 0.8409 (mtmm)
REVERT: B  107 ASP cc_start: 0.8774 (p0) cc_final: 0.8516 (t0)
REVERT: B  135 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8412 (mm)
REVERT: C   44 MET cc_start: 0.8017 (mmm) cc_final: 0.7802 (mmm)
REVERT: C   65 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6583 (t-90)
REVERT: C   99 MET cc_start: 0.8948 (mmm) cc_final: 0.7972 (mmt)
REVERT: C  142 MET cc_start: 0.8837 (mmt) cc_final: 0.8020 (mmp)
REVERT: C  184 ASP cc_start: 0.9308 (m-30) cc_final: 0.8826 (t0)
REVERT: C  186 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7644 (mm)
REVERT: D  136 SER cc_start: 0.8612 (m) cc_final: 0.8244 (t)
REVERT: D  356 MET cc_start: 0.8131 (mtm) cc_final: 0.7774 (mmm)
REVERT: D  408 MET cc_start: 0.2584 (mtt) cc_final: 0.0699 (tmm)
REVERT: D  419 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8516 (m-80)
  outliers start: 24
  outliers final: 14
  residues processed: 81
  average time/residue: 0.1006
  time to fit residues: 11.9940
Evaluate side-chains
  72 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 52
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  120 GLN
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain B residue   41 CYS
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue  135 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   65 HIS
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain D residue  419 PHE
Chi-restraints excluded: chain D residue  450 HIS
Chi-restraints excluded: chain D residue  474 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 54 optimal weight:    0.1980
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 122 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 121 optimal weight:   20.0000
   chunk 92 optimal weight:   10.0000
   chunk 85 optimal weight:    0.0870
   chunk 7 optimal weight:    1.9990
   chunk 120 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.6962

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

Flipped N/Q/H residues before XYZ refinement:
** C 211 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 = 0.4225 r_free = 0.4225 target = 0.102721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.069926 restraints weight = 50808.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.069427 restraints weight = 26575.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.069522 restraints weight = 19183.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.069727 restraints weight = 16592.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.069800 restraints weight = 15153.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.3486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10233  Z= 0.108
  Angle     :  0.600   9.741  13956  Z= 0.297
  Chirality :  0.042   0.148   1542
  Planarity :  0.004   0.043   1777
  Dihedral  :  5.292  56.835   1510
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 19.71 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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 aren not related in a simple way.
  whole:  0.02 (0.24), residues: 1231
  helix:  1.15 (0.51), residues: 112
  sheet:  0.37 (0.22), residues: 521
  loop : -0.45 (0.26), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG C 227 
 TYR   0.016   0.001   TYR D 357 
 PHE   0.017   0.001   PHE C  75 
 TRP   0.035   0.001   TRP D 466 
 HIS   0.003   0.001   HIS B  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (10205)
  covalent geometry    : angle       0.59365 (13892)
  SS BOND              : bond        0.00241 (   20)
  SS BOND              : angle       0.89264 (   40)
  hydrogen bonds       : bond        0.03701 (  353)
  hydrogen bonds       : angle       5.39118 ( 1062)
  link_ALPHA1-3        : bond        0.00614 (    1)
  link_ALPHA1-3        : angle       1.24192 (    3)
  link_BETA1-4         : bond        0.00419 (    3)
  link_BETA1-4         : angle       1.63016 (    9)
  link_NAG-ASN         : bond        0.00193 (    4)
  link_NAG-ASN         : angle       2.51417 (   12)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 51
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8221 (tpp) cc_final: 0.7942 (tpp)
REVERT: A  125 ASN cc_start: 0.8706 (t0) cc_final: 0.8349 (m-40)
REVERT: A  209 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7791 (mm-30)
REVERT: A  211 MET cc_start: 0.8163 (mpp) cc_final: 0.7912 (mpp)
REVERT: A  270 SER cc_start: 0.9388 (m) cc_final: 0.8978 (p)
REVERT: B  135 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8420 (mm)
REVERT: C   44 MET cc_start: 0.8122 (mmm) cc_final: 0.7440 (mmm)
REVERT: C   65 HIS cc_start: 0.7228 (OUTLIER) cc_final: 0.6554 (t-90)
REVERT: C   99 MET cc_start: 0.8925 (mmm) cc_final: 0.7942 (mmt)
REVERT: C  186 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7575 (mm)
REVERT: C  204 MET cc_start: 0.8501 (tpp) cc_final: 0.7960 (tpp)
REVERT: D  136 SER cc_start: 0.8592 (m) cc_final: 0.8221 (t)
REVERT: D  242 ARG cc_start: 0.8743 (mmt180) cc_final: 0.8455 (mmp-170)
REVERT: D  356 MET cc_start: 0.8047 (mtm) cc_final: 0.7754 (mmm)
REVERT: D  408 MET cc_start: 0.2942 (mtt) cc_final: 0.0866 (tmm)
REVERT: D  524 THR cc_start: 0.5860 (p) cc_final: 0.5434 (t)
  outliers start: 32
  outliers final: 20
  residues processed: 78
  average time/residue: 0.0937
  time to fit residues: 11.1097
Evaluate side-chains
  74 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 50
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain B residue   41 CYS
