Starting phenix.real_space_refine
on Sat Jul 26 04:34:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y1t_33572/07_2025/7y1t_33572.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y1t_33572/07_2025/7y1t_33572.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y1t_33572/07_2025/7y1t_33572.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y1t_33572/07_2025/7y1t_33572.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y1t_33572/07_2025/7y1t_33572.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y1t_33572/07_2025/7y1t_33572.cif"
  }
  resolution = 3.24
  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=   0.047
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: 6
    Type Number    sf(0)   Gaussians
     Ca      5      9.91       5
     Mn      1      7.51       5
     S      38      5.16       5
     C    5127      2.51       5
     N    1357      2.21       5
     O    1584      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 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: 8112
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 4114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 534, 4114
          Classifications: {'peptide': 534}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 507}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 345, 2714
          Classifications: {'peptide': 345}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 328}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1038
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 1038
          Classifications: {'peptide': 151}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 6, 'TRANS': 144}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 204
          Unresolved non-hydrogen angles: 253
          Unresolved non-hydrogen dihedrals: 170
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 131
    Chain: "F"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    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: "G"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 72
          Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "A"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 18
          Unusual residues: {' CA': 4, 'NAG': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          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: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 44
          Unusual residues: {' CA': 1, ' MN': 1, 'NAG': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      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
  Time building chain proxies: 5.72, per 1000 atoms: 0.71
  Number of scatterers: 8112
  At special positions: 0
  Unit cell: (100.225, 75.96, 150.865, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      1     24.99
     Ca      5     19.99
     S      38     16.00
     O    1584      8.00
     N    1357      7.00
     C    5127      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  59 " - pdb=" SG  CYS A  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 108 " - pdb=" SG  CYS A 128 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 142 " - pdb=" SG  CYS A 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 401 " - pdb=" SG  CYS B 259 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 479 " - pdb=" SG  CYS A 536 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 169 " - pdb=" SG  CYS B 176 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 224 " - pdb=" SG  CYS B 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 365 " - pdb=" SG  CYS B 377 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA G   3 " - " MAN G   6 "
    ALPHA1-4
      " BMA G   3 " - " MAN G   4 "
    ALPHA1-6
      " MAN G   4 " - " MAN G   5 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " NAG F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
    NAG-ASN
      " NAG A 701 " - " ASN A 525 "
      " NAG B 501 " - " ASN B 389 "
      " NAG B 502 " - " ASN B 191 "
      " NAG B 503 " - " ASN B 360 "
      " NAG C   1 " - " ASN A 260 "
      " NAG D 401 " - " ASN D 107 "
      " NAG E   1 " - " ASN A  44 "
      " NAG F   1 " - " ASN B 414 "
      " NAG G   1 " - " ASN A 266 "
  Time building additional restraints: 2.42
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1890

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 18 sheets defined
      14.3% alpha, 27.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 147 through 152
      removed outlier: 4.459A  pdb=" N   GLY A 151 " --> pdb=" O   ILE A 147 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLN A 152 " --> pdb=" O   ASP A 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 147 through 152'
    Processing helix  chain 'A' and resid 175 through 180
    Processing helix  chain 'A' and resid 188 through 194
    Processing helix  chain 'A' and resid 214 through 218
    Processing helix  chain 'A' and resid 245 through 250
      removed outlier: 3.609A  pdb=" N   THR A 249 " --> pdb=" O   ARG A 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 118
      removed outlier: 3.816A  pdb=" N   HIS B 118 " --> pdb=" O   ALA B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 124
    Processing helix  chain 'B' and resid 126 through 136
      removed outlier: 3.985A  pdb=" N   ASP B 130 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   SER B 132 " --> pdb=" O   GLY B 128 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ARG B 133 " --> pdb=" O   ASN B 129 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS B 134 " --> pdb=" O   ASP B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 173
    Processing helix  chain 'B' and resid 192 through 202
      removed outlier: 3.770A  pdb=" N   HIS B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ARG B 201 " --> pdb=" O   LYS B 197 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLN B 202 " --> pdb=" O   ALA B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 224
    Processing helix  chain 'B' and resid 224 through 229
    Processing helix  chain 'B' and resid 248 through 254
      removed outlier: 4.083A  pdb=" N   SER B 252 " --> pdb=" O   ALA B 249 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU B 254 " --> pdb=" O   ASP B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 293
    Processing helix  chain 'B' and resid 305 through 312
    Processing helix  chain 'B' and resid 330 through 345
