Starting phenix.real_space_refine
on Sun Jul 27 21:20:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d7r_27231/07_2025/8d7r_27231.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d7r_27231/07_2025/8d7r_27231.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d7r_27231/07_2025/8d7r_27231.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d7r_27231/07_2025/8d7r_27231.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d7r_27231/07_2025/8d7r_27231.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d7r_27231/07_2025/8d7r_27231.cif"
  }
  resolution = 3.9
  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=   0.018
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      36      5.16       5
     C    6158      2.51       5
     N    1608      2.21       5
     O    1825      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9627
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "D"
      Number of atoms: 1432
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 1432
          Classifications: {'peptide': 178}
          Link IDs: {'PTRANS': 16, 'TRANS': 161}
    Chain: "C"
      Number of atoms: 1607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1607
          Classifications: {'peptide': 199}
          Link IDs: {'PTRANS': 20, 'TRANS': 178}
    Chain: "B"
      Number of atoms: 3197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 398, 3197
          Classifications: {'peptide': 398}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 378}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 392, 3167
          Classifications: {'peptide': 392}
          Link IDs: {'PTRANS': 25, 'TRANS': 366}
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      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: "I"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 6.68, per 1000 atoms: 0.69
  Number of scatterers: 9627
  At special positions: 0
  Unit cell: (102.34, 144.48, 151.36, 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      36     16.00
     O    1825      8.00
     N    1608      7.00
     C    6158      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 116 " - pdb=" SG  CYS C 127 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 154 " - pdb=" SG  CYS C 164 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 213 " - pdb=" SG  CYS B 270 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 341 " - pdb=" SG  CYS B 351 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 466 " - pdb=" SG  CYS B 511 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 134 " - pdb=" SG  CYS A 144 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 172 " - pdb=" SG  CYS A 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 458 " - pdb=" SG  CYS A 466 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
      " NAG I   1 " - " NAG I   2 "
    NAG-ASN
      " NAG A 701 " - " ASN A 131 "
      " NAG A 702 " - " ASN A 157 "
      " NAG A 703 " - " ASN A 383 "
      " NAG A 704 " - " ASN A 379 "
      " NAG B 901 " - " ASN B 426 "
      " NAG C 401 " - " ASN C 142 "
      " NAG E   1 " - " ASN C 190 "
      " NAG F   1 " - " ASN B 407 "
      " NAG G   1 " - " ASN B 303 "
      " NAG H   1 " - " ASN B 243 "
      " NAG I   1 " - " ASN A 227 "
  Time building additional restraints: 2.40
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2240

