Starting phenix.real_space_refine
on Sun Apr  5 03:42:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ux1_64569/04_2026/9ux1_64569.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ux1_64569/04_2026/9ux1_64569.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ux1_64569/04_2026/9ux1_64569.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ux1_64569/04_2026/9ux1_64569.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ux1_64569/04_2026/9ux1_64569.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ux1_64569/04_2026/9ux1_64569.cif"
  }
  resolution = 2.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.024
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: 5
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     S      49      5.16       5
     C    4954      2.51       5
     N    1273      2.21       5
     O    1460      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7745
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2499
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 2499
          Classifications: {'peptide': 319}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 303}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 2545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 325, 2545
          Classifications: {'peptide': 325}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 2524
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2524
          Classifications: {'peptide': 323}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 307}
    Chain: "A"
      Number of atoms: 59
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 59
          Unusual residues: {'ATP': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 59
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 59
          Unusual residues: {'ATP': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 59
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 59
          Unusual residues: {'ATP': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.73, per 1000 atoms: 0.22
  Number of scatterers: 7745
  At special positions: 0
  Unit cell: (93.12, 88.32, 128.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      49     16.00
     P       9     15.00
     O    1460      8.00
     N    1273      7.00
     C    4954      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 107 " - pdb=" SG  CYS A 153 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 116 " - pdb=" SG  CYS A 137 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 122 " - pdb=" SG  CYS A 147 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 203 " - pdb=" SG  CYS A 213 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 247 " - pdb=" SG  CYS A 256 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 107 " - pdb=" SG  CYS B 153 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 116 " - pdb=" SG  CYS B 137 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 122 " - pdb=" SG  CYS B 147 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 203 " - pdb=" SG  CYS B 213 " distance=2.31
    Simple disulfide: pdb=" SG  CYS B 247 " - pdb=" SG  CYS B 256 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 125 " - pdb=" SG  CYS C 176 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 136 " - pdb=" SG  CYS C 159 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 142 " - pdb=" SG  CYS C 170 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 226 " - pdb=" SG  CYS C 236 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 270 " - pdb=" SG  CYS C 279 " 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
    NAG-ASN
      " NAG A 401 " - " ASN A 290 "
      " NAG A 402 " - " ASN A 170 "
      " NAG B 401 " - " ASN B 290 "
      " NAG B 402 " - " ASN B 170 "
      " NAG C 502 " - " ASN C 194 "
      " NAG C 503 " - " ASN C 133 "
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 233.1 milliseconds
  