    Processing helix  chain 'D' and resid 107 through 115
      removed outlier: 3.989A  pdb=" N   LEU D 111 " --> pdb=" O   ASN D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 171 through 180
      removed outlier: 4.020A  pdb=" N   SER D 180 " --> pdb=" O   ARG D 176 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12
      removed outlier: 6.921A  pdb=" N   ASP A 422 " --> pdb=" O   ALA A 412 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   ALA A 412 " --> pdb=" O   ASP A 422 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   SER A 408 " --> pdb=" O   GLY A 426 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26
    Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81
      removed outlier: 4.016A  pdb=" N   ALA A  81 " --> pdb=" O   ASP A  84 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88
      removed outlier: 4.046A  pdb=" N   HIS A 113 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 100
      removed outlier: 3.958A  pdb=" N   SER A  97 " --> pdb=" O   CYS A 108 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 164
      removed outlier: 3.754A  pdb=" N   SER A 160 " --> pdb=" O   GLY A 172 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG A 168 " --> pdb=" O   THR A 164 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 229
    Processing sheet with id=AA8, first strand: chain 'A' and resid 279 through 283
      removed outlier: 4.020A  pdb=" N   SER A 279 " --> pdb=" O   GLY A 296 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL A 293 " --> pdb=" O   SER A 318 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303
    Processing sheet with id=AB1, first strand: chain 'A' and resid 343 through 348
      removed outlier: 6.330A  pdb=" N   ILE A 344 " --> pdb=" O   ALA A 361 " (cutoff:3.500A)
      removed outlier: 7.921A  pdb=" N   ALA A 361 " --> pdb=" O   ILE A 344 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   ALA A 359 " --> pdb=" O   PRO A 346 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLN A 389 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 537 through 539
      removed outlier: 3.737A  pdb=" N   GLU A 537 " --> pdb=" O   PHE A 478 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   PHE A 478 " --> pdb=" O   GLU A 537 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   VAL A 476 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 524 through 529
      removed outlier: 4.043A  pdb=" N   LYS A 524 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   VAL A 496 " --> pdb=" O   LYS A 524 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ILE A 528 " --> pdb=" O   LEU A 492 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU A 492 " --> pdb=" O   ILE A 528 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 82 through 84
      removed outlier: 3.669A  pdb=" N   HIS B 422 " --> pdb=" O   ILE B  83 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ILE B 407 " --> pdb=" O   GLU B 351 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LYS B 409 " --> pdb=" O   GLN B 349 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 97
      removed outlier: 3.566A  pdb=" N   VAL B 392 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   VAL B 390 " --> pdb=" O   PHE B  93 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU B  95 " --> pdb=" O   PHE B 388 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR B 393 " --> pdb=" O   TYR B 358 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 91 through 97
      removed outlier: 3.566A  pdb=" N   VAL B 392 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   VAL B 390 " --> pdb=" O   PHE B  93 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU B  95 " --> pdb=" O   PHE B 388 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 183 through 189
      removed outlier: 6.411A  pdb=" N   VAL B 185 " --> pdb=" O   SER B 148 " (cutoff:3.500A)
      removed outlier: 8.327A  pdb=" N   SER B 148 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   SER B 187 " --> pdb=" O   PHE B 146 " (cutoff:3.500A)
      removed outlier: 4.672A  pdb=" N   PHE B 146 " --> pdb=" O   SER B 187 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   TYR B 109 " --> pdb=" O   GLY B 145 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   VAL B 111 " --> pdb=" O   GLY B 147 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   TYR B 149 " --> pdb=" O   VAL B 111 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   ASP B 106 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   LEU B 239 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   TYR B 108 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   MET B 241 " --> pdb=" O   TYR B 108 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   LEU B 110 " --> pdb=" O   MET B 241 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ASN B 296 " --> pdb=" O   ARG B 236 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 78 through 83
      removed outlier: 4.052A  pdb=" N   PHE D 228 " --> pdb=" O   ARG D 127 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ARG D 127 " --> pdb=" O   PHE D 228 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 102 through 106
      removed outlier: 3.746A  pdb=" N   ILE D 102 " --> pdb=" O   LEU D 190 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU D 190 " --> pdb=" O   ILE D 102 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   MET D 104 " --> pdb=" O   PHE D 188 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   GLY D 187 " --> pdb=" O   LYS D 144 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS D 144 " --> pdb=" O   GLY D 187 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   VAL D 139 " --> pdb=" O   ARG D 156 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   ARG D 156 " --> pdb=" O   VAL D 139 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   LEU D 141 " --> pdb=" O   SER D 154 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   SER D 154 " --> pdb=" O   LEU D 141 " (cutoff:3.500A)
      removed outlier: 7.129A  pdb=" N   GLN D 143 " --> pdb=" O   TYR D 152 " (cutoff:3.500A)
      removed outlier: 6.051A  pdb=" N   TYR D 152 " --> pdb=" O   GLN D 143 " (cutoff:3.500A)
      removed outlier: 5.775A  pdb=" N   TYR D 145 " --> pdb=" O   TRP D 150 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   TRP D 150 " --> pdb=" O   TYR D 145 " (cutoff:3.500A)

    227 hydrogen bonds defined for protein.