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 21 sheets defined
      12.4% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'D' and resid 35 through 65
      removed outlier: 3.987A  pdb=" N   SER D  39 " --> pdb=" O   GLY D  35 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ILE D  40 " --> pdb=" O   PRO D  36 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLN D  41 " --> pdb=" O   GLY D  37 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 71
      removed outlier: 3.699A  pdb=" N   ASN D  70 " --> pdb=" O   GLY D  66 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   GLU D  71 " --> pdb=" O   PRO D  67 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 66 through 71'
    Processing helix  chain 'D' and resid 90 through 97
      removed outlier: 3.969A  pdb=" N   LEU D  97 " --> pdb=" O   VAL D  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 124
    Processing helix  chain 'D' and resid 126 through 154
    Processing helix  chain 'D' and resid 176 through 210
    Processing helix  chain 'A' and resid 273 through 277
    Processing helix  chain 'A' and resid 355 through 360
    Processing sheet with id=AA1, first strand: chain 'C' and resid 144 through 145
    Processing sheet with id=AA2, first strand: chain 'C' and resid 211 through 214
    Processing sheet with id=AA3, first strand: chain 'C' and resid 256 through 258
    Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 134
    Processing sheet with id=AA5, first strand: chain 'B' and resid 143 through 147
      removed outlier: 3.875A  pdb=" N   ASN B 143 " --> pdb=" O   LYS B 156 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LYS B 156 " --> pdb=" O   ASN B 143 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   THR B 152 " --> pdb=" O   ASP B 147 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   TRP B 157 " --> pdb=" O   HIS B 201 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   HIS B 201 " --> pdb=" O   TRP B 157 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 186 through 192
      removed outlier: 3.565A  pdb=" N   ASN B 191 " --> pdb=" O   VAL B 170 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ARG B 221 " --> pdb=" O   GLU B 173 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LYS B 175 " --> pdb=" O   GLU B 219 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   GLU B 219 " --> pdb=" O   LYS B 175 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU B 177 " --> pdb=" O   PHE B 217 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   HIS B 216 " --> pdb=" O   ILE B 244 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ILE B 244 " --> pdb=" O   HIS B 216 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LYS B 242 " --> pdb=" O   VAL B 218 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 254 through 255
      removed outlier: 3.720A  pdb=" N   ILE B 267 " --> pdb=" O   ILE B 301 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ILE B 301 " --> pdb=" O   ILE B 267 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   PHE B 269 " --> pdb=" O   ILE B 299 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   VAL B 297 " --> pdb=" O   CYS B 271 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 260 through 262
      removed outlier: 3.652A  pdb=" N   ILE B 261 " --> pdb=" O   PHE B 328 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLY B 330 " --> pdb=" O   ILE B 261 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   PHE B 323 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   VAL B 315 " --> pdb=" O   ALA B 280 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   ALA B 280 " --> pdb=" O   VAL B 315 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   THR B 317 " --> pdb=" O   LEU B 278 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 337 through 342
      removed outlier: 5.712A  pdb=" N   GLN B 338 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   ASN B 354 " --> pdb=" O   GLN B 338 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ASN B 340 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER B 352 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 379 through 381
      removed outlier: 3.844A  pdb=" N   VAL B 380 " --> pdb=" O   LEU B 371 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU B 371 " --> pdb=" O   VAL B 380 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   THR B 409 " --> pdb=" O   VAL B 372 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   TYR B 406 " --> pdb=" O   VAL B 425 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL B 425 " --> pdb=" O   TYR B 406 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER B 421 " --> pdb=" O   LEU B 410 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   SER B 419 " --> pdb=" O   ALA B 412 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 477 through 481
      removed outlier: 3.688A  pdb=" N   ARG B 510 " --> pdb=" O   GLU B 467 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLU B 469 " --> pdb=" O   ARG B 508 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ARG B 508 " --> pdb=" O   GLU B 469 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   LYS B 471 " --> pdb=" O   THR B 506 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 136 through 137
      removed outlier: 7.684A  pdb=" N   VAL A 136 " --> pdb=" O   LYS A 221 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 159 through 161
      removed outlier: 3.613A  pdb=" N   LYS A 161 " --> pdb=" O   TRP A 197 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   TRP A 197 " --> pdb=" O   LYS A 161 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 159 through 161
      removed outlier: 3.613A  pdb=" N   LYS A 161 " --> pdb=" O   TRP A 197 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   TRP A 197 " --> pdb=" O   LYS A 161 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ILE A 194 " --> pdb=" O   PHE A 214 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   PHE A 214 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   VAL A 196 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ILE A 212 " --> pdb=" O   VAL A 196 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 226 through 231
      removed outlier: 6.527A  pdb=" N   ASN A 227 " --> pdb=" O   THR A 245 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   THR A 245 " --> pdb=" O   ASN A 227 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   SER A 229 " --> pdb=" O   THR A 243 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR A 243 " --> pdb=" O   SER A 229 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ILE A 231 " --> pdb=" O   LYS A 241 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   LYS A 241 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 270 through 271
      removed outlier: 3.781A  pdb=" N   MET A 302 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ASN A 258 " --> pdb=" O   ARG A 300 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   ARG A 300 " --> pdb=" O   ASN A 258 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLN A 260 " --> pdb=" O   ARG A 298 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ARG A 298 " --> pdb=" O   GLN A 260 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ARG A 262 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   VAL A 296 " --> pdb=" O   ARG A 262 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 347 through 349
      removed outlier: 3.905A  pdb=" N   VAL A 347 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   VAL A 389 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU A 349 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   LEU A 387 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'A' and resid 377 through 378
      removed outlier: 3.748A  pdb=" N   GLN A 378 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   ASP A 365 " --> pdb=" O   ARG A 403 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ARG A 403 " --> pdb=" O   ASP A 365 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU A 397 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   TYR A 396 " --> pdb=" O   ILE A 416 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 431 through 432
    Processing sheet with id=AC2, first strand: chain 'A' and resid 459 through 460
      removed outlier: 4.019A  pdb=" N   CYS A 491 " --> pdb=" O   LEU A 460 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLY A 503 " --> pdb=" O   TYR A 500 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 469 through 474
      removed outlier: 3.568A  pdb=" N   ASP A 469 " --> pdb=" O   TRP A 457 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLN A 471 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   LEU A 455 " --> pdb=" O   GLN A 471 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LYS A 452 " --> pdb=" O   VAL A 499 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL A 499 " --> pdb=" O   LYS A 452 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ILE A 454 " --> pdb=" O   THR A 497 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   TYR A 492 " --> pdb=" O   ALA A 512 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ALA A 512 " --> pdb=" O   TYR A 492 " (cutoff:3.500A)

    213 hydrogen bonds defined for protein.
    585 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: 2.33