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1776

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 12 sheets defined
      23.8% alpha, 24.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 42
      removed outlier: 3.672A  pdb=" N   VAL A  29 " --> pdb=" O   ILE A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 80
      removed outlier: 3.837A  pdb=" N   TYR A  80 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 76 through 80'
    Processing helix  chain 'A' and resid 166 through 170
      removed outlier: 4.129A  pdb=" N   GLU A 169 " --> pdb=" O   MET A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 225
      removed outlier: 3.877A  pdb=" N   ALA A 225 " --> pdb=" O   VAL A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 233
    Processing helix  chain 'A' and resid 266 through 270
    Processing helix  chain 'A' and resid 318 through 343
      removed outlier: 3.690A  pdb=" N   ILE A 322 " --> pdb=" O   ILE A 318 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   THR A 330 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   SER A 331 " --> pdb=" O   ALA A 327 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL A 332 " --> pdb=" O   ALA A 328 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ASP A 340 " --> pdb=" O   THR A 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 43
    Processing helix  chain 'B' and resid 76 through 79
    Processing helix  chain 'B' and resid 118 through 122
      removed outlier: 3.613A  pdb=" N   GLN B 121 " --> pdb=" O   SER B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 170
    Processing helix  chain 'B' and resid 198 through 202
      removed outlier: 3.512A  pdb=" N   LYS B 201 " --> pdb=" O   ARG B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 218 through 222
    Processing helix  chain 'B' and resid 228 through 236
    Processing helix  chain 'B' and resid 266 through 270
    Processing helix  chain 'B' and resid 318 through 346
      removed outlier: 3.786A  pdb=" N   ALA B 327 " --> pdb=" O   ILE B 323 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ALA B 328 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   PHE B 329 " --> pdb=" O   SER B 325 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   THR B 336 " --> pdb=" O   VAL B 332 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL B 337 " --> pdb=" O   GLY B 333 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   ILE B 342 " --> pdb=" O   LEU B 338 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   LEU B 343 " --> pdb=" O   CYS B 339 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 62
    Processing helix  chain 'C' and resid 94 through 97
    Processing helix  chain 'C' and resid 191 through 194
    Processing helix  chain 'C' and resid 241 through 249
    Processing helix  chain 'C' and resid 251 through 256
    Processing helix  chain 'C' and resid 338 through 364
      removed outlier: 3.851A  pdb=" N   ILE C 342 " --> pdb=" O   LEU C 338 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   THR C 350 " --> pdb=" O   ALA C 346 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   SER C 351 " --> pdb=" O   THR C 347 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   VAL C 352 " --> pdb=" O   ALA C 348 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 53
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 50 through 53
    current: chain 'A' and resid 90 through 102
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 90 through 102
    current: chain 'A' and resid 260 through 264
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 260 through 264
    current: chain 'A' and resid 292 through 316
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 65
      removed outlier: 3.703A  pdb=" N   PHE A 186 " --> pdb=" O   PHE A 181 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 70
    Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 107
      removed outlier: 5.683A  pdb=" N   ARG A 136 " --> pdb=" O   GLU A 148 " (cutoff:3.500A)
      removed outlier: 9.035A  pdb=" N   GLN A 150 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
      removed outlier: 8.128A  pdb=" N   THR A 134 " --> pdb=" O   GLN A 150 " (cutoff:3.500A)
      removed outlier: 9.561A  pdb=" N   TRP A 152 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
      removed outlier: 10.188A  pdb=" N   ILE A 132 " --> pdb=" O   TRP A 152 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 53
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 50 through 53
    current: chain 'B' and resid 90 through 108
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 90 through 108
    current: chain 'B' and resid 148 through 153
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 148 through 153
    current: chain 'B' and resid 258 through 264
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 258 through 264
    current: chain 'B' and resid 293 through 316
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 65
      removed outlier: 3.616A  pdb=" N   SER B 178 " --> pdb=" O   SER B  59 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   PHE B 186 " --> pdb=" O   PHE B 181 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 68 through 70
      removed outlier: 3.970A  pdb=" N   GLY B  68 " --> pdb=" O   MET B  75 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 138 through 139
    Processing sheet with id=AA9, first strand: chain 'C' and resid 68 through 70
    Processing sheet with id=AB1, first strand: chain 'C' and resid 78 through 83
    Processing sheet with id=AB2, first strand: chain 'C' and resid 86 through 88
    Processing sheet with id=AB3, first strand: chain 'C' and resid 99 through 100
      removed outlier: 3.747A  pdb=" N   LYS C 100 " --> pdb=" O   SER C 109 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   SER C 109 " --> pdb=" O   LYS C 100 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 107 through 126
    current: chain 'C' and resid 168 through 176
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 168 through 176
    current: chain 'C' and resid 281 through 287
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 281 through 287
    current: chain 'C' and resid 313 through 332
  No H-bonds generated for sheet with id=AB3

    182 hydrogen bonds defined for protein.
    480 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.95

