Starting phenix.real_space_refine
on Fri Feb 14 09:51:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oe4_16824/02_2025/8oe4_16824.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oe4_16824/02_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_16824/02_2025/8oe4_16824.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oe4_16824/02_2025/8oe4_16824.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oe4_16824/02_2025/8oe4_16824.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oe4_16824/02_2025/8oe4_16824.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.07, per 1000 atoms: 0.61
  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: 2.67
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.40
  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: 3.48

  Time building geometry restraints manager: 3.08 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:             1.560
  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:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     25.590
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.950
-------------------------------------------------------------------------------
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  10205  Z= 0.366
  Angle     :  0.848  16.562  13892  Z= 0.468
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (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
 TRP   0.025   0.002   TRP D 466 
 HIS   0.018   0.001   HIS D 438 
 PHE   0.026   0.002   PHE D 208 
 TYR   0.035   0.003   TYR D 357 
 ARG   0.022   0.001   ARG D 536 

*********************** 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  : 1.251 
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: 0.8972 (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: 0.8061 (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: 0.2807
  time to fit residues: 46.4153
Evaluate side-chains
  63 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
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 104 optimal weight:   20.0000
   chunk 93 optimal weight:    0.0060
   chunk 52 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0270
   chunk 63 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9990
   chunk 97 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9980
   chunk 59 optimal weight:    7.9990
   chunk 72 optimal weight:    0.7980
   chunk 112 optimal weight:    1.9990
   overall best weight:    0.5656

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.104873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.071610 restraints weight = 47423.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.071162 restraints weight = 27487.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.071387 restraints weight = 17805.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  10205  Z= 0.207
  Angle     :  0.642   9.970  13892  Z= 0.326
  Chirality :  0.045   0.160   1542
  Planarity :  0.004   0.060   1777
  Dihedral  :  7.349  69.959   1513
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 15.77 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.23), residues: 1231
  helix:  0.66 (0.51), residues: 105
  sheet:  0.36 (0.21), residues: 515
  loop : -0.53 (0.25), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 371 
 HIS   0.006   0.001   HIS D 438 
 PHE   0.025   0.001   PHE C  75 
 TYR   0.019   0.001   TYR D 357 
 ARG   0.006   0.000   ARG A 181 

*********************** 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
  89 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 1.099 
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: 0.8396 (tpp) cc_final: 0.8142 (tpp)
REVERT: A  270 SER cc_start: 0.9242 (m) cc_final: 0.8832 (p)
REVERT: B   39 LYS cc_start: 0.8599 (tttp) cc_final: 0.8288 (mtmm)
REVERT: B  107 ASP cc_start: 0.8904 (p0) cc_final: 0.8508 (t0)
REVERT: C   75 PHE cc_start: 0.7880 (t80) cc_final: 0.7672 (t80)
REVERT: C   99 MET cc_start: 0.8767 (mmm) cc_final: 0.7849 (mmt)
REVERT: C  126 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8585 (p0)
REVERT: C  184 ASP cc_start: 0.9300 (m-30) cc_final: 0.8771 (t0)
REVERT: D  136 SER cc_start: 0.8605 (m) cc_final: 0.8163 (t)
REVERT: D  143 LEU cc_start: 0.8750 (mt) cc_final: 0.8303 (pp)
REVERT: D  356 MET cc_start: 0.8098 (mtm) cc_final: 0.7894 (mtm)
REVERT: D  408 MET cc_start: 0.2454 (mtt) cc_final: 0.0163 (ttp)
  outliers start: 17
  outliers final: 10
  residues processed: 87
  average time/residue: 0.2366
  time to fit residues: 29.1745
Evaluate side-chains
  68 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  233 ILE
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain C residue   26 THR
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  257 THR
Chi-restraints excluded: chain D residue  339 HIS
Chi-restraints excluded: chain D residue  474 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 66 optimal weight:    9.9990
   chunk 67 optimal weight:   20.0000
   chunk 69 optimal weight:    8.9990
   chunk 109 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 91 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 97 optimal weight:   20.0000
   chunk 61 optimal weight:    9.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
C 161 HIS
D 330 GLN
D 339 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.102520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.063447 restraints weight = 48522.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.065340 restraints weight = 21935.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.066457 restraints weight = 14030.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  10205  Z= 0.315
  Angle     :  0.650   9.623  13892  Z= 0.329
  Chirality :  0.045   0.145   1542
  Planarity :  0.004   0.061   1777
  Dihedral  :  6.790  59.443   1510
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.24), residues: 1231
  helix:  1.08 (0.52), residues: 104
  sheet:  0.41 (0.22), residues: 526
  loop : -0.48 (0.26), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  45 
 HIS   0.007   0.001   HIS D 339 
 PHE   0.020   0.002   PHE C  75 
 TYR   0.017   0.002   TYR C 136 
 ARG   0.005   0.001   ARG C  74 