  Time building geometry restraints manager: 2.84 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3010
        1.34 -     1.46: 2438
        1.46 -     1.58: 4403
        1.58 -     1.70: 0
        1.70 -     1.82: 48
  Bond restraints: 9899
  Sorted by residual:
  bond pdb=" C1  NAG F   1 "
       pdb=" O5  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.02e+00
  bond pdb=" C1  NAG A 702 "
       pdb=" O5  NAG A 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.33e+00
  bond pdb=" C1  NAG H   2 "
       pdb=" O5  NAG H   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.21e+00
  bond pdb=" C1  NAG G   2 "
       pdb=" O5  NAG G   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.11e+00
  bond pdb=" C1  NAG B 901 "
       pdb=" O5  NAG B 901 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.09e+00
  ... (remaining 9894 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 13120
        1.41 -     2.82: 318
        2.82 -     4.23: 53
        4.23 -     5.63: 10
        5.63 -     7.04: 7
  Bond angle restraints: 13508
  Sorted by residual:
  angle pdb=" C   PRO A 434 "
        pdb=" N   LYS A 435 "
        pdb=" CA  LYS A 435 "
      ideal   model   delta    sigma   weight residual
     121.54  128.05   -6.51 1.91e+00 2.74e-01 1.16e+01
  angle pdb=" C   ALA B 448 "
        pdb=" N   VAL B 449 "
        pdb=" CA  VAL B 449 "
      ideal   model   delta    sigma   weight residual
     120.49  125.19   -4.70 1.38e+00 5.25e-01 1.16e+01
  angle pdb=" N   ASN A 131 "
        pdb=" CA  ASN A 131 "
        pdb=" CB  ASN A 131 "
      ideal   model   delta    sigma   weight residual
     114.17  110.31    3.86 1.14e+00 7.69e-01 1.15e+01
  angle pdb=" CA  GLY A 361 "
        pdb=" C   GLY A 361 "
        pdb=" N   LYS A 362 "
      ideal   model   delta    sigma   weight residual
     114.23  116.74   -2.51 8.80e-01 1.29e+00 8.14e+00
  angle pdb=" C   LEU B 194 "
        pdb=" N   ASN B 195 "
        pdb=" CA  ASN B 195 "
      ideal   model   delta    sigma   weight residual
     121.54  126.97   -5.43 1.91e+00 2.74e-01 8.08e+00
  ... (remaining 13503 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.88: 5767
       21.88 -    43.76: 270
       43.76 -    65.64: 57
       65.64 -    87.52: 9
       87.52 -   109.39: 26
  Dihedral angle restraints: 6129
    sinusoidal: 2682
      harmonic: 3447
  Sorted by residual:
  dihedral pdb=" CB  CYS A 172 "
           pdb=" SG  CYS A 172 "
           pdb=" SG  CYS A 182 "
           pdb=" CB  CYS A 182 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.22  -80.22     1      1.00e+01 1.00e-02 7.97e+01
  dihedral pdb=" CB  CYS A 458 "
           pdb=" SG  CYS A 458 "
           pdb=" SG  CYS A 466 "
           pdb=" CB  CYS A 466 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -34.89  -51.11     1      1.00e+01 1.00e-02 3.57e+01
  dihedral pdb=" CB  CYS C 116 "
           pdb=" SG  CYS C 116 "
           pdb=" SG  CYS C 127 "
           pdb=" CB  CYS C 127 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   60.67   32.33     1      1.00e+01 1.00e-02 1.49e+01
  ... (remaining 6126 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1270
       0.049 -    0.098: 198
       0.098 -    0.147: 76
       0.147 -    0.196: 2
       0.196 -    0.245: 1
  Chirality restraints: 1547
  Sorted by residual:
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN C 190 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" C1  NAG A 701 "
            pdb=" ND2 ASN A 131 "
            pdb=" C2  NAG A 701 "
            pdb=" O5  NAG A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.24   -0.16 2.00e-01 2.50e+01 6.75e-01
  chirality pdb=" C1  NAG A 703 "
            pdb=" ND2 ASN A 383 "
            pdb=" C2  NAG A 703 "
            pdb=" O5  NAG A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.24   -0.16 2.00e-01 2.50e+01 6.59e-01
  ... (remaining 1544 not shown)

  Planarity restraints: 1696
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D  66 "    0.037 5.00e-02 4.00e+02   5.57e-02 4.96e+00
        pdb=" N   PRO D  67 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO D  67 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO D  67 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 500 "    0.029 5.00e-02 4.00e+02   4.45e-02 3.17e+00
        pdb=" N   PRO B 501 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 501 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 501 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 272 "    0.026 5.00e-02 4.00e+02   3.94e-02 2.49e+00
        pdb=" N   PRO A 273 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 273 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 273 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1693 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 3184
        2.86 -     3.37: 8390
        3.37 -     3.88: 14623
        3.88 -     4.39: 15262
        4.39 -     4.90: 26904
  Nonbonded interactions: 68363
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 262 "
            pdb=" O   THR A 263 "
     model   vdw
     2.345 3.120
  nonbonded pdb=" O   GLU D  92 "
            pdb=" OG  SER D  96 "
     model   vdw
     2.348 3.040
  nonbonded pdb=" O   TYR A 257 "
            pdb=" OG1 THR A 277 "
     model   vdw
     2.370 3.040
  nonbonded pdb=" OG  SER B 374 "
            pdb=" O5  NAG F   1 "
     model   vdw
     2.375 3.040
  nonbonded pdb=" OE1 GLU B 373 "
            pdb=" N   SER B 376 "
     model   vdw
     2.380 3.120
  ... (remaining 68358 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=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:             3.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     24.540
  Find NCS groups from input model:        0.160
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5432
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9923  Z= 0.137
  Angle     :  0.548   7.773  13572  Z= 0.273
  Chirality :  0.042   0.245   1547
  Planarity :  0.004   0.056   1685
  Dihedral  : 15.026 109.395   3865
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.12 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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: -3.25 (0.21), residues: 1157
  helix:  1.59 (0.42), residues: 129
  sheet: -1.70 (0.28), residues: 305
  loop : -3.30 (0.17), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP A 146 
 HIS   0.001   0.000   HIS A 340 
 PHE   0.013   0.000   PHE A 332 
 TYR   0.011   0.001   TYR B 502 
 ARG   0.001   0.000   ARG C 167 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00422 (   11)
  link_NAG-ASN         : angle       2.11636 (   33)
  link_BETA1-4         : bond        0.00317 (    5)
  link_BETA1-4         : angle       1.49354 (   15)
  hydrogen bonds       : bond        0.23422 (  211)
  hydrogen bonds       : angle       8.05712 (  585)
  SS BOND              : bond        0.00222 (    8)
  SS BOND              : angle       0.46437 (   16)
  covalent geometry    : bond        0.00276 ( 9899)
  covalent geometry    : angle       0.53647 (13508)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  438 MET cc_start: 0.5426 (ptp) cc_final: 0.4966 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.2688
  time to fit residues: 65.6744
Evaluate side-chains
  99 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    6.9990
   chunk 86 optimal weight:    0.0030
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 89 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 66 optimal weight:    8.9990
   chunk 103 optimal weight:    8.9990
   overall best weight:    2.1794