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1271
        1.32 -     1.45: 2175
        1.45 -     1.58: 4402
        1.58 -     1.70: 16
        1.70 -     1.83: 65
  Bond restraints: 7929
  Sorted by residual:
  bond pdb=" C   THR B 336 "
       pdb=" N   VAL B 337 "
    ideal  model  delta    sigma   weight residual
    1.334  1.513 -0.179 1.25e-02 6.40e+03 2.05e+02
  bond pdb=" C   SER C 356 "
       pdb=" N   PHE C 357 "
    ideal  model  delta    sigma   weight residual
    1.334  1.487 -0.153 1.20e-02 6.94e+03 1.63e+02
  bond pdb=" C   LEU B  33 "
       pdb=" N   ILE B  34 "
    ideal  model  delta    sigma   weight residual
    1.335  1.453 -0.118 1.19e-02 7.06e+03 9.87e+01
  bond pdb=" C   ILE B  34 "
       pdb=" N   ILE B  35 "
    ideal  model  delta    sigma   weight residual
    1.335  1.214  0.121 1.26e-02 6.30e+03 9.23e+01
  bond pdb=" C   PHE C 357 "
       pdb=" N   LEU C 358 "
    ideal  model  delta    sigma   weight residual
    1.334  1.213  0.122 1.46e-02 4.69e+03 6.97e+01
  ... (remaining 7924 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.71: 10655
        3.71 -     7.43: 96
        7.43 -    11.14: 17
       11.14 -    14.85: 5
       14.85 -    18.56: 4
  Bond angle restraints: 10777
  Sorted by residual:
  angle pdb=" PB  ATP C 501 "
        pdb=" O3B ATP C 501 "
        pdb=" PG  ATP C 501 "
      ideal   model   delta    sigma   weight residual
     139.87  121.31   18.56 1.00e+00 1.00e+00 3.45e+02
  angle pdb=" PA  ATP A 403 "
        pdb=" O3A ATP A 403 "
        pdb=" PB  ATP A 403 "
      ideal   model   delta    sigma   weight residual
     136.83  120.07   16.76 1.00e+00 1.00e+00 2.81e+02
  angle pdb=" PB  ATP A 403 "
        pdb=" O3B ATP A 403 "
        pdb=" PG  ATP A 403 "
      ideal   model   delta    sigma   weight residual
     139.87  123.97   15.90 1.00e+00 1.00e+00 2.53e+02
  angle pdb=" C   CYS A 153 "
        pdb=" N   PRO A 154 "
        pdb=" CA  PRO A 154 "
      ideal   model   delta    sigma   weight residual
     120.14  136.49  -16.35 1.06e+00 8.90e-01 2.38e+02
  angle pdb=" PA  ATP C 501 "
        pdb=" O3A ATP C 501 "
        pdb=" PB  ATP C 501 "
      ideal   model   delta    sigma   weight residual
     136.83  122.69   14.14 1.00e+00 1.00e+00 2.00e+02
  ... (remaining 10772 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.89: 4608
       25.89 -    51.77: 216
       51.77 -    77.66: 26
       77.66 -   103.54: 3
      103.54 -   129.43: 1
  Dihedral angle restraints: 4854
    sinusoidal: 2075
      harmonic: 2779
  Sorted by residual:
  dihedral pdb=" CA  CYS A 153 "
           pdb=" C   CYS A 153 "
           pdb=" N   PRO A 154 "
           pdb=" CA  PRO A 154 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   50.57  129.43     0      5.00e+00 4.00e-02 6.70e+02
  dihedral pdb=" CB  CYS B 203 "
           pdb=" SG  CYS B 203 "
           pdb=" SG  CYS B 213 "
           pdb=" CB  CYS B 213 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -10.86  -75.14     1      1.00e+01 1.00e-02 7.14e+01
  dihedral pdb=" CB  CYS B 247 "
           pdb=" SG  CYS B 247 "
           pdb=" SG  CYS B 256 "
           pdb=" CB  CYS B 256 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  163.32  -70.32     1      1.00e+01 1.00e-02 6.37e+01
  ... (remaining 4851 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 1103
       0.096 -    0.191: 122
       0.191 -    0.287: 1
       0.287 -    0.382: 1
       0.382 -    0.478: 1
  Chirality restraints: 1228
  Sorted by residual:
  chirality pdb=" C1  NAG B 401 "
            pdb=" ND2 ASN B 290 "
            pdb=" C2  NAG B 401 "
            pdb=" O5  NAG B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.92   -0.48 2.00e-01 2.50e+01 5.71e+00
  chirality pdb=" C1  NAG A 401 "
            pdb=" ND2 ASN A 290 "
            pdb=" C2  NAG A 401 "
            pdb=" O5  NAG A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.04   -0.36 2.00e-01 2.50e+01 3.16e+00
  chirality pdb=" C1  NAG C 502 "
            pdb=" ND2 ASN C 194 "
            pdb=" C2  NAG C 502 "
            pdb=" O5  NAG C 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 1225 not shown)

  Planarity restraints: 1347
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 401 "   -0.347 2.00e-02 2.50e+03   2.98e-01 1.11e+03
        pdb=" C7  NAG A 401 "    0.085 2.00e-02 2.50e+03
        pdb=" C8  NAG A 401 "   -0.150 2.00e-02 2.50e+03
        pdb=" N2  NAG A 401 "    0.530 2.00e-02 2.50e+03
        pdb=" O7  NAG A 401 "   -0.119 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 401 "   -0.317 2.00e-02 2.50e+03   2.69e-01 9.05e+02
        pdb=" C7  NAG B 401 "    0.080 2.00e-02 2.50e+03
        pdb=" C8  NAG B 401 "   -0.182 2.00e-02 2.50e+03
        pdb=" N2  NAG B 401 "    0.468 2.00e-02 2.50e+03
        pdb=" O7  NAG B 401 "   -0.050 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 402 "   -0.309 2.00e-02 2.50e+03   2.61e-01 8.52e+02
        pdb=" C7  NAG B 402 "    0.080 2.00e-02 2.50e+03
        pdb=" C8  NAG B 402 "   -0.187 2.00e-02 2.50e+03
        pdb=" N2  NAG B 402 "    0.450 2.00e-02 2.50e+03
        pdb=" O7  NAG B 402 "   -0.034 2.00e-02 2.50e+03
  ... (remaining 1344 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 2465
        2.83 -     3.35: 6124
        3.35 -     3.87: 10829
        3.87 -     4.38: 11637
        4.38 -     4.90: 22352
  Nonbonded interactions: 53407
  Sorted by model distance:
  nonbonded pdb=" O   GLU C  89 "
            pdb=" ND1 HIS C  90 "
     model   vdw
     2.318 3.120
  nonbonded pdb=" O   CYS B 203 "
            pdb=" NH1 ARG B 204 "
     model   vdw
     2.325 3.120
  nonbonded pdb=" O   ILE A 342 "
            pdb=" C   LEU A 343 "
     model   vdw
     2.341 3.270
  nonbonded pdb=" OE1 GLN B  50 "
            pdb=" NH1 ARG B  52 "
     model   vdw
     2.370 3.120
  nonbonded pdb=" O   THR A 202 "
            pdb=" OG1 THR A 202 "
     model   vdw
     2.379 3.040
  ... (remaining 53402 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 'A'
  selection = (chain 'B' and (resid 25 through 343 or resid 401 through 403))
}