*********************** 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
  93 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 61
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8317 (tpp) cc_final: 0.8076 (tpp)
REVERT: A   51 ASP cc_start: 0.8382 (t0) cc_final: 0.7930 (t70)
REVERT: A  270 SER cc_start: 0.9411 (OUTLIER) cc_final: 0.8951 (p)
REVERT: B   39 LYS cc_start: 0.8630 (tttp) cc_final: 0.8350 (mtmm)
REVERT: B  107 ASP cc_start: 0.8944 (p0) cc_final: 0.8619 (t0)
REVERT: C   34 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7859 (pt)
REVERT: C   41 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7547 (tp)
REVERT: C   65 HIS cc_start: 0.7750 (OUTLIER) cc_final: 0.7156 (t-90)
REVERT: C   99 MET cc_start: 0.8992 (mmm) cc_final: 0.8081 (mmt)
REVERT: C  126 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8540 (p0)
REVERT: C  184 ASP cc_start: 0.9243 (m-30) cc_final: 0.8748 (t0)
REVERT: D  136 SER cc_start: 0.8583 (m) cc_final: 0.8200 (t)
REVERT: D  143 LEU cc_start: 0.8557 (mt) cc_final: 0.8075 (pp)
REVERT: D  256 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8957 (pp)
REVERT: D  408 MET cc_start: 0.5631 (mtt) cc_final: 0.3596 (ttp)
  outliers start: 32
  outliers final: 17
  residues processed: 86
  average time/residue: 0.2250
  time to fit residues: 27.8399
Evaluate side-chains
  76 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 53
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   67 GLU
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  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   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  126 ASP
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  229 VAL
Chi-restraints excluded: chain D residue  256 LEU
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 106 optimal weight:   20.0000
   chunk 73 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0870
   chunk 36 optimal weight:    3.9990
   chunk 110 optimal weight:   30.0000
   chunk 80 optimal weight:    3.9990
   chunk 29 optimal weight:    8.9990
   chunk 97 optimal weight:   10.0000
   chunk 114 optimal weight:   50.0000
   chunk 45 optimal weight:    3.9990
   overall best weight:    2.6164

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

Flipped N/Q/H residues before XYZ refinement:
A 216 HIS
D  75 HIS
D 287 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.101961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.068286 restraints weight = 48652.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.068493 restraints weight = 25089.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.068050 restraints weight = 21960.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  10205  Z= 0.310
  Angle     :  0.640   9.489  13892  Z= 0.324
  Chirality :  0.044   0.190   1542
  Planarity :  0.004   0.047   1777
  Dihedral  :  6.048  59.824   1510
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 16.04 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.24), residues: 1231
  helix:  1.05 (0.51), residues: 104
  sheet:  0.28 (0.22), residues: 525
  loop : -0.44 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 466 
 HIS   0.006   0.001   HIS C  65 
 PHE   0.010   0.002   PHE A 140 
 TYR   0.016   0.002   TYR D  36 
 ARG   0.003   0.000   ARG A 250 