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

Flipped N/Q/H residues before XYZ refinement:
D 105 GLN
** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 112 HIS
D 123 GLN
D 135 HIS
D 192 GLN
C 162 ASN
** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 253 GLN
C 256 HIS
B 190 HIS
B 201 HIS
B 226 ASN
B 286 ASN
B 402 ASN
B 420 GLN
B 434 HIS
B 454 HIS
A 137 ASN
A 287 GLN
A 348 GLN
A 471 GLN
A 478 HIS

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.179658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.158336 restraints weight = 19019.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.157639 restraints weight = 24694.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.158249 restraints weight = 21712.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6108
moved from start:          0.3297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.074   9923  Z= 0.241
  Angle     :  0.883  13.680  13572  Z= 0.426
  Chirality :  0.054   0.404   1547
  Planarity :  0.006   0.073   1685
  Dihedral  : 11.808  86.757   1592
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.85 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.46 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.95 (0.22), residues: 1157
  helix:  1.59 (0.46), residues: 135
  sheet: -1.90 (0.25), residues: 365
  loop : -2.88 (0.20), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A 269 
 HIS   0.006   0.001   HIS B 344 
 PHE   0.041   0.003   PHE C 141 
 TYR   0.028   0.003   TYR D  49 
 ARG   0.005   0.001   ARG B 508 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00678 (   11)
  link_NAG-ASN         : angle       3.38266 (   33)
  link_BETA1-4         : bond        0.00864 (    5)
  link_BETA1-4         : angle       1.89180 (   15)
  hydrogen bonds       : bond        0.06987 (  211)
  hydrogen bonds       : angle       6.08168 (  585)
  SS BOND              : bond        0.00474 (    8)
  SS BOND              : angle       1.98525 (   16)
  covalent geometry    : bond        0.00552 ( 9899)
  covalent geometry    : angle       0.86401 (13508)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  252 ASP cc_start: 0.6374 (OUTLIER) cc_final: 0.6058 (t0)
REVERT: B  438 SER cc_start: 0.7293 (p) cc_final: 0.6996 (m)
REVERT: A  213 ASN cc_start: 0.7895 (t0) cc_final: 0.7257 (p0)
REVERT: A  351 TRP cc_start: 0.6521 (p90) cc_final: 0.5694 (p90)
  outliers start: 26
  outliers final: 17
  residues processed: 142
  average time/residue: 0.2576
  time to fit residues: 49.6014
Evaluate side-chains
  117 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  165 THR
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  252 ASP
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  325 THR
Chi-restraints excluded: chain B residue  407 ASN
Chi-restraints excluded: chain B residue  488 GLU
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain A residue  167 HIS
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  478 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 90 optimal weight:    0.5980
   chunk 103 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 102 optimal weight:    3.9990
   chunk 101 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   chunk 100 optimal weight:    0.0370
   chunk 82 optimal weight:    0.6980
   chunk 106 optimal weight:    0.0020
   overall best weight:    0.4266

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

Flipped N/Q/H residues before XYZ refinement:
** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 434 HIS
A 478 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.182939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.159503 restraints weight = 19896.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.158720 restraints weight = 25740.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.160308 restraints weight = 19738.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.4241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6044
moved from start:          0.3399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9923  Z= 0.120
  Angle     :  0.678  11.197  13572  Z= 0.319
  Chirality :  0.048   0.668   1547
  Planarity :  0.004   0.042   1685
  Dihedral  :  9.742  80.770   1592
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.38 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.26 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.42 (0.23), residues: 1157
  helix:  2.55 (0.48), residues: 135
  sheet: -1.59 (0.26), residues: 363
  loop : -2.64 (0.21), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP B 246 
 HIS   0.008   0.001   HIS A 478 
 PHE   0.010   0.001   PHE D 185 
 TYR   0.012   0.001   TYR A 322 
 ARG   0.007   0.001   ARG A 176 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00585 (   11)
  link_NAG-ASN         : angle       3.21431 (   33)
  link_BETA1-4         : bond        0.00372 (    5)
  link_BETA1-4         : angle       1.73671 (   15)
  hydrogen bonds       : bond        0.05247 (  211)
  hydrogen bonds       : angle       5.36199 (  585)
  SS BOND              : bond        0.00379 (    8)
  SS BOND              : angle       1.78334 (   16)
  covalent geometry    : bond        0.00274 ( 9899)
  covalent geometry    : angle       0.65493 (13508)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
REVERT: C  245 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7295 (ptm160)
REVERT: C  252 ASP cc_start: 0.6200 (OUTLIER) cc_final: 0.5926 (t0)
REVERT: A  313 TRP cc_start: 0.7168 (m100) cc_final: 0.6528 (m100)
REVERT: A  328 LYS cc_start: 0.6446 (tmtt) cc_final: 0.6110 (tttm)
REVERT: A  351 TRP cc_start: 0.5870 (p90) cc_final: 0.5570 (p90)
  outliers start: 25
  outliers final: 13
  residues processed: 128
  average time/residue: 0.2432
  time to fit residues: 42.7220
Evaluate side-chains
  113 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  245 ARG
Chi-restraints excluded: chain C residue  252 ASP
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain B residue  334 ASP
Chi-restraints excluded: chain B residue  447 THR
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  226 HIS
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  467 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 52 optimal weight:    0.0040
   chunk 0 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   chunk 67 optimal weight:   10.0000
   chunk 74 optimal weight:    0.0870
   chunk 14 optimal weight:    0.0970
   chunk 18 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.3568

