Starting phenix.real_space_refine
on Sat Aug 23 03:15:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzo_41764/08_2025/8tzo_41764.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzo_41764/08_2025/8tzo_41764.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzo_41764/08_2025/8tzo_41764.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzo_41764/08_2025/8tzo_41764.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tzo_41764/08_2025/8tzo_41764.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzo_41764/08_2025/8tzo_41764.map"
  }
  resolution = 3.1
  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=   0.004 sd=   0.077
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      1      9.91       5
     P       1      5.49       5
     S      73      5.16       5
     C    5627      2.51       5
     N    1450      2.21       5
     O    1585      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8737
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2341
          Classifications: {'peptide': 301}
          Link IDs: {'PTRANS': 11, 'TRANS': 289}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4037
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 496, 4037
          Classifications: {'peptide': 496}
          Link IDs: {'PTRANS': 21, 'TRANS': 474}
    Chain: "C"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2218
          Classifications: {'peptide': 273}
          Link IDs: {'PTRANS': 11, 'TRANS': 261}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 83
          Unusual residues: {'BMA': 1, 'GLC': 1, 'MAN': 3, 'NAG': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 7
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'PAM': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PAM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'POV': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.33, per 1000 atoms: 0.27
  Number of scatterers: 8737
  At special positions: 0
  Unit cell: (106.24, 118.69, 132.8, 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)
     Ca      1     19.99
     S      73     16.00
     P       1     15.00
     O    1585      8.00
     N    1450      7.00
     C    5627      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  38 " - pdb=" SG  CYS A  52 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  73 " - pdb=" SG  CYS A  84 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 123 " - pdb=" SG  CYS A 131 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 202 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 278 " - pdb=" SG  CYS A 309 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 294 " - pdb=" SG  CYS A 304 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 308 " - pdb=" SG  CYS A 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 324 " - pdb=" SG  CYS A 339 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 326 " - pdb=" SG  CYS A 336 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 331 " - pdb=" SG  CYS A 332 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  50 " - pdb=" SG  CYS B  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 162 " - pdb=" SG  CYS B 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 105 " - pdb=" SG  CYS C 137 " 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=1, symmetry=0
  Links applied
    ALPHA1-2
      " MAN D   4 " - " MAN D   5 "
      " MAN D   5 " - " MAN D   6 "
    ALPHA1-3
      " BMA D   3 " - " MAN D   4 "
      " MAN D   6 " - " GLC D   7 "
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    NAG-ASN
      " NAG D   1 " - " ASN A 295 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 259.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1982

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 11 sheets defined
      42.5% alpha, 21.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 55 through 77
      removed outlier: 4.407A  pdb=" N   ILE A  60 " --> pdb=" O   PRO A  56 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   VAL A  61 " --> pdb=" O   ASP A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 125
      removed outlier: 3.571A  pdb=" N   GLN A 125 " --> pdb=" O   ALA A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 151
    Processing helix  chain 'A' and resid 154 through 168
      removed outlier: 3.752A  pdb=" N   TYR A 158 " --> pdb=" O   ALA A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 171
      No H-bonds generated for 'chain 'A' and resid 169 through 171'
    Processing helix  chain 'A' and resid 175 through 195
    Processing helix  chain 'A' and resid 220 through 233
      removed outlier: 3.533A  pdb=" N   LEU A 224 " --> pdb=" O   GLN A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 308
      removed outlier: 3.566A  pdb=" N   CYS A 308 " --> pdb=" O   CYS A 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 35
      removed outlier: 3.649A  pdb=" N   GLY B  32 " --> pdb=" O   ALA B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 81
    Processing helix  chain 'B' and resid 169 through 173
    Processing helix  chain 'B' and resid 227 through 258
      Proline residue:  B 243  - end of helix
    Processing helix  chain 'B' and resid 264 through 282