*********************** 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
  92 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 52
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8336 (tpp) cc_final: 0.8076 (tpp)
REVERT: A  209 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.8022 (mm-30)
REVERT: A  270 SER cc_start: 0.9320 (OUTLIER) cc_final: 0.8920 (p)
REVERT: B   39 LYS cc_start: 0.8617 (tttp) cc_final: 0.8378 (mtmm)
REVERT: B  107 ASP cc_start: 0.8862 (p0) cc_final: 0.8440 (t0)
REVERT: C   34 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7908 (pt)
REVERT: C   65 HIS cc_start: 0.7440 (OUTLIER) cc_final: 0.6830 (t-90)
REVERT: C   99 MET cc_start: 0.8872 (mmm) cc_final: 0.7910 (mmt)
REVERT: C  142 MET cc_start: 0.8925 (mpp) cc_final: 0.8428 (mpp)
REVERT: C  184 ASP cc_start: 0.9285 (m-30) cc_final: 0.8789 (t0)
REVERT: C  204 MET cc_start: 0.8504 (tpp) cc_final: 0.8210 (tpp)
REVERT: D  136 SER cc_start: 0.8721 (m) cc_final: 0.8301 (t)
REVERT: D  143 LEU cc_start: 0.8702 (mt) cc_final: 0.8229 (pp)
REVERT: D  256 LEU cc_start: 0.9087 (tt) cc_final: 0.8885 (pp)
REVERT: D  356 MET cc_start: 0.7950 (mtm) cc_final: 0.7529 (mmm)
REVERT: D  408 MET cc_start: 0.2291 (mtt) cc_final: 0.0476 (tmm)
  outliers start: 40
  outliers final: 28
  residues processed: 84
  average time/residue: 0.2226
  time to fit residues: 28.0355
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  : 1.109 
-------------------------------------------------------------------------------
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   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  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  186 LEU
Chi-restraints excluded: chain C residue  257 TYR
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 102 optimal weight:    7.9990
   chunk 39 optimal weight:    5.9990
   chunk 92 optimal weight:    9.9990
   chunk 18 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 86 optimal weight:    6.9990
   chunk 74 optimal weight:    0.0670
   chunk 111 optimal weight:    7.9990
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.7320

-------------------------------------------------------------------------------
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 = 0.4227 r_free = 0.4227 target = 0.103126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.069884 restraints weight = 48807.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.069172 restraints weight = 27730.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.069450 restraints weight = 17461.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  10205  Z= 0.166
  Angle     :  0.561   9.519  13892  Z= 0.284
  Chirality :  0.042   0.165   1542
  Planarity :  0.004   0.057   1777
  Dihedral  :  5.242  56.741   1510
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.06 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.24), residues: 1231
  helix:  1.23 (0.53), residues: 110
  sheet:  0.42 (0.22), residues: 520
  loop : -0.43 (0.26), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP D 466 
 HIS   0.003   0.001   HIS C  65 
 PHE   0.013   0.001   PHE A 140 
 TYR   0.015   0.001   TYR D 357 
 ARG   0.006   0.000   ARG C  74 

*********************** 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
  83 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 57
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8275 (tpp) cc_final: 0.7994 (tpp)
REVERT: A  209 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8011 (mm-30)
REVERT: A  270 SER cc_start: 0.9355 (m) cc_final: 0.8954 (p)
REVERT: B   39 LYS cc_start: 0.8643 (tttp) cc_final: 0.8427 (mtmm)
REVERT: B  107 ASP cc_start: 0.8761 (p0) cc_final: 0.8420 (t0)
REVERT: C   34 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7700 (pt)
REVERT: C   41 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7341 (mm)
REVERT: C   44 MET cc_start: 0.7767 (mmm) cc_final: 0.7193 (mmm)
REVERT: C   65 HIS cc_start: 0.7548 (OUTLIER) cc_final: 0.6949 (t-90)
REVERT: C   99 MET cc_start: 0.8908 (mmm) cc_final: 0.7979 (mmt)
REVERT: C  142 MET cc_start: 0.8943 (mpp) cc_final: 0.8206 (mpp)
REVERT: C  204 MET cc_start: 0.8450 (tpp) cc_final: 0.8242 (tpp)
REVERT: D  136 SER cc_start: 0.8660 (m) cc_final: 0.8227 (t)
REVERT: D  143 LEU cc_start: 0.8694 (mt) cc_final: 0.8218 (pp)
REVERT: D  256 LEU cc_start: 0.9160 (tt) cc_final: 0.8931 (pp)
REVERT: D  356 MET cc_start: 0.8093 (mtm) cc_final: 0.7748 (mmm)
REVERT: D  408 MET cc_start: 0.2577 (mtt) cc_final: 0.0528 (tmm)
  outliers start: 26
  outliers final: 17
  residues processed: 78
  average time/residue: 0.2213
  time to fit residues: 25.0676
Evaluate side-chains
  72 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 51
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  192 GLU
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 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  186 LEU
Chi-restraints excluded: chain C residue  257 TYR
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  257 THR
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 117 optimal weight:    8.9990
   chunk 116 optimal weight:    8.9990
   chunk 63 optimal weight:   20.0000
   chunk 58 optimal weight:    8.9990
   chunk 78 optimal weight:    8.9990
   chunk 99 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   chunk 27 optimal weight:    7.9990
   chunk 102 optimal weight:   20.0000
   chunk 43 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   overall best weight:    4.1186