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue  135 LEU
Chi-restraints excluded: chain C residue   26 THR
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   65 HIS
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  142 MET
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  164 ASN
Chi-restraints excluded: chain D residue  300 THR
Chi-restraints excluded: chain D residue  419 PHE
Chi-restraints excluded: chain D residue  450 HIS
Chi-restraints excluded: chain D residue  474 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 92 optimal weight:    9.9990
   chunk 112 optimal weight:    0.0980
   chunk 91 optimal weight:   10.0000
   chunk 57 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0870
   chunk 70 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 79 optimal weight:    0.7980
   chunk 17 optimal weight:    7.9990
   chunk 54 optimal weight:    0.0030
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.3768

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

Flipped N/Q/H residues before XYZ refinement:
** C 211 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 = 0.4223 r_free = 0.4223 target = 0.102814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.069558 restraints weight = 49029.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.068339 restraints weight = 28041.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.068826 restraints weight = 18466.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.068907 restraints weight = 17288.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.069005 restraints weight = 14562.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.3609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  10233  Z= 0.102
  Angle     :  0.597  10.715  13956  Z= 0.297
  Chirality :  0.042   0.143   1542
  Planarity :  0.004   0.045   1777
  Dihedral  :  5.185  55.457   1510
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 20.16 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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 aren not related in a simple way.
  whole:  0.04 (0.24), residues: 1231
  helix:  0.70 (0.48), residues: 118
  sheet:  0.50 (0.23), residues: 502
  loop : -0.45 (0.26), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  74 
 TYR   0.015   0.001   TYR D 357 
 PHE   0.021   0.001   PHE C  75 
 TRP   0.037   0.001   TRP D 466 
 HIS   0.002   0.001   HIS B  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (10205)
  covalent geometry    : angle       0.58687 (13892)
  SS BOND              : bond        0.00337 (   20)
  SS BOND              : angle       1.46703 (   40)
  hydrogen bonds       : bond        0.03516 (  353)
  hydrogen bonds       : angle       5.36092 ( 1062)
  link_ALPHA1-3        : bond        0.00847 (    1)
  link_ALPHA1-3        : angle       1.20550 (    3)
  link_BETA1-4         : bond        0.00366 (    3)
  link_BETA1-4         : angle       1.42570 (    9)
  link_NAG-ASN         : bond        0.00311 (    4)
  link_NAG-ASN         : angle       2.49613 (   12)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 53
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7385 (mt0)
REVERT: A  125 ASN cc_start: 0.8746 (t0) cc_final: 0.8423 (m-40)
REVERT: A  209 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7795 (mm-30)
REVERT: A  211 MET cc_start: 0.8177 (mpp) cc_final: 0.7935 (mpp)
REVERT: A  270 SER cc_start: 0.9375 (m) cc_final: 0.8994 (p)
REVERT: B  112 GLU cc_start: 0.7735 (pp20) cc_final: 0.7422 (pp20)
REVERT: B  135 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8440 (mm)
REVERT: C   44 MET cc_start: 0.7995 (mmm) cc_final: 0.7422 (mmm)
REVERT: C   65 HIS cc_start: 0.7390 (OUTLIER) cc_final: 0.6749 (t-90)
REVERT: C   99 MET cc_start: 0.8934 (mmm) cc_final: 0.7944 (mmt)
REVERT: C  186 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7629 (mm)
REVERT: C  204 MET cc_start: 0.8419 (tpp) cc_final: 0.7927 (tpp)
REVERT: D  136 SER cc_start: 0.8565 (m) cc_final: 0.8190 (t)
REVERT: D  356 MET cc_start: 0.8049 (mtm) cc_final: 0.7767 (mmm)
REVERT: D  408 MET cc_start: 0.2901 (mtt) cc_final: 0.0842 (tmm)
REVERT: D  524 THR cc_start: 0.5813 (p) cc_final: 0.5393 (t)
  outliers start: 26
  outliers final: 18
  residues processed: 75
  average time/residue: 0.1023
  time to fit residues: 11.3322
Evaluate side-chains
  71 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 48
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  120 GLN
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   41 CYS
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue  135 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue   65 HIS
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  300 THR
Chi-restraints excluded: chain D residue  419 PHE
Chi-restraints excluded: chain D residue  450 HIS
Chi-restraints excluded: chain D residue  474 CYS
Chi-restraints excluded: chain D residue  518 VAL
Chi-restraints excluded: chain D residue  535 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 99 optimal weight:    0.5980
   chunk 57 optimal weight:    9.9990
   chunk 68 optimal weight:    7.9990
   chunk 90 optimal weight:   20.0000
   chunk 86 optimal weight:    2.9990
   chunk 107 optimal weight:   10.0000
   chunk 66 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 34 optimal weight:    7.9990
   chunk 74 optimal weight:    0.0060
   overall best weight:    1.2400