    594 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: 2.44

  Time building geometry restraints manager: 2.79 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: 2645
        1.34 -     1.46: 1943
        1.46 -     1.58: 3630
        1.58 -     1.70: 0
        1.70 -     1.82: 60
  Bond restraints: 8278
  Sorted by residual:
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.489 -0.083 2.00e-02 2.50e+03 1.71e+01
  bond pdb=" C1  MAN G   4 "
       pdb=" C2  MAN G   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.566 -0.040 2.00e-02 2.50e+03 3.91e+00
  bond pdb=" C1  MAN G   4 "
       pdb=" O5  MAN G   4 "
    ideal  model  delta    sigma   weight residual
    1.399  1.434 -0.035 2.00e-02 2.50e+03 2.98e+00
  bond pdb=" C1  MAN G   6 "
       pdb=" C2  MAN G   6 "
    ideal  model  delta    sigma   weight residual
    1.526  1.558 -0.032 2.00e-02 2.50e+03 2.61e+00
  bond pdb=" C1  NAG F   3 "
       pdb=" O5  NAG F   3 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.37e+00
  ... (remaining 8273 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 10800
        1.31 -     2.63: 318
        2.63 -     3.94: 81
        3.94 -     5.26: 20
        5.26 -     6.57: 11
  Bond angle restraints: 11230
  Sorted by residual:
  angle pdb=" C   ASP A 288 "
        pdb=" N   ASP A 289 "
        pdb=" CA  ASP A 289 "
      ideal   model   delta    sigma   weight residual
     124.31  130.49   -6.18 1.67e+00 3.59e-01 1.37e+01
  angle pdb=" C   SER A 201 "
        pdb=" N   ILE A 202 "
        pdb=" CA  ILE A 202 "
      ideal   model   delta    sigma   weight residual
     121.97  126.30   -4.33 1.80e+00 3.09e-01 5.80e+00
  angle pdb=" CA  ASP A 289 "
        pdb=" CB  ASP A 289 "
        pdb=" CG  ASP A 289 "
      ideal   model   delta    sigma   weight residual
     112.60  114.90   -2.30 1.00e+00 1.00e+00 5.27e+00
  angle pdb=" CA  CYS B 259 "
        pdb=" CB  CYS B 259 "
        pdb=" SG  CYS B 259 "
      ideal   model   delta    sigma   weight residual
     114.40  119.52   -5.12 2.30e+00 1.89e-01 4.96e+00
  angle pdb=" C   PHE B 195 "
        pdb=" N   GLU B 196 "
        pdb=" CA  GLU B 196 "
      ideal   model   delta    sigma   weight residual
     120.31  117.19    3.12 1.52e+00 4.33e-01 4.21e+00
  ... (remaining 11225 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.77: 4778
       22.77 -    45.55: 283
       45.55 -    68.32: 58
       68.32 -    91.10: 20
       91.10 -   113.87: 19
  Dihedral angle restraints: 5158
    sinusoidal: 2207
      harmonic: 2951
  Sorted by residual:
  dihedral pdb=" CB  CYS A 142 "
           pdb=" SG  CYS A 142 "
           pdb=" SG  CYS A 155 "
           pdb=" CB  CYS A 155 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -38.55  -47.45     1      1.00e+01 1.00e-02 3.11e+01
  dihedral pdb=" CB  CYS A 401 "
           pdb=" SG  CYS A 401 "
           pdb=" SG  CYS B 259 "
           pdb=" CB  CYS B 259 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.14   40.14     1      1.00e+01 1.00e-02 2.26e+01
  dihedral pdb=" CA  ALA B 329 "
           pdb=" C   ALA B 329 "
           pdb=" N   ASN B 330 "
           pdb=" CA  ASN B 330 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.80   22.20     0      5.00e+00 4.00e-02 1.97e+01
  ... (remaining 5155 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.316: 1286
       0.316 -    0.633: 2
       0.633 -    0.949: 1
       0.949 -    1.266: 0
       1.266 -    1.582: 3
  Chirality restraints: 1292
  Sorted by residual:
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.93   -0.47 2.00e-02 2.50e+03 5.47e+02
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN A 266 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.82   -1.58 2.00e-01 2.50e+01 6.26e+01
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN B 414 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.95   -1.45 2.00e-01 2.50e+01 5.28e+01
  ... (remaining 1289 not shown)

  Planarity restraints: 1458
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 266 "   -0.163 2.00e-02 2.50e+03   2.04e-01 5.21e+02
        pdb=" CG  ASN A 266 "    0.069 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 266 "    0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 266 "    0.340 2.00e-02 2.50e+03
        pdb=" C1  NAG G   1 "   -0.248 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 414 "   -0.152 2.00e-02 2.50e+03   1.93e-01 4.67e+02
        pdb=" CG  ASN B 414 "    0.063 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 414 "   -0.003 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 414 "    0.325 2.00e-02 2.50e+03
        pdb=" C1  NAG F   1 "   -0.233 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 525 "   -0.115 2.00e-02 2.50e+03   1.34e-01 2.23e+02
        pdb=" CG  ASN A 525 "    0.046 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 525 "    0.014 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 525 "    0.217 2.00e-02 2.50e+03
        pdb=" C1  NAG A 701 "   -0.163 2.00e-02 2.50e+03
  ... (remaining 1455 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 88
        2.58 -     3.16: 6368
        3.16 -     3.74: 11799
        3.74 -     4.32: 16459
        4.32 -     4.90: 27765
  Nonbonded interactions: 62479
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 217 "
            pdb="MN    MN B 505 "
     model   vdw
     1.998 2.320
  nonbonded pdb=" OG  SER A 144 "
            pdb=" OD1 ASP A 146 "
     model   vdw
     2.130 3.040
  nonbonded pdb=" NZ  LYS B 327 "
            pdb=" O   ALA B 329 "
     model   vdw
     2.182 3.120
  nonbonded pdb=" OD1 ASP B 130 "
            pdb=" ND2 ASN B 332 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" OD1 ASP A  24 "
            pdb=" N   PHE A  25 "
     model   vdw
     2.233 3.120