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

Flipped N/Q/H residues before XYZ refinement:
D 180 GLN
** C 147 HIS ** 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 = 0.4511 r_free = 0.4511 target = 0.183159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.159462 restraints weight = 18975.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.159416 restraints weight = 22858.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.160737 restraints weight = 17308.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.4243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6023
moved from start:          0.3571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9923  Z= 0.115
  Angle     :  0.659  15.582  13572  Z= 0.308
  Chirality :  0.046   0.560   1547
  Planarity :  0.004   0.046   1685
  Dihedral  :  8.393  71.570   1592
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.56 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.20 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.24), residues: 1157
  helix:  2.80 (0.47), residues: 135
  sheet: -1.33 (0.26), residues: 366
  loop : -2.47 (0.21), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 519 
 HIS   0.019   0.001   HIS A 478 
 PHE   0.009   0.001   PHE A 332 
 TYR   0.008   0.001   TYR A 295 
 ARG   0.008   0.000   ARG B 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00897 (   11)
  link_NAG-ASN         : angle       3.89645 (   33)
  link_BETA1-4         : bond        0.00492 (    5)
  link_BETA1-4         : angle       1.71495 (   15)
  hydrogen bonds       : bond        0.04619 (  211)
  hydrogen bonds       : angle       4.99565 (  585)
  SS BOND              : bond        0.00490 (    8)
  SS BOND              : angle       1.98160 (   16)
  covalent geometry    : bond        0.00261 ( 9899)
  covalent geometry    : angle       0.62604 (13508)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   57 LEU cc_start: 0.8783 (tt) cc_final: 0.8554 (tp)
REVERT: C  245 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7266 (ptm160)
REVERT: C  275 GLU cc_start: 0.5508 (mm-30) cc_final: 0.5184 (tm-30)
REVERT: A  313 TRP cc_start: 0.7177 (m100) cc_final: 0.6547 (m100)
REVERT: A  328 LYS cc_start: 0.6519 (tmtt) cc_final: 0.6207 (tttm)
REVERT: A  351 TRP cc_start: 0.5916 (p90) cc_final: 0.5599 (p90)
  outliers start: 24
  outliers final: 15
  residues processed: 124
  average time/residue: 0.2475
  time to fit residues: 41.9735
Evaluate side-chains
  116 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  165 THR
Chi-restraints excluded: chain C residue  142 ASN
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  245 ARG
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain B residue  334 ASP
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  447 THR
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  226 HIS
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  402 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 79 optimal weight:    0.7980
   chunk 38 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 95 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9990
   chunk 105 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 72 optimal weight:    0.0770
   overall best weight:    0.6140

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.181560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.159541 restraints weight = 18982.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.158906 restraints weight = 26068.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.160169 restraints weight = 20177.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.4244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6036
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9923  Z= 0.118
  Angle     :  0.653  12.270  13572  Z= 0.308
  Chirality :  0.045   0.447   1547
  Planarity :  0.004   0.043   1685
  Dihedral  :  7.589  60.516   1592
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.08 %
    Favored  : 90.92 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 18.34 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.24), residues: 1157
  helix:  3.24 (0.46), residues: 129
  sheet: -1.11 (0.27), residues: 360
  loop : -2.33 (0.21), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 443 
 HIS   0.012   0.001   HIS A 478 
 PHE   0.009   0.001   PHE D 185 
 TYR   0.024   0.001   TYR B 502 
 ARG   0.007   0.000   ARG A 176 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00514 (   11)
  link_NAG-ASN         : angle       3.42284 (   33)
  link_BETA1-4         : bond        0.00424 (    5)
  link_BETA1-4         : angle       1.80309 (   15)
  hydrogen bonds       : bond        0.04746 (  211)
  hydrogen bonds       : angle       4.81115 (  585)
  SS BOND              : bond        0.00777 (    8)
  SS BOND              : angle       2.14839 (   16)
  covalent geometry    : bond        0.00270 ( 9899)
  covalent geometry    : angle       0.62559 (13508)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   57 LEU cc_start: 0.8806 (tt) cc_final: 0.8535 (tp)
REVERT: C  245 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7171 (ptm160)
REVERT: C  275 GLU cc_start: 0.5631 (mm-30) cc_final: 0.5368 (tm-30)
REVERT: A  313 TRP cc_start: 0.7154 (m100) cc_final: 0.6642 (m100)
REVERT: A  328 LYS cc_start: 0.6601 (tmtt) cc_final: 0.6297 (tttm)
REVERT: A  351 TRP cc_start: 0.6048 (p90) cc_final: 0.5766 (p90)
  outliers start: 27
  outliers final: 17
  residues processed: 128
  average time/residue: 0.2482
  time to fit residues: 43.8841
Evaluate side-chains
  122 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  165 THR
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain C residue  142 ASN
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  245 ARG
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  447 THR
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  226 HIS
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  467 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 113 optimal weight:    0.2980
   chunk 17 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 12 optimal weight:    0.5980
   chunk 96 optimal weight:    0.0970
   chunk 27 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0270
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.3436