-------------------------------------------------------------------------------
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 = 0.4178 r_free = 0.4178 target = 0.100421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.066687 restraints weight = 49501.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.066760 restraints weight = 26200.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.066313 restraints weight = 22569.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.3472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.063  10205  Z= 0.458
  Angle     :  0.719   9.788  13892  Z= 0.365
  Chirality :  0.046   0.152   1542
  Planarity :  0.005   0.063   1777
  Dihedral  :  5.971  56.630   1510
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 17.42 %
    Favored  : 78.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.24), residues: 1231
  helix:  0.71 (0.51), residues: 101
  sheet:  0.28 (0.22), residues: 522
  loop : -0.64 (0.26), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  45 
 HIS   0.007   0.002   HIS C  65 
 PHE   0.015   0.002   PHE A 273 
 TYR   0.023   0.002   TYR D  36 
 ARG   0.008   0.001   ARG C  74 

*********************** 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
  97 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 56
  time to evaluate  : 1.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8283 (tpp) cc_final: 0.8008 (tpp)
REVERT: A  209 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7934 (mm-30)
REVERT: A  270 SER cc_start: 0.9283 (OUTLIER) cc_final: 0.8868 (p)
REVERT: B   39 LYS cc_start: 0.8596 (tttp) cc_final: 0.8367 (mtmm)
REVERT: B  107 ASP cc_start: 0.8776 (p0) cc_final: 0.8533 (t0)
REVERT: C   44 MET cc_start: 0.7741 (mmm) cc_final: 0.7302 (mmm)
REVERT: C   65 HIS cc_start: 0.7140 (OUTLIER) cc_final: 0.6444 (t-90)
REVERT: C   99 MET cc_start: 0.8868 (mmm) cc_final: 0.7892 (mmt)
REVERT: C  142 MET cc_start: 0.9064 (mpp) cc_final: 0.8627 (mpp)
REVERT: C  184 ASP cc_start: 0.9317 (m-30) cc_final: 0.8807 (t0)
REVERT: D  136 SER cc_start: 0.8771 (m) cc_final: 0.8253 (p)
REVERT: D  356 MET cc_start: 0.8057 (mtm) cc_final: 0.7749 (mmm)
REVERT: D  408 MET cc_start: 0.2677 (mtt) cc_final: 0.0812 (tmm)
  outliers start: 41
  outliers final: 31
  residues processed: 93
  average time/residue: 0.2210
  time to fit residues: 30.1403
Evaluate side-chains
  86 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 52
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
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   67 GLU
Chi-restraints excluded: chain A residue  141 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  192 GLU
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  175 VAL
Chi-restraints excluded: chain C residue   26 THR
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  186 LEU
Chi-restraints excluded: chain C residue  257 TYR
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  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 112 optimal weight:   20.0000
   chunk 18 optimal weight:    0.9980
   chunk 85 optimal weight:    6.9990
   chunk 67 optimal weight:   10.0000
   chunk 70 optimal weight:    7.9990
   chunk 116 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   chunk 4 optimal weight:    0.3980
   chunk 57 optimal weight:    9.9990
   chunk 0 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
B 170 GLN
** 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 = 0.4209 r_free = 0.4209 target = 0.101940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.068947 restraints weight = 51305.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.068355 restraints weight = 26839.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.068203 restraints weight = 20084.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.3572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10205  Z= 0.220
  Angle     :  0.607  10.848  13892  Z= 0.302
  Chirality :  0.043   0.153   1542
  Planarity :  0.005   0.075   1777
  Dihedral  :  5.556  59.683   1510
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.97 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.24), residues: 1231
  helix:  1.26 (0.52), residues: 101
  sheet:  0.24 (0.22), residues: 530
  loop : -0.45 (0.27), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 466 
 HIS   0.003   0.001   HIS C  65 
 PHE   0.011   0.001   PHE A 140 
 TYR   0.018   0.001   TYR D 357 
 ARG   0.009   0.001   ARG C  74 