  ... (remaining 62474 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 'C'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             3.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.520
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.070
  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:             0.010
  Load rotamer database and sin/cos tables:3.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
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   0.083   8304  Z= 0.170
  Angle     :  0.884  30.865  11300  Z= 0.353
  Chirality :  0.087   1.582   1292
  Planarity :  0.004   0.104   1449
  Dihedral  : 16.885 113.873   3244
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.27), residues: 1014
  helix:  1.39 (0.57), residues: 98
  sheet:  0.21 (0.29), residues: 337
  loop : -1.33 (0.26), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 179 
 HIS   0.002   0.000   HIS A 113 
 PHE   0.017   0.001   PHE B 137 
 TYR   0.011   0.001   TYR A 200 
 ARG   0.005   0.000   ARG D 226 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.03297 (    9)
  link_NAG-ASN         : angle      11.79741 (   27)
  link_ALPHA1-4        : bond        0.01084 (    1)
  link_ALPHA1-4        : angle       1.68503 (    3)
  link_ALPHA1-6        : bond        0.00378 (    1)
  link_ALPHA1-6        : angle       1.48862 (    3)
  link_BETA1-4         : bond        0.01420 (    6)
  link_BETA1-4         : angle       7.97537 (   18)
  link_ALPHA1-3        : bond        0.00416 (    1)
  link_ALPHA1-3        : angle       1.80026 (    3)
  hydrogen bonds       : bond        0.25773 (  222)
  hydrogen bonds       : angle      10.45088 (  594)
  SS BOND              : bond        0.00256 (    8)
  SS BOND              : angle       0.87807 (   16)
  covalent geometry    : bond        0.00324 ( 8278)
  covalent geometry    : angle       0.58807 (11230)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
REVERT: A  474 PHE cc_start: 0.3816 (p90) cc_final: 0.3565 (p90)
REVERT: B  250 LEU cc_start: 0.8421 (mt) cc_final: 0.8081 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1936
  time to fit residues: 33.8669
Evaluate side-chains
  87 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 52 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 92 optimal weight:    4.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 182 GLN
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 118 HIS
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.132476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.104762 restraints weight = 14098.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 2.93
r_work: 0.3444 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8304  Z= 0.176
  Angle     :  0.682   9.531  11300  Z= 0.325
  Chirality :  0.048   0.275   1292
  Planarity :  0.004   0.078   1449
  Dihedral  : 12.284  96.129   1472
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 10.34 %
    Favored  : 88.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.27), residues: 1014
  helix:  1.74 (0.56), residues: 100
  sheet: -0.02 (0.27), residues: 373
  loop : -1.21 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  61 
 HIS   0.004   0.001   HIS A 113 
 PHE   0.029   0.002   PHE B 137 
 TYR   0.013   0.002   TYR A 178 
 ARG   0.005   0.001   ARG D 215 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00589 (    9)
  link_NAG-ASN         : angle       2.63032 (   27)
  link_ALPHA1-4        : bond        0.01236 (    1)
  link_ALPHA1-4        : angle       1.00762 (    3)
  link_ALPHA1-6        : bond        0.00260 (    1)
  link_ALPHA1-6        : angle       1.37511 (    3)
  link_BETA1-4         : bond        0.00599 (    6)
  link_BETA1-4         : angle       1.98330 (   18)
  link_ALPHA1-3        : bond        0.01421 (    1)
  link_ALPHA1-3        : angle       2.20218 (    3)
  hydrogen bonds       : bond        0.03387 (  222)
  hydrogen bonds       : angle       7.12175 (  594)
  SS BOND              : bond        0.00714 (    8)
  SS BOND              : angle       1.45272 (   16)
  covalent geometry    : bond        0.00406 ( 8278)
  covalent geometry    : angle       0.66344 (11230)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 2.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7003 (p0)
REVERT: A  474 PHE cc_start: 0.3557 (p90) cc_final: 0.3303 (p90)
REVERT: B  224 CYS cc_start: 0.7716 (m) cc_final: 0.7475 (m)
  outliers start: 10
  outliers final: 7
  residues processed: 97
  average time/residue: 0.3150
  time to fit residues: 44.6893
Evaluate side-chains
  88 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain D residue  108 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 67 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 78 optimal weight:    0.0980
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.129024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.101144 restraints weight = 14192.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 2.92
r_work: 0.3386 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.2404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8304  Z= 0.146
  Angle     :  0.640  15.479  11300  Z= 0.305
  Chirality :  0.048   0.305   1292
  Planarity :  0.004   0.056   1449
  Dihedral  : 10.360  94.138   1472
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.02 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.27), residues: 1014
  helix:  1.83 (0.58), residues: 96
  sheet: -0.06 (0.27), residues: 374
  loop : -1.15 (0.27), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  61 
 HIS   0.004   0.001   HIS A 113 
 PHE   0.022   0.001   PHE B 137 
 TYR   0.014   0.001   TYR A 420 
 ARG   0.003   0.000   ARG D 215 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00433 (    9)