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:             3.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.960
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
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      :  0.007   0.281   7950  Z= 0.522
  Angle     :  1.082  32.089  10825  Z= 0.743
  Chirality :  0.056   0.478   1228
  Planarity :  0.016   0.298   1341
  Dihedral  : 14.202 129.429   3033
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.22 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.44 (0.22), residues: 961
  helix: -2.47 (0.28), residues: 199
  sheet: -0.06 (0.30), residues: 227
  loop : -3.40 (0.20), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 264 
 TYR   0.015   0.001   TYR C  45 
 PHE   0.012   0.002   PHE A 282 
 TRP   0.016   0.002   TRP C 268 
 HIS   0.003   0.001   HIS C 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00678 ( 7929)
  covalent geometry    : angle       1.01671 (10777)
  SS BOND              : bond        0.07324 (   15)
  SS BOND              : angle       6.34225 (   30)
  hydrogen bonds       : bond        0.15257 (  182)
  hydrogen bonds       : angle       6.53052 (  480)
  link_NAG-ASN         : bond        0.00925 (    6)
  link_NAG-ASN         : angle       4.18557 (   18)

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

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 1
  residues processed: 97
  average time/residue: 0.6788
  time to fit residues: 68.9306
Evaluate side-chains
  62 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  248 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  45 HIS
A 185 ASN
B  27 ASN
B  31 GLN
B 139 ASN
C  64 GLN
C 204 HIS
C 229 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.098641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.064926 restraints weight = 17948.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.2879 rms_B_bonded: 4.19
r_work: 0.2728 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7950  Z= 0.161
  Angle     :  0.768  12.126  10825  Z= 0.387
  Chirality :  0.052   0.376   1228
  Planarity :  0.006   0.099   1341
  Dihedral  : 12.034 116.397   1275
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.04 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.19 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.22 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.62 (0.23), residues: 961
  helix: -1.02 (0.34), residues: 194
  sheet:  0.05 (0.30), residues: 241
  loop : -3.07 (0.21), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 198 
 TYR   0.013   0.001   TYR C  45 
 PHE   0.013   0.001   PHE A 184 
 TRP   0.014   0.002   TRP C 361 
 HIS   0.005   0.001   HIS C 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 7929)
  covalent geometry    : angle       0.74285 (10777)
  SS BOND              : bond        0.00514 (   15)
  SS BOND              : angle       1.87483 (   30)
  hydrogen bonds       : bond        0.05851 (  182)
  hydrogen bonds       : angle       5.31040 (  480)
  link_NAG-ASN         : bond        0.01001 (    6)
  link_NAG-ASN         : angle       4.33060 (   18)

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

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  288 MET cc_start: 0.8028 (ppp) cc_final: 0.7788 (ppp)
REVERT: B   75 MET cc_start: 0.9185 (mmm) cc_final: 0.8930 (mmm)
REVERT: B  248 ASP cc_start: 0.8739 (t0) cc_final: 0.8239 (t0)
  outliers start: 12
  outliers final: 4
  residues processed: 77
  average time/residue: 0.5551
  time to fit residues: 45.2602
Evaluate side-chains
  60 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 CYS
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue  203 CYS
Chi-restraints excluded: chain B residue  267 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A  45 HIS
C  64 GLN
C 344 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.098628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.065372 restraints weight = 17988.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 4.15
r_work: 0.2739 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   7950  Z= 0.157
  Angle     :  0.731  11.057  10825  Z= 0.376
  Chirality :  0.051   0.343   1228
  Planarity :  0.005   0.089   1341
  Dihedral  : 11.004  80.535   1273
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 14.05 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.22 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.34 (0.24), residues: 961
  helix: -0.43 (0.36), residues: 192
  sheet:  0.06 (0.30), residues: 248
  loop : -2.98 (0.22), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 136 
 TYR   0.012   0.001   TYR C  45 
 PHE   0.011   0.001   PHE A 301 
 TRP   0.028   0.002   TRP C  58 
 HIS   0.007   0.001   HIS A  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 7929)
  covalent geometry    : angle       0.70660 (10777)
  SS BOND              : bond        0.00503 (   15)
  SS BOND              : angle       2.00536 (   30)
  hydrogen bonds       : bond        0.05606 (  182)
  hydrogen bonds       : angle       5.18071 (  480)
  link_NAG-ASN         : bond        0.00957 (    6)
  link_NAG-ASN         : angle       4.00574 (   18)