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.182515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.162523 restraints weight = 19280.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.161807 restraints weight = 24243.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.162286 restraints weight = 23113.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.4267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5959
moved from start:          0.3972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9923  Z= 0.109
  Angle     :  0.633  11.457  13572  Z= 0.299
  Chirality :  0.043   0.301   1547
  Planarity :  0.004   0.045   1685
  Dihedral  :  7.235  55.589   1592
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.38 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.71 %
    Favored  : 78.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.24), residues: 1157
  helix:  3.38 (0.46), residues: 129
  sheet: -0.97 (0.27), residues: 363
  loop : -2.20 (0.22), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 203 
 HIS   0.009   0.001   HIS A 478 
 PHE   0.007   0.001   PHE C 243 
 TYR   0.007   0.001   TYR A 295 
 ARG   0.011   0.000   ARG A 176 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00523 (   11)
  link_NAG-ASN         : angle       3.15420 (   33)
  link_BETA1-4         : bond        0.00498 (    5)
  link_BETA1-4         : angle       1.79842 (   15)
  hydrogen bonds       : bond        0.04316 (  211)
  hydrogen bonds       : angle       4.60850 (  585)
  SS BOND              : bond        0.00737 (    8)
  SS BOND              : angle       1.94859 (   16)
  covalent geometry    : bond        0.00250 ( 9899)
  covalent geometry    : angle       0.60885 (13508)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 115
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   86 ARG cc_start: 0.6613 (mmt90) cc_final: 0.6356 (mmm160)
REVERT: C  245 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7233 (ptm160)
REVERT: A  206 LYS cc_start: 0.3884 (pptt) cc_final: 0.3087 (pptt)
REVERT: A  313 TRP cc_start: 0.7154 (m100) cc_final: 0.6781 (m100)
REVERT: A  328 LYS cc_start: 0.6606 (tmtt) cc_final: 0.6325 (tttm)
  outliers start: 26
  outliers final: 17
  residues processed: 132
  average time/residue: 0.2483
  time to fit residues: 44.8409
Evaluate side-chains
  121 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  165 THR
Chi-restraints excluded: chain C residue  127 CYS
Chi-restraints excluded: chain C residue  142 ASN
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  245 ARG
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  447 THR
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  226 HIS
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  402 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 80 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   chunk 87 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   chunk 21 optimal weight:    9.9990
   chunk 70 optimal weight:    0.4980
   chunk 76 optimal weight:    0.4980
   chunk 104 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0020
   overall best weight:    1.1992

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

Flipped N/Q/H residues before XYZ refinement:
C 298 HIS
B 434 HIS
A 348 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.176557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.155125 restraints weight = 19241.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.154449 restraints weight = 25434.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.155248 restraints weight = 22844.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.4179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6179
moved from start:          0.4561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9923  Z= 0.147
  Angle     :  0.697  12.492  13572  Z= 0.333
  Chirality :  0.045   0.255   1547
  Planarity :  0.005   0.043   1685
  Dihedral  :  7.040  56.953   1592
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.08 %
    Favored  : 90.92 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 18.53 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.24), residues: 1157
  helix:  3.25 (0.46), residues: 129
  sheet: -1.06 (0.26), residues: 372
  loop : -2.18 (0.22), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 351 
 HIS   0.007   0.001   HIS A 478 
 PHE   0.013   0.001   PHE D 185 
 TYR   0.021   0.001   TYR A 322 
 ARG   0.010   0.001   ARG A 176 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00477 (   11)
  link_NAG-ASN         : angle       3.05315 (   33)
  link_BETA1-4         : bond        0.00467 (    5)
  link_BETA1-4         : angle       1.82874 (   15)
  hydrogen bonds       : bond        0.05417 (  211)
  hydrogen bonds       : angle       4.69572 (  585)
  SS BOND              : bond        0.00779 (    8)
  SS BOND              : angle       1.94641 (   16)
  covalent geometry    : bond        0.00342 ( 9899)
  covalent geometry    : angle       0.67568 (13508)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 107
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   86 ARG cc_start: 0.6673 (mmt90) cc_final: 0.6299 (mmm160)
REVERT: C  245 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7333 (ptm160)
REVERT: A  206 LYS cc_start: 0.4216 (pptt) cc_final: 0.3355 (pptt)
REVERT: A  313 TRP cc_start: 0.7348 (m100) cc_final: 0.6944 (m100)
REVERT: A  328 LYS cc_start: 0.6856 (tmtt) cc_final: 0.6575 (tttm)
  outliers start: 38
  outliers final: 26
  residues processed: 133
  average time/residue: 0.2431
  time to fit residues: 44.5791
Evaluate side-chains
  130 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   75 ASN
Chi-restraints excluded: chain D residue  165 THR
Chi-restraints excluded: chain C residue  127 CYS
Chi-restraints excluded: chain C residue  142 ASN
Chi-restraints excluded: chain C residue  151 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  245 ARG
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  407 ASN
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  434 HIS
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  447 THR
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  226 HIS
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  467 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 87 optimal weight:    0.4980
   chunk 90 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    1.6988