*********************** 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
  88 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 54
  time to evaluate  : 1.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8227 (tpp) cc_final: 0.7926 (tpp)
REVERT: A  209 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7978 (mm-30)
REVERT: A  270 SER cc_start: 0.9302 (m) cc_final: 0.8914 (p)
REVERT: B   39 LYS cc_start: 0.8667 (tttp) cc_final: 0.8446 (mtmm)
REVERT: B  107 ASP cc_start: 0.8708 (p0) cc_final: 0.8471 (t0)
REVERT: C   34 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7802 (pt)
REVERT: C   44 MET cc_start: 0.7676 (mmm) cc_final: 0.7090 (mmm)
REVERT: C   65 HIS cc_start: 0.7303 (OUTLIER) cc_final: 0.6660 (t-90)
REVERT: C   99 MET cc_start: 0.8849 (mmm) cc_final: 0.7875 (mmt)
REVERT: C  142 MET cc_start: 0.8988 (mpp) cc_final: 0.8536 (mpp)
REVERT: C  184 ASP cc_start: 0.9335 (m-30) cc_final: 0.8849 (t0)
REVERT: C  204 MET cc_start: 0.8451 (tpp) cc_final: 0.7923 (tpp)
REVERT: D  136 SER cc_start: 0.8673 (m) cc_final: 0.8306 (t)
REVERT: D  356 MET cc_start: 0.8135 (mtm) cc_final: 0.7761 (mmm)
REVERT: D  408 MET cc_start: 0.3147 (mtt) cc_final: 0.0540 (tmm)
  outliers start: 34
  outliers final: 24
  residues processed: 83
  average time/residue: 0.2029
  time to fit residues: 24.9938
Evaluate side-chains
  78 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 51
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
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  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  192 GLU
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 C residue   26 THR
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  144 CYS
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  257 TYR
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  164 ASN
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  535 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 78 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 101 optimal weight:   20.0000
   chunk 71 optimal weight:    9.9990
   chunk 105 optimal weight:   20.0000
   chunk 94 optimal weight:    9.9990
   chunk 98 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 90 optimal weight:   30.0000
   chunk 33 optimal weight:    0.0470
   overall best weight:    2.3482

-------------------------------------------------------------------------------
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 = 0.4193 r_free = 0.4193 target = 0.100975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.067829 restraints weight = 48667.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.067420 restraints weight = 28542.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.067311 restraints weight = 19797.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.3783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10205  Z= 0.280
  Angle     :  0.624   9.355  13892  Z= 0.311
  Chirality :  0.043   0.154   1542
  Planarity :  0.005   0.078   1777
  Dihedral  :  5.558  59.536   1510
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 19.16 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.24), residues: 1231
  helix:  1.25 (0.52), residues: 101
  sheet:  0.22 (0.22), residues: 529
  loop : -0.47 (0.26), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  45 
 HIS   0.005   0.001   HIS C  65 
 PHE   0.014   0.002   PHE B 109 
 TYR   0.018   0.002   TYR D  36 
 ARG   0.010   0.001   ARG C  74 