      removed outlier: 3.563A  pdb=" N   ILE B 280 " --> pdb=" O   SER B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 288
    Processing helix  chain 'B' and resid 295 through 322
    Processing helix  chain 'B' and resid 331 through 334
    Processing helix  chain 'B' and resid 335 through 361
      Proline residue:  B 341  - end of helix
      removed outlier: 4.589A  pdb=" N   VAL B 359 " --> pdb=" O   CYS B 355 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLN B 360 " --> pdb=" O   GLU B 356 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU B 361 " --> pdb=" O   ARG B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 370
    Processing helix  chain 'B' and resid 371 through 412
      removed outlier: 4.251A  pdb=" N   SER B 412 " --> pdb=" O   SER B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 417
    Processing helix  chain 'B' and resid 418 through 456
    Processing helix  chain 'B' and resid 469 through 492
      removed outlier: 4.025A  pdb=" N   PHE B 474 " --> pdb=" O   ASN B 470 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 36
      removed outlier: 3.788A  pdb=" N   SER C  35 " --> pdb=" O   ASP C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 122
      removed outlier: 3.827A  pdb=" N   MET C 122 " --> pdb=" O   GLN C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 200
    Processing helix  chain 'C' and resid 302 through 307
      removed outlier: 3.861A  pdb=" N   ILE C 305 " --> pdb=" O   ASP C 302 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   TYR C 306 " --> pdb=" O   PRO C 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 335 through 377
      removed outlier: 5.147A  pdb=" N   VAL C 349 " --> pdb=" O   GLU C 345 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   ALA C 352 " --> pdb=" O   GLY C 348 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   ALA C 353 " --> pdb=" O   VAL C 349 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LYS C 377 " --> pdb=" O   ASP C 373 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 202
    Processing sheet with id=AA2, first strand: chain 'A' and resid 251 through 254
      removed outlier: 4.640A  pdb=" N   PHE A 251 " --> pdb=" O   VAL A 241 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 293 through 294
      removed outlier: 3.956A  pdb=" N   TYR A 346 " --> pdb=" O   CYS A 294 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 324
    Processing sheet with id=AA5, first strand: chain 'B' and resid 40 through 46
      removed outlier: 3.963A  pdb=" N   GLU B 215 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ASP B 117 " --> pdb=" O   LYS B 217 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   ILE B 219 " --> pdb=" O   GLN B 115 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   GLN B 115 " --> pdb=" O   ILE B 219 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   LEU B 221 " --> pdb=" O   ILE B 113 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ILE B 113 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   GLY B 223 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   LEU B 111 " --> pdb=" O   GLY B 223 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   MET B 110 " --> pdb=" O   GLU B 186 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   GLU B 186 " --> pdb=" O   MET B 110 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   PHE B 112 " --> pdb=" O   PHE B 184 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 74
      removed outlier: 4.538A  pdb=" N   LYS B  49 " --> pdb=" O   ILE B  74 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ARG B 200 " --> pdb=" O   ASP B 135 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   TYR B 140 " --> pdb=" O   GLU B 150 " (cutoff:3.500A)
      removed outlier: 5.614A  pdb=" N   GLU B 150 " --> pdb=" O   TYR B 140 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 459 through 462
    Processing sheet with id=AA8, first strand: chain 'C' and resid 21 through 25
      removed outlier: 3.503A  pdb=" N   PHE C 330 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   THR C 325 " --> pdb=" O   THR C  68 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 25
      removed outlier: 3.503A  pdb=" N   PHE C 330 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   PHE C 327 " --> pdb=" O   LYS C  98 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   LYS C  98 " --> pdb=" O   PHE C 327 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   ASN C 329 " --> pdb=" O   THR C  96 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   THR C  96 " --> pdb=" O   ASN C 329 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   TYR C 182 " --> pdb=" O   SER C 193 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   SER C 193 " --> pdb=" O   TYR C 182 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   VAL C 184 " --> pdb=" O   VAL C 191 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 39
      removed outlier: 5.314A  pdb=" N   GLY C 312 " --> pdb=" O   PHE C  81 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   TRP C 319 " --> pdb=" O   GLY C 107 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 37 through 39
      removed outlier: 5.314A  pdb=" N   GLY C 312 " --> pdb=" O   PHE C  81 " (cutoff:3.500A)

    459 hydrogen bonds defined for protein.