  link_NAG-ASN         : angle       2.33555 (   27)
  link_ALPHA1-4        : bond        0.01444 (    1)
  link_ALPHA1-4        : angle       1.10407 (    3)
  link_ALPHA1-6        : bond        0.00604 (    1)
  link_ALPHA1-6        : angle       1.41629 (    3)
  link_BETA1-4         : bond        0.00561 (    6)
  link_BETA1-4         : angle       2.13021 (   18)
  link_ALPHA1-3        : bond        0.01529 (    1)
  link_ALPHA1-3        : angle       1.84903 (    3)
  hydrogen bonds       : bond        0.03432 (  222)
  hydrogen bonds       : angle       6.46569 (  594)
  SS BOND              : bond        0.00546 (    8)
  SS BOND              : angle       1.72186 (   16)
  covalent geometry    : bond        0.00334 ( 8278)
  covalent geometry    : angle       0.62080 (11230)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.949 
Fit side-chains
REVERT: A  108 CYS cc_start: 0.7109 (m) cc_final: 0.6665 (m)
REVERT: A  474 PHE cc_start: 0.3620 (p90) cc_final: 0.3289 (p90)
REVERT: B  141 ASP cc_start: 0.7709 (t0) cc_final: 0.6455 (p0)
REVERT: B  224 CYS cc_start: 0.7666 (m) cc_final: 0.7459 (m)
  outliers start: 13
  outliers final: 6
  residues processed: 90
  average time/residue: 0.2015
  time to fit residues: 25.2700
Evaluate side-chains
  81 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain D residue   99 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 37 optimal weight:    0.0970
   chunk 51 optimal weight:    4.9990
   chunk 95 optimal weight:   10.0000
   chunk 77 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 94 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.126731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.098836 restraints weight = 14024.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 2.90
r_work: 0.3352 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8304  Z= 0.159
  Angle     :  0.640  13.701  11300  Z= 0.307
  Chirality :  0.047   0.301   1292
  Planarity :  0.004   0.050   1449
  Dihedral  :  9.893  91.587   1472
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.87 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.27), residues: 1014
  helix:  1.67 (0.57), residues: 100
  sheet: -0.19 (0.27), residues: 374
  loop : -1.12 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  61 
 HIS   0.002   0.001   HIS A 113 
 PHE   0.019   0.001   PHE B 137 
 TYR   0.011   0.001   TYR A 562 
 ARG   0.004   0.000   ARG D 226 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00411 (    9)
  link_NAG-ASN         : angle       2.26841 (   27)
  link_ALPHA1-4        : bond        0.01541 (    1)
  link_ALPHA1-4        : angle       1.17321 (    3)
  link_ALPHA1-6        : bond        0.00482 (    1)
  link_ALPHA1-6        : angle       1.40699 (    3)
  link_BETA1-4         : bond        0.00536 (    6)
  link_BETA1-4         : angle       2.16337 (   18)
  link_ALPHA1-3        : bond        0.01632 (    1)
  link_ALPHA1-3        : angle       1.35095 (    3)
  hydrogen bonds       : bond        0.03066 (  222)
  hydrogen bonds       : angle       6.19122 (  594)
  SS BOND              : bond        0.00819 (    8)
  SS BOND              : angle       2.35246 (   16)
  covalent geometry    : bond        0.00372 ( 8278)
  covalent geometry    : angle       0.61937 (11230)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.884 
Fit side-chains
REVERT: A   60 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7087 (p0)
REVERT: A  368 ASP cc_start: 0.8156 (t0) cc_final: 0.7864 (t0)
REVERT: A  474 PHE cc_start: 0.3099 (p90) cc_final: 0.2849 (p90)
REVERT: B  141 ASP cc_start: 0.7650 (t0) cc_final: 0.6450 (p0)
REVERT: B  224 CYS cc_start: 0.7599 (m) cc_final: 0.7376 (m)
  outliers start: 20
  outliers final: 13
  residues processed: 92
  average time/residue: 0.2088
  time to fit residues: 26.9670
Evaluate side-chains
  90 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  374 MET
Chi-restraints excluded: chain D residue   99 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 61 optimal weight:    0.2980
   chunk 63 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0870
   chunk 19 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 45 optimal weight:    7.9990
   chunk 24 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    0.6560

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.125973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.098071 restraints weight = 13908.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 2.88
r_work: 0.3338 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8304  Z= 0.145
  Angle     :  0.623  13.477  11300  Z= 0.296
  Chirality :  0.046   0.295   1292
  Planarity :  0.004   0.047   1449
  Dihedral  :  9.611  90.868   1472
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 16.18 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.27), residues: 1014
  helix:  1.57 (0.56), residues: 102
  sheet: -0.18 (0.27), residues: 373
  loop : -1.10 (0.27), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  61 
 HIS   0.002   0.001   HIS A 113 
 PHE   0.018   0.001   PHE B 137 
 TYR   0.012   0.001   TYR A 420 
 ARG   0.003   0.000   ARG D 226 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00387 (    9)
  link_NAG-ASN         : angle       2.20536 (   27)
  link_ALPHA1-4        : bond        0.01520 (    1)
  link_ALPHA1-4        : angle       1.10085 (    3)
  link_ALPHA1-6        : bond        0.00507 (    1)
  link_ALPHA1-6        : angle       1.41838 (    3)
  link_BETA1-4         : bond        0.00520 (    6)
  link_BETA1-4         : angle       2.25833 (   18)
  link_ALPHA1-3        : bond        0.01532 (    1)
  link_ALPHA1-3        : angle       1.23544 (    3)
  hydrogen bonds       : bond        0.02972 (  222)
  hydrogen bonds       : angle       6.02192 (  594)