*********************** 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
  86 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 50
  time to evaluate  : 1.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8287 (tpp) cc_final: 0.7984 (tpp)
REVERT: A  209 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7935 (mm-30)
REVERT: A  270 SER cc_start: 0.9309 (OUTLIER) cc_final: 0.8915 (p)
REVERT: B  107 ASP cc_start: 0.8751 (p0) cc_final: 0.8506 (t0)
REVERT: C   34 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7991 (pt)
REVERT: C   44 MET cc_start: 0.7743 (mmm) cc_final: 0.7192 (mmm)
REVERT: C   65 HIS cc_start: 0.7267 (OUTLIER) cc_final: 0.6573 (t-90)
REVERT: C   99 MET cc_start: 0.8857 (mmm) cc_final: 0.7877 (mmt)
REVERT: C  142 MET cc_start: 0.8919 (mpp) cc_final: 0.8367 (mpp)
REVERT: C  184 ASP cc_start: 0.9294 (m-30) cc_final: 0.8777 (t0)
REVERT: C  204 MET cc_start: 0.8474 (tpp) cc_final: 0.8020 (tpp)
REVERT: D  136 SER cc_start: 0.8661 (m) cc_final: 0.8288 (t)
REVERT: D  356 MET cc_start: 0.8056 (mtm) cc_final: 0.7699 (mmm)
REVERT: D  408 MET cc_start: 0.2396 (mtt) cc_final: 0.0441 (tmm)
  outliers start: 36
  outliers final: 27
  residues processed: 80
  average time/residue: 0.2071
  time to fit residues: 24.8504
Evaluate side-chains
  80 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 49
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   62 LEU
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  192 GLU
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 C residue   26 THR
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  144 CYS
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  257 TYR
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  164 ASN
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 117 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0980
   chunk 114 optimal weight:    7.9990
   chunk 108 optimal weight:   30.0000
   chunk 55 optimal weight:    3.9990
   chunk 44 optimal weight:    0.3980
   chunk 6 optimal weight:    4.9990
   chunk 94 optimal weight:    9.9990
   chunk 71 optimal weight:    7.9990
   overall best weight:    2.2986

-------------------------------------------------------------------------------
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 = 0.4191 r_free = 0.4191 target = 0.100953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.065346 restraints weight = 49329.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.066273 restraints weight = 25855.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.066359 restraints weight = 16613.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.3944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10205  Z= 0.275
  Angle     :  0.625  12.633  13892  Z= 0.312
  Chirality :  0.043   0.154   1542
  Planarity :  0.005   0.085   1777
  Dihedral  :  5.548  57.915   1510
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 19.43 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.24), residues: 1231
  helix:  1.03 (0.51), residues: 101
  sheet:  0.29 (0.22), residues: 520
  loop : -0.50 (0.26), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  45 
 HIS   0.005   0.001   HIS C  65 
 PHE   0.012   0.002   PHE B 109 
 TYR   0.018   0.002   TYR D  36 
 ARG   0.014   0.001   ARG C  74 

*********************** 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
  79 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 47
  time to evaluate  : 1.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8237 (tpp) cc_final: 0.7904 (tpp)
REVERT: A  209 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7965 (mm-30)
REVERT: A  270 SER cc_start: 0.9276 (OUTLIER) cc_final: 0.8890 (p)
REVERT: C   34 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7874 (pt)
REVERT: C   44 MET cc_start: 0.7523 (mmm) cc_final: 0.6973 (mmm)
REVERT: C   65 HIS cc_start: 0.7143 (OUTLIER) cc_final: 0.6431 (t-90)
REVERT: C   99 MET cc_start: 0.8835 (mmm) cc_final: 0.7841 (mmt)
REVERT: C  142 MET cc_start: 0.8942 (mpp) cc_final: 0.8503 (mpp)
REVERT: C  184 ASP cc_start: 0.9365 (m-30) cc_final: 0.8924 (t0)
REVERT: C  204 MET cc_start: 0.8616 (tpp) cc_final: 0.8277 (tpp)
REVERT: D  136 SER cc_start: 0.8739 (m) cc_final: 0.8341 (t)
REVERT: D  356 MET cc_start: 0.8202 (mtm) cc_final: 0.7867 (mmm)
REVERT: D  408 MET cc_start: 0.3750 (mtt) cc_final: 0.1301 (tmm)
  outliers start: 32
  outliers final: 27
  residues processed: 73
  average time/residue: 0.2001
  time to fit residues: 22.1071
Evaluate side-chains
  77 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 46
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   62 LEU
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  192 GLU
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 C residue   26 THR
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   77 ILE
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  144 CYS
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  257 TYR
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  164 ASN
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  535 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 90 optimal weight:    9.9990
   chunk 69 optimal weight:    9.9990
   chunk 70 optimal weight:   20.0000
   chunk 77 optimal weight:    0.2980
   chunk 115 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 21 optimal weight:    0.1980
   chunk 101 optimal weight:   20.0000
   chunk 78 optimal weight:    6.9990
   overall best weight:    1.5982