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

Flipped N/Q/H residues before XYZ refinement:
D 106 ASN
** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 255 GLN
** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.172313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.150064 restraints weight = 19357.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.149106 restraints weight = 26285.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.150011 restraints weight = 21872.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.4112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6347
moved from start:          0.5133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9923  Z= 0.177
  Angle     :  0.738  13.863  13572  Z= 0.359
  Chirality :  0.046   0.224   1547
  Planarity :  0.005   0.047   1685
  Dihedral  :  7.003  58.204   1592
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.42 %
    Favored  : 90.58 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 19.00 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.24), residues: 1157
  helix:  2.79 (0.46), residues: 132
  sheet: -1.15 (0.26), residues: 362
  loop : -2.38 (0.22), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 351 
 HIS   0.045   0.002   HIS B 434 
 PHE   0.018   0.002   PHE A 332 
 TYR   0.018   0.002   TYR A 322 
 ARG   0.011   0.001   ARG A 176 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00487 (   11)
  link_NAG-ASN         : angle       3.02016 (   33)
  link_BETA1-4         : bond        0.00473 (    5)
  link_BETA1-4         : angle       1.88699 (   15)
  hydrogen bonds       : bond        0.06217 (  211)
  hydrogen bonds       : angle       4.88167 (  585)
  SS BOND              : bond        0.00757 (    8)
  SS BOND              : angle       1.93019 (   16)
  covalent geometry    : bond        0.00412 ( 9899)
  covalent geometry    : angle       0.71823 (13508)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 112
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   88 THR cc_start: 0.7093 (p) cc_final: 0.6862 (p)
REVERT: D  113 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8151 (mp)
REVERT: C  236 GLU cc_start: 0.6206 (mm-30) cc_final: 0.5884 (mm-30)
REVERT: C  245 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7424 (ptm160)
REVERT: A  206 LYS cc_start: 0.4568 (pptt) cc_final: 0.3621 (pptt)
REVERT: A  328 LYS cc_start: 0.7200 (tmtt) cc_final: 0.6961 (tttm)
  outliers start: 39
  outliers final: 31
  residues processed: 136
  average time/residue: 0.2382
  time to fit residues: 44.6405
Evaluate side-chains
  135 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 102
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   75 ASN
Chi-restraints excluded: chain D residue  106 ASN
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  151 MET
Chi-restraints excluded: chain D residue  165 THR
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain C residue  127 CYS
Chi-restraints excluded: chain C residue  142 ASN
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  245 ARG
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain B residue  201 HIS
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  407 ASN
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  447 THR
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  226 HIS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  402 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 103 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0670
   chunk 71 optimal weight:    9.9990
   chunk 55 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 87 optimal weight:    0.4980
   chunk 3 optimal weight:    0.7980
   chunk 61 optimal weight:    0.1980
   chunk 80 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
** A 471 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 = 0.4425 r_free = 0.4425 target = 0.175601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.154071 restraints weight = 19072.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.153447 restraints weight = 25186.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.154757 restraints weight = 21066.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.4171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6206
moved from start:          0.5102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9923  Z= 0.123
  Angle     :  0.691  12.286  13572  Z= 0.333
  Chirality :  0.044   0.220   1547
  Planarity :  0.004   0.052   1685
  Dihedral  :  6.727  56.874   1592
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 19.94 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.24), residues: 1157
  helix:  3.37 (0.45), residues: 126
  sheet: -1.00 (0.26), residues: 373
  loop : -2.28 (0.22), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 519 
 HIS   0.009   0.001   HIS B 434 
 PHE   0.019   0.001   PHE A 332 
 TYR   0.024   0.001   TYR D 110 
 ARG   0.013   0.001   ARG A 176 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00521 (   11)
  link_NAG-ASN         : angle       2.91833 (   33)
  link_BETA1-4         : bond        0.00520 (    5)
  link_BETA1-4         : angle       1.86502 (   15)
  hydrogen bonds       : bond        0.05170 (  211)
  hydrogen bonds       : angle       4.67078 (  585)
  SS BOND              : bond        0.00663 (    8)
  SS BOND              : angle       1.63751 (   16)
  covalent geometry    : bond        0.00278 ( 9899)
  covalent geometry    : angle       0.67261 (13508)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 1.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   86 ARG cc_start: 0.6937 (mmm160) cc_final: 0.6670 (mmm160)
REVERT: D  113 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8071 (mp)
REVERT: C  245 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7204 (ptm160)
REVERT: A  206 LYS cc_start: 0.4348 (pptt) cc_final: 0.3431 (pptt)
REVERT: A  348 GLN cc_start: 0.7004 (tp-100) cc_final: 0.6486 (tt0)
REVERT: A  414 LEU cc_start: 0.6893 (tt) cc_final: 0.6454 (tp)
  outliers start: 27
  outliers final: 21
  residues processed: 124
  average time/residue: 0.2432
  time to fit residues: 41.9585
Evaluate side-chains