    1287 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.51

  Time building geometry restraints manager: 1.13 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1400
        1.31 -     1.44: 2525
        1.44 -     1.56: 4924
        1.56 -     1.69: 3
        1.69 -     1.82: 107
  Bond restraints: 8959
  Sorted by residual:
  bond pdb=" C31 POV B 601 "
       pdb=" O31 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.327  1.418 -0.091 2.00e-02 2.50e+03 2.08e+01
  bond pdb=" C21 POV B 601 "
       pdb=" O21 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.330  1.420 -0.090 2.00e-02 2.50e+03 2.00e+01
  bond pdb="C210 POV B 601 "
       pdb="C211 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.497  1.558 -0.061 2.00e-02 2.50e+03 9.16e+00
  bond pdb=" N   POV B 601 "
       pdb=" C14 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.490  1.435  0.055 2.00e-02 2.50e+03 7.59e+00
  bond pdb=" N   POV B 601 "
       pdb=" C12 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.508  1.455  0.053 2.00e-02 2.50e+03 6.95e+00
  ... (remaining 8954 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 11914
        2.49 -     4.99: 155
        4.99 -     7.48: 17
        7.48 -     9.97: 7
        9.97 -    12.47: 2
  Bond angle restraints: 12095
  Sorted by residual:
  angle pdb=" O11 POV B 601 "
        pdb=" P   POV B 601 "
        pdb=" O12 POV B 601 "
      ideal   model   delta    sigma   weight residual
      97.67  110.14  -12.47 3.00e+00 1.11e-01 1.73e+01
  angle pdb=" O13 POV B 601 "
        pdb=" P   POV B 601 "
        pdb=" O14 POV B 601 "
      ideal   model   delta    sigma   weight residual
     121.11  109.16   11.95 3.00e+00 1.11e-01 1.59e+01
  angle pdb=" C22 POV B 601 "
        pdb=" C21 POV B 601 "
        pdb=" O21 POV B 601 "
      ideal   model   delta    sigma   weight residual
     111.03  120.33   -9.30 3.00e+00 1.11e-01 9.61e+00
  angle pdb=" C32 POV B 601 "
        pdb=" C31 POV B 601 "
        pdb=" O31 POV B 601 "
      ideal   model   delta    sigma   weight residual
     110.66  119.95   -9.29 3.00e+00 1.11e-01 9.60e+00
  angle pdb=" N   POV B 601 "
        pdb=" C12 POV B 601 "
        pdb=" C11 POV B 601 "
      ideal   model   delta    sigma   weight residual
     118.03  108.89    9.14 3.00e+00 1.11e-01 9.28e+00
  ... (remaining 12090 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.27: 4952
       21.27 -    42.54: 362
       42.54 -    63.81: 63
       63.81 -    85.08: 27
       85.08 -   106.36: 18
  Dihedral angle restraints: 5422
    sinusoidal: 2338
      harmonic: 3084
  Sorted by residual:
  dihedral pdb=" CB  CYS A 324 "
           pdb=" SG  CYS A 324 "
           pdb=" SG  CYS A 339 "
           pdb=" CB  CYS A 339 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.31  -80.31     1      1.00e+01 1.00e-02 7.98e+01
  dihedral pdb=" CA  CYS A 331 "
           pdb=" C   CYS A 331 "
           pdb=" N   CYS A 332 "
           pdb=" CA  CYS A 332 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.60  -29.40     0      5.00e+00 4.00e-02 3.46e+01
  dihedral pdb=" CA  PHE A 328 "
           pdb=" C   PHE A 328 "
           pdb=" N   HIS A 329 "
           pdb=" CA  HIS A 329 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.02   22.98     0      5.00e+00 4.00e-02 2.11e+01
  ... (remaining 5419 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1089
       0.057 -    0.114: 190
       0.114 -    0.171: 18
       0.171 -    0.227: 2
       0.227 -    0.284: 1
  Chirality restraints: 1300
  Sorted by residual:
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.56    0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" C2  MAN D   4 "
            pdb=" C1  MAN D   4 "
            pdb=" C3  MAN D   4 "
            pdb=" O2  MAN D   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.52    2.73   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 295 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 1297 not shown)

  Planarity restraints: 1526
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 177 "   -0.057 5.00e-02 4.00e+02   8.74e-02 1.22e+01
        pdb=" N   PRO C 178 "    0.151 5.00e-02 4.00e+02
        pdb=" CA  PRO C 178 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO C 178 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 281 "    0.058 5.00e-02 4.00e+02   8.58e-02 1.18e+01