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

Flipped N/Q/H residues before XYZ refinement:
B 125 HIS
** 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 = 0.4201 r_free = 0.4201 target = 0.101420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.062398 restraints weight = 48544.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.064404 restraints weight = 21817.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.065455 restraints weight = 13757.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.4050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10205  Z= 0.215
  Angle     :  0.602  12.042  13892  Z= 0.299
  Chirality :  0.042   0.151   1542
  Planarity :  0.005   0.088   1777
  Dihedral  :  5.303  55.757   1510
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 19.98 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.24), residues: 1231
  helix:  1.36 (0.52), residues: 101
  sheet:  0.28 (0.22), residues: 524
  loop : -0.47 (0.26), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D 466 
 HIS   0.004   0.001   HIS C  65 
 PHE   0.011   0.001   PHE A 140 
 TYR   0.017   0.001   TYR D  36 
 ARG   0.014   0.001   ARG C  74 

********************** 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: 29
    poor density    : 45
  time to evaluate  : 1.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7877 (mm-30)
REVERT: A  270 SER cc_start: 0.9389 (OUTLIER) cc_final: 0.8967 (p)
REVERT: C   34 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7836 (pt)
REVERT: C   44 MET cc_start: 0.7608 (mmm) cc_final: 0.7032 (mmm)
REVERT: C   65 HIS cc_start: 0.7386 (OUTLIER) cc_final: 0.6679 (t-90)
REVERT: C   99 MET cc_start: 0.8911 (mmm) cc_final: 0.7962 (mmt)
REVERT: C  204 MET cc_start: 0.8429 (tpp) cc_final: 0.8083 (tpp)
REVERT: D  136 SER cc_start: 0.8657 (m) cc_final: 0.8262 (t)
REVERT: D  356 MET cc_start: 0.8228 (mtm) cc_final: 0.7942 (mmm)
REVERT: D  408 MET cc_start: 0.5991 (mtt) cc_final: 0.3407 (tmm)
  outliers start: 29
  outliers final: 25
  residues processed: 69
  average time/residue: 0.2154
  time to fit residues: 22.5572
Evaluate side-chains
  73 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 44
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
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  147 THR
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  192 GLU
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 C residue   26 THR
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  186 LEU
Chi-restraints excluded: chain C residue  257 TYR
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  164 ASN
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  535 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 21 optimal weight:    0.0770
   chunk 62 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9980
   chunk 91 optimal weight:   30.0000
   chunk 7 optimal weight:    0.5980
   chunk 85 optimal weight:    0.0770
   chunk 84 optimal weight:    0.9980
   chunk 109 optimal weight:   50.0000
   chunk 9 optimal weight:    2.9990
   chunk 104 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.5296

-------------------------------------------------------------------------------
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 = 0.4231 r_free = 0.4231 target = 0.102787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.071305 restraints weight = 50454.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.070688 restraints weight = 25513.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.070280 restraints weight = 23148.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.4095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  10205  Z= 0.153
  Angle     :  0.573   9.935  13892  Z= 0.285
  Chirality :  0.042   0.154   1542
  Planarity :  0.005   0.088   1777
  Dihedral  :  4.900  53.362   1510
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 20.44 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.24), residues: 1231
  helix:  0.94 (0.51), residues: 115
  sheet:  0.45 (0.22), residues: 514
  loop : -0.46 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP D 466 
 HIS   0.003   0.001   HIS A 216 
 PHE   0.014   0.001   PHE A 140 
 TYR   0.017   0.001   TYR D 357 
 ARG   0.014   0.000   ARG C  74 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3997.03 seconds
wall clock time: 72 minutes 11.48 seconds (4331.48 seconds total)