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

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.8243 (mmp80) cc_final: 0.7504 (mmp80)
REVERT: A  288 MET cc_start: 0.8273 (ppp) cc_final: 0.8009 (ppp)
REVERT: B  248 ASP cc_start: 0.8929 (t0) cc_final: 0.8329 (t0)
REVERT: C   59 TYR cc_start: 0.8909 (t80) cc_final: 0.8634 (t80)
REVERT: C   64 GLN cc_start: 0.9112 (pt0) cc_final: 0.8820 (pm20)
REVERT: C   71 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7921 (tp30)
REVERT: C  344 ASN cc_start: 0.8564 (m-40) cc_final: 0.8339 (m110)
  outliers start: 15
  outliers final: 8
  residues processed: 72
  average time/residue: 0.5140
  time to fit residues: 39.4019
Evaluate side-chains
  64 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  203 CYS
Chi-restraints excluded: chain B residue  137 CYS
Chi-restraints excluded: chain B residue  203 CYS
Chi-restraints excluded: chain B residue  251 LYS
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain C residue   71 GLU
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  219 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 90 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0370
   overall best weight:    1.5664

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

Flipped N/Q/H residues before XYZ refinement:
A  45 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.096197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.062633 restraints weight = 18337.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.2840 rms_B_bonded: 4.18
r_work: 0.2688 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   7950  Z= 0.203
  Angle     :  0.764  11.305  10825  Z= 0.396
  Chirality :  0.052   0.350   1228
  Planarity :  0.005   0.096   1341
  Dihedral  : 10.944  85.427   1273
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.88 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.22 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.31 (0.24), residues: 961
  helix: -0.09 (0.37), residues: 194
  sheet:  0.01 (0.30), residues: 244
  loop : -3.06 (0.22), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  52 
 TYR   0.012   0.001   TYR C  45 
 PHE   0.013   0.001   PHE A 301 
 TRP   0.029   0.002   TRP C  58 
 HIS   0.007   0.001   HIS A  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 7929)
  covalent geometry    : angle       0.74039 (10777)
  SS BOND              : bond        0.00444 (   15)
  SS BOND              : angle       2.01717 (   30)
  hydrogen bonds       : bond        0.05912 (  182)
  hydrogen bonds       : angle       5.20932 (  480)
  link_NAG-ASN         : bond        0.00868 (    6)
  link_NAG-ASN         : angle       4.02318 (   18)

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

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 59
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A   32 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9106 (mm)
REVERT: A  288 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.8001 (ppp)
REVERT: B  115 ARG cc_start: 0.8495 (mtp180) cc_final: 0.8207 (mtp180)
REVERT: B  116 CYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5724 (t)
REVERT: B  147 CYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7022 (m)
REVERT: B  248 ASP cc_start: 0.8999 (t0) cc_final: 0.8381 (t0)
REVERT: C   59 TYR cc_start: 0.8854 (t80) cc_final: 0.8615 (t80)
REVERT: C   64 GLN cc_start: 0.9138 (pt0) cc_final: 0.8827 (pm20)
REVERT: C   71 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8017 (tp30)
REVERT: C  344 ASN cc_start: 0.8604 (m-40) cc_final: 0.8391 (m110)
  outliers start: 20
  outliers final: 8
  residues processed: 73
  average time/residue: 0.4957
  time to fit residues: 38.7499
Evaluate side-chains
  67 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  203 CYS
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain B residue  116 CYS
Chi-restraints excluded: chain B residue  137 CYS
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  203 CYS
Chi-restraints excluded: chain B residue  251 LYS
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain C residue   71 GLU
Chi-restraints excluded: chain C residue  219 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0000
   chunk 69 optimal weight:    0.6980
   chunk 47 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
A  45 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.097151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.063938 restraints weight = 18195.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 4.16
r_work: 0.2723 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7950  Z= 0.144
  Angle     :  0.718  12.363  10825  Z= 0.365
  Chirality :  0.051   0.354   1228
  Planarity :  0.005   0.088   1341
  Dihedral  : 10.300  87.887   1273
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 15.71 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.22 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.13 (0.25), residues: 961
  helix:  0.11 (0.38), residues: 199
  sheet: -0.01 (0.29), residues: 256
  loop : -2.97 (0.23), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  52 
 TYR   0.012   0.001   TYR C  45 
 PHE   0.010   0.001   PHE A 301 
 TRP   0.032   0.002   TRP C  58 
 HIS   0.008   0.001   HIS A  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 7929)
  covalent geometry    : angle       0.69767 (10777)
  SS BOND              : bond        0.00414 (   15)
  SS BOND              : angle       1.44363 (   30)
  hydrogen bonds       : bond        0.05225 (  182)
  hydrogen bonds       : angle       5.02689 (  480)
  link_NAG-ASN         : bond        0.00906 (    6)
  link_NAG-ASN         : angle       3.88653 (   18)