        pdb=" N   PRO A 282 "   -0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO A 282 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A 282 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 298 "    0.034 5.00e-02 4.00e+02   5.07e-02 4.11e+00
        pdb=" N   PRO A 299 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 299 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 299 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1523 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1883
        2.78 -     3.31: 8331
        3.31 -     3.84: 14574
        3.84 -     4.37: 17165
        4.37 -     4.90: 29956
  Nonbonded interactions: 71909
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 173 "
            pdb=" OG1 THR A 178 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OE2 GLU B 285 "
            pdb=" NH2 ARG B 303 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" NE2 HIS A 329 "
            pdb=" OE2 GLU B 205 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OH  TYR C 128 "
            pdb=" O3  GLC D   7 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" NH2 ARG A 342 "
            pdb=" OD2 ASP C 201 "
     model   vdw
     2.359 3.120
  ... (remaining 71904 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             3.230
  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:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     10.120
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
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      :  0.004   0.091   8982  Z= 0.200
  Angle     :  0.714  12.465  12146  Z= 0.356
  Chirality :  0.043   0.284   1300
  Planarity :  0.005   0.087   1525
  Dihedral  : 17.023 106.355   3395
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  8.93 %
    Favored  : 90.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.26), residues: 1060
  helix:  2.15 (0.25), residues: 399
  sheet: -0.52 (0.37), residues: 206
  loop : -0.33 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 254 
 TYR   0.020   0.001   TYR C 338 
 PHE   0.015   0.001   PHE C 342 
 TRP   0.018   0.001   TRP B 481 
 HIS   0.003   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 8959)
  covalent geometry    : angle       0.70348 (12095)
  SS BOND              : bond        0.00270 (   15)
  SS BOND              : angle       1.04407 (   30)
  hydrogen bonds       : bond        0.15403 (  437)
  hydrogen bonds       : angle       6.87683 ( 1287)
  Misc. bond           : bond        0.00023 (    1)
  link_ALPHA1-2        : bond        0.00357 (    2)
  link_ALPHA1-2        : angle       3.36655 (    6)
  link_ALPHA1-3        : bond        0.00567 (    2)
  link_ALPHA1-3        : angle       1.49758 (    6)
  link_BETA1-4         : bond        0.00547 (    2)
  link_BETA1-4         : angle       2.80386 (    6)
  link_NAG-ASN         : bond        0.00377 (    1)
  link_NAG-ASN         : angle       3.53799 (    3)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: B  254 ARG cc_start: 0.8247 (mtp85) cc_final: 0.7965 (mtp85)
  outliers start: 2
  outliers final: 1
  residues processed: 100
  average time/residue: 0.0888
  time to fit residues: 12.9664
Evaluate side-chains
  94 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   66 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.0010
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0770
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0980
   overall best weight:    0.3344

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

Flipped N/Q/H residues before XYZ refinement:
A 325 ASN
B 459 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.195215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.122920 restraints weight = 9851.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.44
r_work: 0.3316 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.0740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8982  Z= 0.114
  Angle     :  0.557   9.447  12146  Z= 0.286
  Chirality :  0.042   0.225   1300
  Planarity :  0.005   0.063   1525
  Dihedral  : 12.441  88.881   1331
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  8.40 %
    Favored  : 89.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.26), residues: 1060
  helix:  2.53 (0.25), residues: 386
  sheet: -0.18 (0.38), residues: 198
  loop : -0.29 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 254 
 TYR   0.016   0.001   TYR A 318 
 PHE   0.017   0.001   PHE C 113 