  SS BOND              : bond        0.00749 (    8)
  SS BOND              : angle       2.07400 (   16)
  covalent geometry    : bond        0.00337 ( 8278)
  covalent geometry    : angle       0.60322 (11230)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 1.040 
Fit side-chains
REVERT: A   60 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7306 (p0)
REVERT: A  368 ASP cc_start: 0.8187 (t0) cc_final: 0.7825 (t0)
REVERT: A  474 PHE cc_start: 0.3123 (p90) cc_final: 0.2886 (p90)
REVERT: B  141 ASP cc_start: 0.7633 (t0) cc_final: 0.6417 (p0)
  outliers start: 16
  outliers final: 10
  residues processed: 93
  average time/residue: 0.1889
  time to fit residues: 25.2174
Evaluate side-chains
  88 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  374 MET
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain D residue   99 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 88 optimal weight:    7.9990
   chunk 17 optimal weight:    0.6980
   chunk 94 optimal weight:    0.0980
   chunk 42 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 ASN
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.125128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.097240 restraints weight = 14130.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 2.90
r_work: 0.3322 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.3256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8304  Z= 0.147
  Angle     :  0.627  12.682  11300  Z= 0.299
  Chirality :  0.047   0.290   1292
  Planarity :  0.004   0.048   1449
  Dihedral  :  9.434  89.606   1472
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 16.55 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.27), residues: 1014
  helix:  1.57 (0.57), residues: 102
  sheet: -0.23 (0.27), residues: 372
  loop : -1.04 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  61 
 HIS   0.002   0.001   HIS B 307 
 PHE   0.027   0.001   PHE B 137 
 TYR   0.010   0.001   TYR A 420 
 ARG   0.003   0.000   ARG D 215 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00376 (    9)
  link_NAG-ASN         : angle       2.18692 (   27)
  link_ALPHA1-4        : bond        0.01460 (    1)
  link_ALPHA1-4        : angle       1.09747 (    3)
  link_ALPHA1-6        : bond        0.00494 (    1)
  link_ALPHA1-6        : angle       1.40706 (    3)
  link_BETA1-4         : bond        0.00500 (    6)
  link_BETA1-4         : angle       2.32403 (   18)
  link_ALPHA1-3        : bond        0.01440 (    1)
  link_ALPHA1-3        : angle       1.15820 (    3)
  hydrogen bonds       : bond        0.02957 (  222)
  hydrogen bonds       : angle       5.94459 (  594)
  SS BOND              : bond        0.00583 (    8)
  SS BOND              : angle       2.25369 (   16)
  covalent geometry    : bond        0.00344 ( 8278)
  covalent geometry    : angle       0.60560 (11230)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7128 (p0)
REVERT: A  368 ASP cc_start: 0.8245 (t0) cc_final: 0.7841 (t0)
REVERT: A  474 PHE cc_start: 0.3134 (p90) cc_final: 0.2878 (p90)
REVERT: B  141 ASP cc_start: 0.7648 (t0) cc_final: 0.6425 (p0)
  outliers start: 20
  outliers final: 13
  residues processed: 92
  average time/residue: 0.1850
  time to fit residues: 24.3350
Evaluate side-chains
  89 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  374 MET
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain D residue   99 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 95 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 ASN
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.123640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.095588 restraints weight = 14187.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.91
r_work: 0.3293 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.3514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8304  Z= 0.180
  Angle     :  0.648  13.169  11300  Z= 0.312
  Chirality :  0.048   0.291   1292
  Planarity :  0.004   0.048   1449
  Dihedral  :  9.380  88.544   1472
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 16.79 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.27), residues: 1014
  helix:  1.55 (0.57), residues: 102
  sheet: -0.20 (0.27), residues: 372
  loop : -1.05 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  61 
 HIS   0.003   0.001   HIS B 307 
 PHE   0.027   0.001   PHE B 137 
 TYR   0.012   0.001   TYR A 562 
 ARG   0.003   0.000   ARG D 215 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00393 (    9)
  link_NAG-ASN         : angle       2.23550 (   27)
  link_ALPHA1-4        : bond        0.01406 (    1)
  link_ALPHA1-4        : angle       1.13561 (    3)
  link_ALPHA1-6        : bond        0.00568 (    1)
  link_ALPHA1-6        : angle       1.42520 (    3)
  link_BETA1-4         : bond        0.00466 (    6)
  link_BETA1-4         : angle       2.38638 (   18)
  link_ALPHA1-3        : bond        0.01403 (    1)
  link_ALPHA1-3        : angle       1.12263 (    3)
  hydrogen bonds       : bond        0.03208 (  222)
  hydrogen bonds       : angle       5.99336 (  594)
  SS BOND              : bond        0.00951 (    8)
  SS BOND              : angle       2.32025 (   16)
  covalent geometry    : bond        0.00423 ( 8278)
  covalent geometry    : angle       0.62647 (11230)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7150 (p0)
REVERT: A  225 SER cc_start: 0.8741 (t) cc_final: 0.8459 (p)
REVERT: A  275 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.7602 (m-80)
REVERT: A  368 ASP cc_start: 0.8319 (t0) cc_final: 0.7918 (t0)
REVERT: A  474 PHE cc_start: 0.3124 (p90) cc_final: 0.2848 (p90)
REVERT: A  483 ASP cc_start: 0.7346 (t70) cc_final: 0.7063 (t70)
REVERT: B  141 ASP cc_start: 0.7742 (t0) cc_final: 0.6421 (p0)
REVERT: D  140 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5560 (tp30)