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

Flipped N/Q/H residues before XYZ refinement:
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 211 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 = 0.4212 r_free = 0.4212 target = 0.102065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.067094 restraints weight = 48814.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.068025 restraints weight = 23910.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.067959 restraints weight = 16252.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.068237 restraints weight = 15060.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.068357 restraints weight = 12825.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10233  Z= 0.122
  Angle     :  0.583  12.302  13956  Z= 0.290
  Chirality :  0.042   0.144   1542
  Planarity :  0.004   0.060   1777
  Dihedral  :  5.070  56.662   1510
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 20.07 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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 aren not related in a simple way.
  whole:  0.15 (0.24), residues: 1231
  helix:  1.24 (0.49), residues: 112
  sheet:  0.51 (0.23), residues: 511
  loop : -0.42 (0.26), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG C 227 
 TYR   0.015   0.001   TYR D 357 
 PHE   0.010   0.001   PHE A 140 
 TRP   0.027   0.001   TRP D 466 
 HIS   0.003   0.001   HIS C  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (10205)
  covalent geometry    : angle       0.57513 (13892)
  SS BOND              : bond        0.00290 (   20)
  SS BOND              : angle       1.02554 (   40)
  hydrogen bonds       : bond        0.03639 (  353)
  hydrogen bonds       : angle       5.18521 ( 1062)
  link_ALPHA1-3        : bond        0.00658 (    1)
  link_ALPHA1-3        : angle       1.43344 (    3)
  link_BETA1-4         : bond        0.00206 (    3)
  link_BETA1-4         : angle       1.70081 (    9)
  link_NAG-ASN         : bond        0.00296 (    4)
  link_NAG-ASN         : angle       2.55691 (   12)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 48
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7302 (mt0)
REVERT: A  125 ASN cc_start: 0.8711 (t0) cc_final: 0.8348 (m-40)
REVERT: A  209 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7799 (mm-30)
REVERT: A  211 MET cc_start: 0.8189 (mpp) cc_final: 0.7934 (mpp)
REVERT: A  270 SER cc_start: 0.9351 (m) cc_final: 0.8939 (p)
REVERT: B  112 GLU cc_start: 0.7759 (pp20) cc_final: 0.7465 (pp20)
REVERT: B  135 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8483 (mm)
REVERT: C   44 MET cc_start: 0.8004 (mmm) cc_final: 0.7363 (mmm)
REVERT: C   65 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.6743 (t-90)
REVERT: C   99 MET cc_start: 0.8979 (mmm) cc_final: 0.7988 (mmt)
REVERT: C  186 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7594 (mm)
REVERT: C  204 MET cc_start: 0.8463 (tpp) cc_final: 0.8052 (tpp)
REVERT: D  136 SER cc_start: 0.8612 (m) cc_final: 0.8209 (t)
REVERT: D  356 MET cc_start: 0.8061 (mtm) cc_final: 0.7789 (mmm)
REVERT: D  408 MET cc_start: 0.2653 (mtt) cc_final: 0.0831 (tmm)
REVERT: D  524 THR cc_start: 0.5932 (p) cc_final: 0.5526 (t)
  outliers start: 28
  outliers final: 22
  residues processed: 73
  average time/residue: 0.0987
  time to fit residues: 10.7526
Evaluate side-chains
  74 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 47
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  120 GLN
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   41 CYS
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue  135 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue   65 HIS
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain C residue  144 CYS
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  164 ASN
Chi-restraints excluded: chain D residue  300 THR
Chi-restraints excluded: chain D residue  419 PHE
Chi-restraints excluded: chain D residue  450 HIS
Chi-restraints excluded: chain D residue  474 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 121 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 97 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 57 optimal weight:   10.0000
   chunk 105 optimal weight:   20.0000
   chunk 54 optimal weight:   10.0000
   chunk 0 optimal weight:    4.9990
   chunk 65 optimal weight:    7.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 519 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 = 0.4176 r_free = 0.4176 target = 0.100115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.066938 restraints weight = 49072.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.065458 restraints weight = 31210.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.065536 restraints weight = 20989.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.065664 restraints weight = 19671.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.065850 restraints weight = 16738.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.4067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  10233  Z= 0.276
  Angle     :  0.717  12.244  13956  Z= 0.359
  Chirality :  0.046   0.170   1542
  Planarity :  0.005   0.048   1777
  Dihedral  :  5.819  59.923   1510
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 20.07 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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 aren not related in a simple way.