 TRP   0.015   0.001   TRP B 481 
 HIS   0.003   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 8959)
  covalent geometry    : angle       0.54792 (12095)
  SS BOND              : bond        0.00333 (   15)
  SS BOND              : angle       0.90961 (   30)
  hydrogen bonds       : bond        0.04271 (  437)
  hydrogen bonds       : angle       4.87404 ( 1287)
  Misc. bond           : bond        0.00003 (    1)
  link_ALPHA1-2        : bond        0.00522 (    2)
  link_ALPHA1-2        : angle       2.56557 (    6)
  link_ALPHA1-3        : bond        0.00835 (    2)
  link_ALPHA1-3        : angle       1.92570 (    6)
  link_BETA1-4         : bond        0.00247 (    2)
  link_BETA1-4         : angle       2.12938 (    6)
  link_NAG-ASN         : bond        0.00248 (    1)
  link_NAG-ASN         : angle       3.04658 (    3)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.304 
Fit side-chains
REVERT: B   79 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7757 (mt-10)
REVERT: B  254 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7972 (mtp85)
REVERT: C  168 PHE cc_start: 0.5311 (t80) cc_final: 0.4949 (t80)
REVERT: C  169 THR cc_start: 0.6926 (m) cc_final: 0.6533 (p)
REVERT: C  357 MET cc_start: 0.6300 (tpp) cc_final: 0.6028 (tpt)
  outliers start: 18
  outliers final: 9
  residues processed: 121
  average time/residue: 0.0916
  time to fit residues: 15.9717
Evaluate side-chains
  108 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  399 MET
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue  195 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 94 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 104 optimal weight:    5.9990
   chunk 80 optimal weight:    6.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 459 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.190045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.116644 restraints weight = 9934.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 2.45
r_work: 0.3225 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.0986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059   8982  Z= 0.281
  Angle     :  0.650   8.241  12146  Z= 0.330
  Chirality :  0.046   0.221   1300
  Planarity :  0.005   0.054   1525
  Dihedral  : 11.120  87.005   1329
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.55 %
    Favored  : 87.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.26), residues: 1060
  helix:  2.07 (0.24), residues: 388
  sheet: -0.53 (0.37), residues: 198
  loop : -0.43 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 200 
 TYR   0.017   0.002   TYR A 318 
 PHE   0.022   0.002   PHE C 113 
 TRP   0.018   0.002   TRP A 147 
 HIS   0.007   0.001   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00694 ( 8959)
  covalent geometry    : angle       0.64226 (12095)
  SS BOND              : bond        0.00476 (   15)
  SS BOND              : angle       1.02644 (   30)
  hydrogen bonds       : bond        0.05088 (  437)
  hydrogen bonds       : angle       4.86563 ( 1287)
  Misc. bond           : bond        0.00055 (    1)
  link_ALPHA1-2        : bond        0.00357 (    2)
  link_ALPHA1-2        : angle       2.51763 (    6)
  link_ALPHA1-3        : bond        0.00406 (    2)
  link_ALPHA1-3        : angle       2.28125 (    6)
  link_BETA1-4         : bond        0.00228 (    2)
  link_BETA1-4         : angle       1.94920 (    6)
  link_NAG-ASN         : bond        0.00267 (    1)
  link_NAG-ASN         : angle       2.77688 (    3)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.337 
Fit side-chains
REVERT: B   76 ASP cc_start: 0.7747 (p0) cc_final: 0.7508 (p0)
REVERT: B  143 ASP cc_start: 0.7715 (p0) cc_final: 0.7238 (t0)
REVERT: B  254 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7932 (mtp85)
REVERT: C  120 THR cc_start: 0.8293 (p) cc_final: 0.7976 (t)
REVERT: C  168 PHE cc_start: 0.5562 (t80) cc_final: 0.5006 (t80)
REVERT: C  318 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7228 (pp)
REVERT: C  357 MET cc_start: 0.6390 (tpp) cc_final: 0.6065 (tpt)
  outliers start: 19
  outliers final: 13
  residues processed: 114
  average time/residue: 0.0879
  time to fit residues: 14.5624
Evaluate side-chains
  110 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  459 HIS
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  201 ASP