  125 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  165 THR
Chi-restraints excluded: chain C residue  127 CYS
Chi-restraints excluded: chain C residue  142 ASN
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  245 ARG
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain B residue  201 HIS
Chi-restraints excluded: chain B residue  338 GLN
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  447 THR
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  226 HIS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  467 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 109 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 107 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0980
   chunk 61 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 90 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 67 optimal weight:    8.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
D 106 ASN
** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 477 GLN
** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.170766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.148641 restraints weight = 19235.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.147469 restraints weight = 25607.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.148879 restraints weight = 22166.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.4096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6389
moved from start:          0.5638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9923  Z= 0.170
  Angle     :  0.752  12.786  13572  Z= 0.366
  Chirality :  0.046   0.260   1547
  Planarity :  0.005   0.059   1685
  Dihedral  :  6.797  54.527   1592
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.29 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 20.42 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.24), residues: 1157
  helix:  3.08 (0.45), residues: 126
  sheet: -1.21 (0.27), residues: 362
  loop : -2.35 (0.22), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 232 
 HIS   0.006   0.001   HIS A 478 
 PHE   0.014   0.002   PHE D 185 
 TYR   0.019   0.002   TYR A 366 
 ARG   0.013   0.001   ARG A 176 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00594 (   11)
  link_NAG-ASN         : angle       2.99723 (   33)
  link_BETA1-4         : bond        0.00406 (    5)
  link_BETA1-4         : angle       1.85140 (   15)
  hydrogen bonds       : bond        0.06376 (  211)
  hydrogen bonds       : angle       4.91799 (  585)
  SS BOND              : bond        0.00725 (    8)
  SS BOND              : angle       1.83723 (   16)
  covalent geometry    : bond        0.00396 ( 9899)
  covalent geometry    : angle       0.73366 (13508)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 105
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   86 ARG cc_start: 0.7034 (mmm160) cc_final: 0.6791 (mmm160)
REVERT: D  113 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8224 (mp)
REVERT: C  236 GLU cc_start: 0.6209 (mm-30) cc_final: 0.5965 (mm-30)
REVERT: C  245 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6846 (ptm160)
REVERT: A  206 LYS cc_start: 0.4487 (pptt) cc_final: 0.3405 (pptt)
REVERT: A  348 GLN cc_start: 0.7144 (tp-100) cc_final: 0.6794 (tt0)
REVERT: A  414 LEU cc_start: 0.7077 (tt) cc_final: 0.6676 (tp)
  outliers start: 26
  outliers final: 21
  residues processed: 121
  average time/residue: 0.2523
  time to fit residues: 41.6429
Evaluate side-chains
  124 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  151 MET
Chi-restraints excluded: chain D residue  165 THR
Chi-restraints excluded: chain C residue  127 CYS
Chi-restraints excluded: chain C residue  142 ASN
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  245 ARG
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain B residue  201 HIS
Chi-restraints excluded: chain B residue  338 GLN
Chi-restraints excluded: chain B residue  407 ASN
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  447 THR
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  226 HIS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  402 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 97 optimal weight:    0.3980
   chunk 54 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 31 optimal weight:    0.2980
   chunk 111 optimal weight:    4.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 471 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 = 0.4401 r_free = 0.4401 target = 0.173832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.151652 restraints weight = 19011.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.150840 restraints weight = 24177.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.152703 restraints weight = 19986.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6281
moved from start:          0.5617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9923  Z= 0.127
  Angle     :  0.697  11.179  13572  Z= 0.338
  Chirality :  0.044   0.232   1547
  Planarity :  0.005   0.056   1685
  Dihedral  :  6.595  55.231   1592
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.16 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 20.89 %
    Favored  : 76.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.24), residues: 1157
  helix:  3.25 (0.44), residues: 126
  sheet: -1.06 (0.27), residues: 363
  loop : -2.29 (0.22), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 519 
 HIS   0.005   0.001   HIS A 478 
 PHE   0.013   0.001   PHE A 169 
 TYR   0.010   0.001   TYR D  49 
 ARG   0.014   0.001   ARG A 176 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00532 (   11)
  link_NAG-ASN         : angle       2.79999 (   33)
  link_BETA1-4         : bond        0.00492 (    5)
  link_BETA1-4         : angle       1.81400 (   15)
  hydrogen bonds       : bond        0.05332 (  211)
  hydrogen bonds       : angle       4.67455 (  585)
  SS BOND              : bond        0.00661 (    8)
  SS BOND              : angle       1.54809 (   16)
  covalent geometry    : bond        0.00289 ( 9899)
  covalent geometry    : angle       0.67980 (13508)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3340.88 seconds
wall clock time: 58 minutes 40.44 seconds (3520.44 seconds total)