  outliers start: 23
  outliers final: 17
  residues processed: 95
  average time/residue: 0.1915
  time to fit residues: 26.0127
Evaluate side-chains
  98 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  374 MET
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain B residue  421 ILE
Chi-restraints excluded: chain D residue   99 THR
Chi-restraints excluded: chain D residue  140 GLU
Chi-restraints excluded: chain D residue  234 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0980
   chunk 51 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.123942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.095963 restraints weight = 14286.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 2.92
r_work: 0.3296 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8304  Z= 0.148
  Angle     :  0.627  12.225  11300  Z= 0.301
  Chirality :  0.047   0.287   1292
  Planarity :  0.004   0.050   1449
  Dihedral  :  9.273  88.136   1472
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 17.40 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.27), residues: 1014
  helix:  1.45 (0.56), residues: 103
  sheet: -0.18 (0.27), residues: 371
  loop : -1.01 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  61 
 HIS   0.002   0.001   HIS B 307 
 PHE   0.026   0.001   PHE B 137 
 TYR   0.009   0.001   TYR A 562 
 ARG   0.003   0.000   ARG D 215 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00368 (    9)
  link_NAG-ASN         : angle       2.17075 (   27)
  link_ALPHA1-4        : bond        0.01425 (    1)
  link_ALPHA1-4        : angle       1.12347 (    3)
  link_ALPHA1-6        : bond        0.00489 (    1)
  link_ALPHA1-6        : angle       1.40184 (    3)
  link_BETA1-4         : bond        0.00491 (    6)
  link_BETA1-4         : angle       2.44490 (   18)
  link_ALPHA1-3        : bond        0.01317 (    1)
  link_ALPHA1-3        : angle       1.08923 (    3)
  hydrogen bonds       : bond        0.03047 (  222)
  hydrogen bonds       : angle       5.92398 (  594)
  SS BOND              : bond        0.00541 (    8)
  SS BOND              : angle       2.08073 (   16)
  covalent geometry    : bond        0.00347 ( 8278)
  covalent geometry    : angle       0.60588 (11230)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 ASP cc_start: 0.7772 (t70) cc_final: 0.7143 (p0)
REVERT: A  225 SER cc_start: 0.8778 (t) cc_final: 0.8505 (p)
REVERT: A  275 TYR cc_start: 0.8840 (OUTLIER) cc_final: 0.7373 (m-80)
REVERT: A  368 ASP cc_start: 0.8320 (t0) cc_final: 0.7920 (t0)
REVERT: A  409 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8667 (ptp)
REVERT: A  474 PHE cc_start: 0.3283 (p90) cc_final: 0.2998 (p90)
REVERT: A  483 ASP cc_start: 0.7374 (t70) cc_final: 0.7130 (t70)
REVERT: D  140 GLU cc_start: 0.6011 (tp30) cc_final: 0.5567 (tp30)
  outliers start: 22
  outliers final: 15
  residues processed: 99
  average time/residue: 0.1950
  time to fit residues: 27.6357
Evaluate side-chains
  93 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  409 MET
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  374 MET
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain D residue   99 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0070
   chunk 0 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0980
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.124180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.096510 restraints weight = 14464.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 2.82
r_work: 0.3311 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.3678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8304  Z= 0.135
  Angle     :  0.625  11.189  11300  Z= 0.298
  Chirality :  0.047   0.285   1292
  Planarity :  0.004   0.051   1449
  Dihedral  :  9.154  87.289   1472
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 17.76 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.27), residues: 1014
  helix:  1.48 (0.56), residues: 103
  sheet: -0.13 (0.27), residues: 361
  loop : -1.02 (0.28), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  61 
 HIS   0.002   0.001   HIS B 307 
 PHE   0.024   0.001   PHE B 137 
 TYR   0.011   0.001   TYR A 562 
 ARG   0.002   0.000   ARG D 215 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00361 (    9)
  link_NAG-ASN         : angle       2.12900 (   27)
  link_ALPHA1-4        : bond        0.01444 (    1)
  link_ALPHA1-4        : angle       1.13441 (    3)
  link_ALPHA1-6        : bond        0.00509 (    1)
  link_ALPHA1-6        : angle       1.40263 (    3)
  link_BETA1-4         : bond        0.00503 (    6)
  link_BETA1-4         : angle       2.48063 (   18)
  link_ALPHA1-3        : bond        0.01293 (    1)
  link_ALPHA1-3        : angle       1.09874 (    3)
  hydrogen bonds       : bond        0.02953 (  222)
  hydrogen bonds       : angle       5.88228 (  594)
  SS BOND              : bond        0.00606 (    8)
  SS BOND              : angle       1.93615 (   16)
  covalent geometry    : bond        0.00315 ( 8278)
  covalent geometry    : angle       0.60487 (11230)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 1.817 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 ASP cc_start: 0.7733 (t70) cc_final: 0.7141 (p0)
REVERT: A  225 SER cc_start: 0.8772 (t) cc_final: 0.8511 (p)
REVERT: A  275 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.7533 (m-80)
REVERT: A  368 ASP cc_start: 0.8290 (t0) cc_final: 0.7938 (t0)
REVERT: A  409 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8662 (ptp)
REVERT: A  483 ASP cc_start: 0.7398 (t70) cc_final: 0.7154 (t70)
REVERT: A  497 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6689 (pp20)
REVERT: D  140 GLU cc_start: 0.6061 (OUTLIER) cc_final: 0.5688 (tp30)
  outliers start: 23