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 69 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   chunk 73 optimal weight:    0.6980
   chunk 17 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:
C  94 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.193646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.121299 restraints weight = 10013.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.45
r_work: 0.3289 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.1118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8982  Z= 0.131
  Angle     :  0.549   7.063  12146  Z= 0.282
  Chirality :  0.042   0.234   1300
  Planarity :  0.004   0.048   1525
  Dihedral  : 10.214  83.220   1329
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 11.09 %
    Favored  : 86.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.26), residues: 1060
  helix:  2.50 (0.25), residues: 382
  sheet: -0.48 (0.37), residues: 199
  loop : -0.35 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 254 
 TYR   0.013   0.001   TYR A 318 
 PHE   0.016   0.001   PHE C 113 
 TRP   0.014   0.001   TRP B 481 
 HIS   0.012   0.001   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8959)
  covalent geometry    : angle       0.54115 (12095)
  SS BOND              : bond        0.00309 (   15)
  SS BOND              : angle       0.88761 (   30)
  hydrogen bonds       : bond        0.04181 (  437)
  hydrogen bonds       : angle       4.53813 ( 1287)
  Misc. bond           : bond        0.00035 (    1)
  link_ALPHA1-2        : bond        0.00421 (    2)
  link_ALPHA1-2        : angle       2.23667 (    6)
  link_ALPHA1-3        : bond        0.00646 (    2)
  link_ALPHA1-3        : angle       2.08813 (    6)
  link_BETA1-4         : bond        0.00145 (    2)
  link_BETA1-4         : angle       1.98851 (    6)
  link_NAG-ASN         : bond        0.00360 (    1)
  link_NAG-ASN         : angle       2.70684 (    3)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: B  254 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7951 (mtp85)
REVERT: B  285 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8538 (mp0)
REVERT: B  323 MET cc_start: 0.8463 (mmm) cc_final: 0.8199 (mmm)
REVERT: B  461 LYS cc_start: 0.8088 (tptp) cc_final: 0.7860 (tptp)
REVERT: C  120 THR cc_start: 0.8352 (p) cc_final: 0.8041 (t)
REVERT: C  168 PHE cc_start: 0.5541 (t80) cc_final: 0.5221 (t80)
REVERT: C  318 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7195 (pp)
REVERT: C  357 MET cc_start: 0.6356 (tpp) cc_final: 0.6066 (tpp)
  outliers start: 21
  outliers final: 15
  residues processed: 118
  average time/residue: 0.0917
  time to fit residues: 15.4951
Evaluate side-chains
  115 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  323 GLN
Chi-restraints excluded: chain B residue    7 GLU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  201 ASP
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 6 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 89 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 4 optimal weight:    0.4980
   chunk 27 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 459 HIS
C  26 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.193044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.121095 restraints weight = 9854.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 2.41
r_work: 0.3298 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8982  Z= 0.130
  Angle     :  0.533   7.683  12146  Z= 0.272
  Chirality :  0.041   0.216   1300
  Planarity :  0.004   0.046   1525
  Dihedral  :  9.049  76.473   1329
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.63 %
    Favored  : 86.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.26), residues: 1060
  helix:  2.65 (0.25), residues: 385
  sheet: -0.42 (0.38), residues: 192
  loop : -0.41 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 254 
 TYR   0.014   0.001   TYR C 150 
 PHE   0.016   0.001   PHE C 113 
 TRP   0.013   0.001   TRP B 481 
 HIS   0.003   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8959)
  covalent geometry    : angle       0.52437 (12095)
  SS BOND              : bond        0.00358 (   15)
  SS BOND              : angle       1.09182 (   30)
  hydrogen bonds       : bond        0.03963 (  437)
  hydrogen bonds       : angle       4.34874 ( 1287)
  Misc. bond           : bond        0.00014 (    1)
  link_ALPHA1-2        : bond        0.00405 (    2)