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

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: A  147 CYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6135 (m)
REVERT: A  288 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8046 (ppp)
REVERT: B  147 CYS cc_start: 0.7752 (OUTLIER) cc_final: 0.6868 (m)
REVERT: B  248 ASP cc_start: 0.9005 (t0) cc_final: 0.8461 (t0)
REVERT: C   59 TYR cc_start: 0.8824 (t80) cc_final: 0.8615 (t80)
REVERT: C   64 GLN cc_start: 0.9187 (pt0) cc_final: 0.8869 (pm20)
REVERT: C   71 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8024 (tp30)
  outliers start: 22
  outliers final: 10
  residues processed: 75
  average time/residue: 0.5043
  time to fit residues: 40.3281
Evaluate side-chains
  67 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 53
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  147 CYS
Chi-restraints excluded: chain A residue  203 CYS
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  137 CYS
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  203 CYS
Chi-restraints excluded: chain B residue  251 LYS
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain C residue   71 GLU
Chi-restraints excluded: chain C residue  219 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 2 optimal weight:    0.3980
   chunk 23 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 73 optimal weight:    0.0030
   chunk 30 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 94 optimal weight:    4.9990
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
A  45 HIS
C 344 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.098276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.065047 restraints weight = 18260.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 4.19
r_work: 0.2745 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7950  Z= 0.125
  Angle     :  0.690  12.009  10825  Z= 0.352
  Chirality :  0.050   0.367   1228
  Planarity :  0.005   0.083   1341
  Dihedral  :  9.845  80.935   1273
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 16.07 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.22 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.93 (0.25), residues: 961
  helix:  0.38 (0.38), residues: 197
  sheet:  0.12 (0.29), residues: 255
  loop : -2.88 (0.24), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 115 
 TYR   0.012   0.001   TYR C  45 
 PHE   0.009   0.001   PHE C 336 
 TRP   0.035   0.002   TRP C  58 
 HIS   0.007   0.001   HIS A  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7929)
  covalent geometry    : angle       0.67015 (10777)
  SS BOND              : bond        0.00419 (   15)
  SS BOND              : angle       1.32723 (   30)
  hydrogen bonds       : bond        0.04886 (  182)
  hydrogen bonds       : angle       4.88784 (  480)
  link_NAG-ASN         : bond        0.00951 (    6)
  link_NAG-ASN         : angle       3.78431 (   18)

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

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 58
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A  147 CYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6089 (m)
REVERT: A  288 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8088 (ppp)
REVERT: B  116 CYS cc_start: 0.5865 (OUTLIER) cc_final: 0.5543 (t)
REVERT: B  147 CYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7215 (m)
REVERT: B  248 ASP cc_start: 0.9026 (t0) cc_final: 0.8469 (t0)
REVERT: C   64 GLN cc_start: 0.9271 (pt0) cc_final: 0.8948 (pm20)
  outliers start: 23
  outliers final: 11
  residues processed: 72
  average time/residue: 0.4475
  time to fit residues: 34.6725
Evaluate side-chains
  68 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 53
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  147 CYS
Chi-restraints excluded: chain A residue  203 CYS
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  116 CYS
Chi-restraints excluded: chain B residue  137 CYS
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  203 CYS
Chi-restraints excluded: chain B residue  251 LYS
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  219 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 78 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0970
   chunk 16 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 17 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.098264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.065021 restraints weight = 18058.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.2898 rms_B_bonded: 4.16
r_work: 0.2745 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7950  Z= 0.130
  Angle     :  0.696  12.338  10825  Z= 0.353
  Chirality :  0.050   0.377   1228
  Planarity :  0.005   0.085   1341
  Dihedral  :  9.744  76.850   1273
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 17.50 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.22 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.78 (0.26), residues: 961
  helix:  0.62 (0.39), residues: 194
  sheet:  0.20 (0.29), residues: 259
  loop : -2.82 (0.24), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  52 
 TYR   0.012   0.001   TYR C  45 
 PHE   0.009   0.001   PHE A 301 
 TRP   0.040   0.002   TRP C  58 
 HIS   0.002   0.001   HIS C 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 7929)
  covalent geometry    : angle       0.67656 (10777)
  SS BOND              : bond        0.00408 (   15)
  SS BOND              : angle       1.23899 (   30)
  hydrogen bonds       : bond        0.04743 (  182)
  hydrogen bonds       : angle       4.81593 (  480)
  link_NAG-ASN         : bond        0.00954 (    6)
  link_NAG-ASN         : angle       3.78272 (   18)