  whole: -0.16 (0.24), residues: 1231
  helix:  1.13 (0.50), residues: 101
  sheet:  0.23 (0.23), residues: 521
  loop : -0.54 (0.26), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  86 
 TYR   0.017   0.002   TYR D 357 
 PHE   0.016   0.002   PHE B 109 
 TRP   0.028   0.002   TRP D 466 
 HIS   0.007   0.001   HIS A 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00623 (10205)
  covalent geometry    : angle       0.70461 (13892)
  SS BOND              : bond        0.00393 (   20)
  SS BOND              : angle       1.16358 (   40)
  hydrogen bonds       : bond        0.04735 (  353)
  hydrogen bonds       : angle       5.61291 ( 1062)
  link_ALPHA1-3        : bond        0.00156 (    1)
  link_ALPHA1-3        : angle       2.03816 (    3)
  link_BETA1-4         : bond        0.00993 (    3)
  link_BETA1-4         : angle       2.78338 (    9)
  link_NAG-ASN         : bond        0.00810 (    4)
  link_NAG-ASN         : angle       3.48611 (   12)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 48
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7252 (mt0)
REVERT: A  125 ASN cc_start: 0.8753 (t0) cc_final: 0.8289 (m-40)
REVERT: A  209 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7757 (mm-30)
REVERT: A  270 SER cc_start: 0.9340 (m) cc_final: 0.8908 (p)
REVERT: B  112 GLU cc_start: 0.7726 (pp20) cc_final: 0.7394 (pp20)
REVERT: B  135 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8621 (mm)
REVERT: C   44 MET cc_start: 0.7809 (mmm) cc_final: 0.7471 (mmm)
REVERT: C   99 MET cc_start: 0.8858 (mmm) cc_final: 0.7865 (mmt)
REVERT: C  186 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7677 (mm)
REVERT: C  204 MET cc_start: 0.8674 (tpp) cc_final: 0.8396 (tpp)
REVERT: D  136 SER cc_start: 0.8718 (m) cc_final: 0.8334 (t)
REVERT: D  356 MET cc_start: 0.8074 (mtm) cc_final: 0.7804 (mmm)
REVERT: D  408 MET cc_start: 0.3438 (mtt) cc_final: 0.1120 (tmm)
  outliers start: 32
  outliers final: 25
  residues processed: 76
  average time/residue: 0.0996
  time to fit residues: 11.1730
Evaluate side-chains
  76 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 47
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  120 GLN
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain B residue   41 CYS
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue  135 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  164 ASN
Chi-restraints excluded: chain D residue  300 THR
Chi-restraints excluded: chain D residue  419 PHE
Chi-restraints excluded: chain D residue  450 HIS
Chi-restraints excluded: chain D residue  474 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 109 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   chunk 82 optimal weight:    3.9990
   chunk 123 optimal weight:   20.0000
   chunk 101 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 97 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
B 125 HIS
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 211 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 = 0.4203 r_free = 0.4203 target = 0.101446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.070283 restraints weight = 50482.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.068141 restraints weight = 32489.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.068057 restraints weight = 25186.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.068298 restraints weight = 24741.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.068663 restraints weight = 19196.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.4074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10233  Z= 0.152
  Angle     :  0.631  11.356  13956  Z= 0.314
  Chirality :  0.043   0.148   1542
  Planarity :  0.004   0.048   1777
  Dihedral  :  5.469  57.176   1510
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 20.44 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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 aren not related in a simple way.