  link_ALPHA1-2        : angle       2.08966 (    6)
  link_ALPHA1-3        : bond        0.00709 (    2)
  link_ALPHA1-3        : angle       1.79434 (    6)
  link_BETA1-4         : bond        0.00312 (    2)
  link_BETA1-4         : angle       1.98007 (    6)
  link_NAG-ASN         : bond        0.00493 (    1)
  link_NAG-ASN         : angle       2.85372 (    3)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.404 
Fit side-chains
REVERT: B  254 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7938 (mtp85)
REVERT: B  258 MET cc_start: 0.8142 (mtp) cc_final: 0.7727 (mtp)
REVERT: B  323 MET cc_start: 0.8442 (mmm) cc_final: 0.8159 (mmm)
REVERT: B  405 ARG cc_start: 0.7637 (tpt170) cc_final: 0.7202 (ttp-170)
REVERT: B  461 LYS cc_start: 0.8118 (tptp) cc_final: 0.7864 (tptp)
REVERT: C   98 LYS cc_start: 0.7123 (ptmt) cc_final: 0.6815 (ptmt)
REVERT: C  120 THR cc_start: 0.8415 (p) cc_final: 0.8117 (t)
REVERT: C  318 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7195 (pp)
REVERT: C  357 MET cc_start: 0.6396 (tpp) cc_final: 0.6134 (tpp)
REVERT: C  358 LYS cc_start: 0.5976 (ptmt) cc_final: 0.5693 (pptt)
  outliers start: 20
  outliers final: 14
  residues processed: 124
  average time/residue: 0.0878
  time to fit residues: 15.7695
Evaluate side-chains
  117 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain B residue    7 GLU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  459 HIS
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  201 ASP
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   chunk 37 optimal weight:    5.9990
   chunk 63 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0970
   chunk 51 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
B 322 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.193552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.123117 restraints weight = 9865.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 2.87
r_work: 0.3284 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8982  Z= 0.120
  Angle     :  0.523   7.738  12146  Z= 0.266
  Chirality :  0.041   0.201   1300
  Planarity :  0.004   0.044   1525
  Dihedral  :  8.365  74.019   1329
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 12.27 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.26), residues: 1060
  helix:  2.71 (0.25), residues: 385
  sheet: -0.44 (0.38), residues: 193
  loop : -0.38 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 422 
 TYR   0.011   0.001   TYR C 150 
 PHE   0.015   0.001   PHE C 113 
 TRP   0.013   0.001   TRP B 481 
 HIS   0.004   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8959)
  covalent geometry    : angle       0.51411 (12095)
  SS BOND              : bond        0.00281 (   15)
  SS BOND              : angle       0.87124 (   30)
  hydrogen bonds       : bond        0.03836 (  437)
  hydrogen bonds       : angle       4.28632 ( 1287)
  Misc. bond           : bond        0.00013 (    1)
  link_ALPHA1-2        : bond        0.00414 (    2)
  link_ALPHA1-2        : angle       2.12753 (    6)
  link_ALPHA1-3        : bond        0.00728 (    2)
  link_ALPHA1-3        : angle       1.75497 (    6)
  link_BETA1-4         : bond        0.00268 (    2)
  link_BETA1-4         : angle       2.06520 (    6)
  link_NAG-ASN         : bond        0.00558 (    1)
  link_NAG-ASN         : angle       2.99716 (    3)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A  342 ARG cc_start: 0.8043 (ttm170) cc_final: 0.7821 (ttp-110)
REVERT: B  254 ARG cc_start: 0.8250 (mtp85) cc_final: 0.7969 (mtp85)
REVERT: B  258 MET cc_start: 0.8158 (mtp) cc_final: 0.7764 (mtp)
REVERT: B  285 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8558 (mp0)
REVERT: B  323 MET cc_start: 0.8430 (mmm) cc_final: 0.8121 (mmm)
REVERT: B  405 ARG cc_start: 0.7628 (tpt170) cc_final: 0.7177 (ttp-170)
REVERT: B  461 LYS cc_start: 0.8091 (tptp) cc_final: 0.7841 (tptp)
REVERT: C   98 LYS cc_start: 0.7125 (ptmt) cc_final: 0.6775 (ptmt)
REVERT: C  120 THR cc_start: 0.8371 (p) cc_final: 0.8089 (t)
REVERT: C  318 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7262 (pp)
REVERT: C  357 MET cc_start: 0.6456 (tpp) cc_final: 0.6140 (tpp)
  outliers start: 16
  outliers final: 13
  residues processed: 116
  average time/residue: 0.0925
  time to fit residues: 15.4173
Evaluate side-chains
  113 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain B residue    7 GLU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 98 optimal weight:    0.1980