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

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 CYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6075 (m)
REVERT: A  288 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8150 (ppp)
REVERT: B  116 CYS cc_start: 0.6155 (OUTLIER) cc_final: 0.5673 (t)
REVERT: B  147 CYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7231 (m)
REVERT: B  248 ASP cc_start: 0.9025 (t0) cc_final: 0.8465 (t0)
REVERT: B  288 MET cc_start: 0.8933 (ttp) cc_final: 0.8665 (ttp)
REVERT: C   64 GLN cc_start: 0.9286 (pt0) cc_final: 0.8990 (pm20)
REVERT: C   71 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8036 (tp30)
REVERT: C  344 ASN cc_start: 0.8510 (m-40) cc_final: 0.8283 (m110)
  outliers start: 20
  outliers final: 12
  residues processed: 75
  average time/residue: 0.5185
  time to fit residues: 41.7339
Evaluate side-chains
  71 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  147 CYS
Chi-restraints excluded: chain A residue  203 CYS
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  116 CYS
Chi-restraints excluded: chain B residue  137 CYS
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  203 CYS
Chi-restraints excluded: chain B residue  251 LYS
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain C residue   71 GLU
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  219 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 17 optimal weight:    9.9990
   chunk 38 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 87 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  45 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.097868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.064603 restraints weight = 18157.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.2885 rms_B_bonded: 4.17
r_work: 0.2732 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7950  Z= 0.144
  Angle     :  0.713  13.459  10825  Z= 0.364
  Chirality :  0.051   0.379   1228
  Planarity :  0.005   0.086   1341
  Dihedral  :  9.613  75.062   1273
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 17.50 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.22 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.75 (0.26), residues: 961
  helix:  0.64 (0.38), residues: 198
  sheet:  0.17 (0.29), residues: 259
  loop : -2.81 (0.24), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  52 
 TYR   0.012   0.001   TYR C  45 
 PHE   0.011   0.001   PHE A 301 
 TRP   0.041   0.002   TRP C  58 
 HIS   0.007   0.001   HIS A  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 7929)
  covalent geometry    : angle       0.69324 (10777)
  SS BOND              : bond        0.00349 (   15)
  SS BOND              : angle       1.34393 (   30)
  hydrogen bonds       : bond        0.04855 (  182)
  hydrogen bonds       : angle       4.78067 (  480)
  link_NAG-ASN         : bond        0.00940 (    6)
  link_NAG-ASN         : angle       3.85323 (   18)

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

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 59
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.8415 (mmm160) cc_final: 0.8184 (mmm160)
REVERT: A  147 CYS cc_start: 0.7129 (OUTLIER) cc_final: 0.5983 (m)
REVERT: A  288 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8114 (ppp)
REVERT: B  116 CYS cc_start: 0.6164 (OUTLIER) cc_final: 0.5696 (t)
REVERT: B  147 CYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7361 (m)
REVERT: B  248 ASP cc_start: 0.9022 (t0) cc_final: 0.8459 (t0)
REVERT: B  288 MET cc_start: 0.8828 (ttp) cc_final: 0.8605 (ttp)
REVERT: C   64 GLN cc_start: 0.9317 (pt0) cc_final: 0.9046 (pm20)
REVERT: C   71 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8038 (tp30)
REVERT: C  344 ASN cc_start: 0.8572 (m-40) cc_final: 0.8364 (m110)
  outliers start: 23
  outliers final: 11
  residues processed: 72
  average time/residue: 0.4835
  time to fit residues: 37.2835
Evaluate side-chains
  71 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  147 CYS
Chi-restraints excluded: chain A residue  203 CYS
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  116 CYS
Chi-restraints excluded: chain B residue  137 CYS
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  203 CYS
Chi-restraints excluded: chain B residue  251 LYS
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain C residue   71 GLU
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  219 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 93 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9990
   chunk 86 optimal weight:    0.0000
   chunk 18 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.6184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.098517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.065314 restraints weight = 18141.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 4.17
r_work: 0.2744 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.2867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7950  Z= 0.130
  Angle     :  0.705  13.694  10825  Z= 0.358
  Chirality :  0.050   0.372   1228
  Planarity :  0.005   0.083   1341
  Dihedral  :  9.369  73.105   1273
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 17.98 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.22 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.26), residues: 961
  helix:  0.73 (0.39), residues: 198
  sheet:  0.23 (0.29), residues: 259
  loop : -2.72 (0.24), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  52 
 TYR   0.012   0.001   TYR C  45 
 PHE   0.009   0.001   PHE C 336 
 TRP   0.044   0.002   TRP C  58 
 HIS   0.002   0.001   HIS C 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7929)
  covalent geometry    : angle       0.68599 (10777)
  SS BOND              : bond        0.00337 (   15)
  SS BOND              : angle       1.24904 (   30)
  hydrogen bonds       : bond        0.04565 (  182)
  hydrogen bonds       : angle       4.73912 (  480)
  link_NAG-ASN         : bond        0.00983 (    6)
  link_NAG-ASN         : angle       3.83792 (   18)