  outliers final: 18
  residues processed: 97
  average time/residue: 0.3166
  time to fit residues: 43.1599
Evaluate side-chains
  98 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  409 MET
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  349 GLN
Chi-restraints excluded: chain B residue  374 MET
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain B residue  421 ILE
Chi-restraints excluded: chain D residue   99 THR
Chi-restraints excluded: chain D residue  140 GLU
Chi-restraints excluded: chain D residue  222 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 15 optimal weight:    0.2980
   chunk 79 optimal weight:    2.9990
   chunk 59 optimal weight:    0.1980
   chunk 50 optimal weight:    0.3980
   chunk 56 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0870
   chunk 23 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9980
   chunk 12 optimal weight:    0.4980
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.2958

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.125730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.097821 restraints weight = 14071.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.87
r_work: 0.3333 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.3667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8304  Z= 0.107
  Angle     :  0.607  10.479  11300  Z= 0.288
  Chirality :  0.046   0.280   1292
  Planarity :  0.004   0.052   1449
  Dihedral  :  8.978  85.970   1472
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.00 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.27), residues: 1014
  helix:  1.61 (0.56), residues: 103
  sheet: -0.09 (0.27), residues: 361
  loop : -1.01 (0.28), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  61 
 HIS   0.002   0.001   HIS B 307 
 PHE   0.023   0.001   PHE B 137 
 TYR   0.010   0.001   TYR A 562 
 ARG   0.002   0.000   ARG A 398 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00356 (    9)
  link_NAG-ASN         : angle       2.04060 (   27)
  link_ALPHA1-4        : bond        0.01320 (    1)
  link_ALPHA1-4        : angle       1.03222 (    3)
  link_ALPHA1-6        : bond        0.00481 (    1)
  link_ALPHA1-6        : angle       1.40326 (    3)
  link_BETA1-4         : bond        0.00525 (    6)
  link_BETA1-4         : angle       2.50338 (   18)
  link_ALPHA1-3        : bond        0.01286 (    1)
  link_ALPHA1-3        : angle       1.16177 (    3)
  hydrogen bonds       : bond        0.02777 (  222)
  hydrogen bonds       : angle       5.77846 (  594)
  SS BOND              : bond        0.00451 (    8)
  SS BOND              : angle       1.71456 (   16)
  covalent geometry    : bond        0.00243 ( 8278)
  covalent geometry    : angle       0.58754 (11230)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 1.256 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 ASP cc_start: 0.7626 (t70) cc_final: 0.7080 (p0)
REVERT: A  225 SER cc_start: 0.8766 (t) cc_final: 0.8510 (p)
REVERT: A  275 TYR cc_start: 0.8737 (OUTLIER) cc_final: 0.7594 (m-80)
REVERT: A  368 ASP cc_start: 0.8302 (t0) cc_final: 0.7993 (t0)
REVERT: A  483 ASP cc_start: 0.7400 (t70) cc_final: 0.7166 (t70)
REVERT: A  497 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6666 (pp20)
REVERT: D  140 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5749 (tp30)
  outliers start: 18
  outliers final: 11
  residues processed: 92
  average time/residue: 0.2718
  time to fit residues: 35.6534
Evaluate side-chains
  92 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain D residue  140 GLU
Chi-restraints excluded: chain D residue  222 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 83 optimal weight:    0.0070
   chunk 15 optimal weight:    0.4980
   chunk 17 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0770
   chunk 43 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.4356

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.125344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.097489 restraints weight = 14208.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.93
r_work: 0.3325 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.3790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8304  Z= 0.117
  Angle     :  0.606  10.762  11300  Z= 0.286
  Chirality :  0.046   0.282   1292
  Planarity :  0.004   0.051   1449
  Dihedral  :  8.763  82.052   1472
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 17.76 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.27), residues: 1014
  helix:  1.66 (0.56), residues: 103
  sheet: -0.04 (0.27), residues: 361
  loop : -1.00 (0.28), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  61 
 HIS   0.002   0.001   HIS B 307 
 PHE   0.022   0.001   PHE B 137 
 TYR   0.010   0.001   TYR A 562 
 ARG   0.002   0.000   ARG D 214 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00343 (    9)
  link_NAG-ASN         : angle       2.07433 (   27)
  link_ALPHA1-4        : bond        0.01418 (    1)
  link_ALPHA1-4        : angle       1.16116 (    3)
  link_ALPHA1-6        : bond        0.00516 (    1)
  link_ALPHA1-6        : angle       1.38678 (    3)
  link_BETA1-4         : bond        0.00510 (    6)
  link_BETA1-4         : angle       2.54837 (   18)
  link_ALPHA1-3        : bond        0.01183 (    1)
  link_ALPHA1-3        : angle       1.14320 (    3)
  hydrogen bonds       : bond        0.02732 (  222)
  hydrogen bonds       : angle       5.67555 (  594)
  SS BOND              : bond        0.00495 (    8)
  SS BOND              : angle       1.65145 (   16)
  covalent geometry    : bond        0.00268 ( 8278)
  covalent geometry    : angle       0.58628 (11230)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4328.80 seconds
wall clock time: 78 minutes 32.86 seconds (4712.86 seconds total)