  whole: -0.05 (0.24), residues: 1231
  helix:  1.55 (0.51), residues: 101
  sheet:  0.24 (0.23), residues: 522
  loop : -0.47 (0.26), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  74 
 TYR   0.018   0.001   TYR D 357 
 PHE   0.012   0.001   PHE B 109 
 TRP   0.033   0.001   TRP D 466 
 HIS   0.004   0.001   HIS D 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (10205)
  covalent geometry    : angle       0.62235 (13892)
  SS BOND              : bond        0.00302 (   20)
  SS BOND              : angle       1.01127 (   40)
  hydrogen bonds       : bond        0.04039 (  353)
  hydrogen bonds       : angle       5.43488 ( 1062)
  link_ALPHA1-3        : bond        0.00617 (    1)
  link_ALPHA1-3        : angle       1.32188 (    3)
  link_BETA1-4         : bond        0.00366 (    3)
  link_BETA1-4         : angle       1.89103 (    9)
  link_NAG-ASN         : bond        0.00338 (    4)
  link_NAG-ASN         : angle       2.78677 (   12)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 46
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7239 (mt0)
REVERT: A  125 ASN cc_start: 0.8736 (t0) cc_final: 0.8318 (m-40)
REVERT: A  209 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7761 (mm-30)
REVERT: A  270 SER cc_start: 0.9331 (m) cc_final: 0.8957 (p)
REVERT: B  112 GLU cc_start: 0.7707 (pp20) cc_final: 0.7448 (pp20)
REVERT: B  135 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8533 (mm)
REVERT: C   34 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7780 (pt)
REVERT: C   44 MET cc_start: 0.7780 (mmm) cc_final: 0.7178 (mmm)
REVERT: C   99 MET cc_start: 0.8843 (mmm) cc_final: 0.7876 (mmt)
REVERT: C  186 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7686 (mm)
REVERT: C  204 MET cc_start: 0.8626 (tpp) cc_final: 0.8350 (tpp)
REVERT: D  136 SER cc_start: 0.8640 (m) cc_final: 0.8288 (t)
REVERT: D  356 MET cc_start: 0.8015 (mtm) cc_final: 0.7804 (mmm)
REVERT: D  408 MET cc_start: 0.3519 (mtt) cc_final: 0.1283 (tmm)
  outliers start: 28
  outliers final: 21
  residues processed: 71
  average time/residue: 0.0979
  time to fit residues: 10.3808
Evaluate side-chains
  71 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 45
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  120 GLN
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   41 CYS
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue  135 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  164 ASN
Chi-restraints excluded: chain D residue  300 THR
Chi-restraints excluded: chain D residue  419 PHE
Chi-restraints excluded: chain D residue  450 HIS
Chi-restraints excluded: chain D residue  474 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 99 optimal weight:    5.9990
   chunk 43 optimal weight:    0.6980
   chunk 32 optimal weight:    6.9990
   chunk 29 optimal weight:    8.9990
   chunk 58 optimal weight:    3.9990
   chunk 111 optimal weight:    9.9990
   chunk 87 optimal weight:   10.0000
   chunk 82 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 88 optimal weight:    0.6980
   chunk 59 optimal weight:    0.6980
   overall best weight:    2.0184

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

Flipped N/Q/H residues before XYZ refinement:
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 519 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.100915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.067384 restraints weight = 49632.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.067012 restraints weight = 26749.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.066965 restraints weight = 19054.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.067108 restraints weight = 17574.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.067243 restraints weight = 15696.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.4202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10233  Z= 0.167
  Angle     :  0.627  11.069  13956  Z= 0.313
  Chirality :  0.043   0.145   1542
  Planarity :  0.004   0.048   1777
  Dihedral  :  5.400  56.611   1510
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 20.71 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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 aren not related in a simple way.
  whole: -0.06 (0.24), residues: 1231
  helix:  1.58 (0.51), residues: 101
  sheet:  0.19 (0.23), residues: 523
  loop : -0.45 (0.26), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  74 
 TYR   0.017   0.001   TYR D  36 
 PHE   0.013   0.001   PHE B 109 
 TRP   0.036   0.001   TRP D 466 
 HIS   0.004   0.001   HIS C  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (10205)
  covalent geometry    : angle       0.61845 (13892)
  SS BOND              : bond        0.00297 (   20)
  SS BOND              : angle       0.95064 (   40)
  hydrogen bonds       : bond        0.04017 (  353)
  hydrogen bonds       : angle       5.40927 ( 1062)
  link_ALPHA1-3        : bond        0.00414 (    1)
  link_ALPHA1-3        : angle       1.34280 (    3)
  link_BETA1-4         : bond        0.00311 (    3)
  link_BETA1-4         : angle       1.98556 (    9)
  link_NAG-ASN         : bond        0.00360 (    4)
  link_NAG-ASN         : angle       2.77087 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2362.66 seconds
wall clock time: 41 minutes 25.15 seconds (2485.15 seconds total)