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

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 59
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.8451 (mmm160) cc_final: 0.8214 (mmm160)
REVERT: A  147 CYS cc_start: 0.7088 (OUTLIER) cc_final: 0.5942 (m)
REVERT: A  288 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8123 (ppp)
REVERT: B  147 CYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7389 (m)
REVERT: B  248 ASP cc_start: 0.9017 (t0) cc_final: 0.8451 (t0)
REVERT: B  288 MET cc_start: 0.8819 (ttp) cc_final: 0.8544 (ttp)
REVERT: C   64 GLN cc_start: 0.9334 (pt0) cc_final: 0.9059 (pm20)
REVERT: C   71 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7996 (tp30)
REVERT: C  344 ASN cc_start: 0.8546 (m-40) cc_final: 0.8315 (m110)
  outliers start: 20
  outliers final: 9
  residues processed: 74
  average time/residue: 0.4751
  time to fit residues: 37.7436
Evaluate side-chains
  70 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  147 CYS
Chi-restraints excluded: chain A residue  203 CYS
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  203 CYS
Chi-restraints excluded: chain B residue  251 LYS
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain C residue   71 GLU
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  219 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 83 optimal weight:    0.4980
   chunk 29 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 63 optimal weight:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  45 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.098107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.064898 restraints weight = 18107.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.2891 rms_B_bonded: 4.16
r_work: 0.2739 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7950  Z= 0.139
  Angle     :  0.728  14.989  10825  Z= 0.367
  Chirality :  0.051   0.371   1228
  Planarity :  0.005   0.081   1341
  Dihedral  :  9.302  72.576   1273
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 18.57 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.22 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.60 (0.26), residues: 961
  helix:  0.75 (0.39), residues: 198
  sheet:  0.23 (0.29), residues: 259
  loop : -2.68 (0.24), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  52 
 TYR   0.012   0.001   TYR C  45 
 PHE   0.010   0.001   PHE A 301 
 TRP   0.045   0.002   TRP C  58 
 HIS   0.006   0.001   HIS A  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7929)
  covalent geometry    : angle       0.70454 (10777)
  SS BOND              : bond        0.00415 (   15)
  SS BOND              : angle       2.03479 (   30)
  hydrogen bonds       : bond        0.04626 (  182)
  hydrogen bonds       : angle       4.73790 (  480)
  link_NAG-ASN         : bond        0.00967 (    6)
  link_NAG-ASN         : angle       3.86856 (   18)

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

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.8491 (mmm160) cc_final: 0.8252 (mmm160)
REVERT: A  147 CYS cc_start: 0.7097 (OUTLIER) cc_final: 0.5943 (m)
REVERT: A  288 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8110 (ppp)
REVERT: B  147 CYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7165 (m)
REVERT: B  248 ASP cc_start: 0.8982 (t0) cc_final: 0.8411 (t0)
REVERT: B  288 MET cc_start: 0.8816 (ttp) cc_final: 0.8581 (ttp)
REVERT: C   64 GLN cc_start: 0.9342 (pt0) cc_final: 0.9067 (pm20)
REVERT: C   71 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8002 (tp30)
REVERT: C  344 ASN cc_start: 0.8479 (m-40) cc_final: 0.8219 (m110)
  outliers start: 15
  outliers final: 9
  residues processed: 70
  average time/residue: 0.4889
  time to fit residues: 36.6800
Evaluate side-chains
  72 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  147 CYS
Chi-restraints excluded: chain A residue  203 CYS
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  203 CYS
Chi-restraints excluded: chain B residue  251 LYS
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain C residue   71 GLU
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  219 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 12 optimal weight:    6.9990
   chunk 54 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0000
   chunk 85 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 77 optimal weight:    0.1980
   chunk 39 optimal weight:    0.5980
   chunk 69 optimal weight:    0.0070
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.2802

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

Flipped N/Q/H residues before XYZ refinement:
A  45 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.100464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.067454 restraints weight = 18105.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 4.17
r_work: 0.2797 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.3133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7950  Z= 0.118
  Angle     :  0.697  14.387  10825  Z= 0.348
  Chirality :  0.050   0.360   1228
  Planarity :  0.004   0.058   1341
  Dihedral  :  8.840  70.502   1273
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 19.52 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.22 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.26), residues: 961
  helix:  1.08 (0.40), residues: 189
  sheet:  0.28 (0.29), residues: 272
  loop : -2.55 (0.25), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 115 
 TYR   0.012   0.001   TYR C  45 
 PHE   0.009   0.001   PHE C 336 
 TRP   0.044   0.002   TRP C  58 
 HIS   0.009   0.001   HIS A  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7929)
  covalent geometry    : angle       0.67842 (10777)
  SS BOND              : bond        0.00302 (   15)
  SS BOND              : angle       1.21148 (   30)
  hydrogen bonds       : bond        0.04111 (  182)
  hydrogen bonds       : angle       4.66808 (  480)
  link_NAG-ASN         : bond        0.01011 (    6)
  link_NAG-ASN         : angle       3.78927 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2541.01 seconds
wall clock time: 43 minutes 53.19 seconds (2633.19 seconds total)