   chunk 77 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 94 optimal weight:   10.0000
   chunk 80 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN
B 459 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.193548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.122889 restraints weight = 9990.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.81
r_work: 0.3282 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8982  Z= 0.125
  Angle     :  0.522   7.155  12146  Z= 0.266
  Chirality :  0.041   0.175   1300
  Planarity :  0.004   0.042   1525
  Dihedral  :  7.616  70.017   1329
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 12.06 %
    Favored  : 85.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.26), residues: 1060
  helix:  2.72 (0.24), residues: 385
  sheet: -0.35 (0.38), residues: 189
  loop : -0.41 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 422 
 TYR   0.010   0.001   TYR B 177 
 PHE   0.015   0.001   PHE C 113 
 TRP   0.012   0.001   TRP B 481 
 HIS   0.004   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8959)
  covalent geometry    : angle       0.51367 (12095)
  SS BOND              : bond        0.00288 (   15)
  SS BOND              : angle       0.84096 (   30)
  hydrogen bonds       : bond        0.03844 (  437)
  hydrogen bonds       : angle       4.24164 ( 1287)
  Misc. bond           : bond        0.00009 (    1)
  link_ALPHA1-2        : bond        0.00407 (    2)
  link_ALPHA1-2        : angle       2.15166 (    6)
  link_ALPHA1-3        : bond        0.00687 (    2)
  link_ALPHA1-3        : angle       1.59269 (    6)
  link_BETA1-4         : bond        0.00202 (    2)
  link_BETA1-4         : angle       2.17354 (    6)
  link_NAG-ASN         : bond        0.00588 (    1)
  link_NAG-ASN         : angle       3.25171 (    3)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  181 ASN cc_start: 0.8905 (m-40) cc_final: 0.8518 (m-40)
REVERT: A  342 ARG cc_start: 0.8006 (ttm170) cc_final: 0.7800 (ttp-110)
REVERT: B  254 ARG cc_start: 0.8283 (mtp85) cc_final: 0.8006 (mtp85)
REVERT: B  258 MET cc_start: 0.8174 (mtp) cc_final: 0.7769 (mtp)
REVERT: B  285 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8582 (mp0)
REVERT: B  323 MET cc_start: 0.8450 (mmm) cc_final: 0.8112 (mmm)
REVERT: B  405 ARG cc_start: 0.7702 (tpt170) cc_final: 0.7234 (ttp80)
REVERT: C   98 LYS cc_start: 0.7179 (ptmt) cc_final: 0.6840 (ptmt)
REVERT: C  120 THR cc_start: 0.8343 (p) cc_final: 0.8084 (t)
REVERT: C  318 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7233 (pp)
REVERT: C  357 MET cc_start: 0.6291 (tpp) cc_final: 0.6085 (tpp)
  outliers start: 21
  outliers final: 16
  residues processed: 117
  average time/residue: 0.0873
  time to fit residues: 14.8113
Evaluate side-chains
  114 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain B residue    7 GLU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  459 HIS
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   56 PHE
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  201 ASP
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0370
   chunk 40 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
B 459 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.193965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.123445 restraints weight = 9861.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.84
r_work: 0.3292 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8982  Z= 0.119
  Angle     :  0.519   6.791  12146  Z= 0.265
  Chirality :  0.041   0.169   1300
  Planarity :  0.004   0.041   1525
  Dihedral  :  7.363  68.080   1329
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.02 %
    Favored  : 85.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.26), residues: 1060
  helix:  2.76 (0.24), residues: 385
  sheet: -0.36 (0.38), residues: 189
  loop : -0.42 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 422 
 TYR   0.010   0.001   TYR B 492 
 PHE   0.016   0.001   PHE C 113 
 TRP   0.012   0.001   TRP B 481 
 HIS   0.008   0.001   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8959)
  covalent geometry    : angle       0.51005 (12095)
  SS BOND              : bond        0.00279 (   15)
  SS BOND              : angle       0.84912 (   30)
  hydrogen bonds       : bond        0.03795 (  437)
  hydrogen bonds       : angle       4.20249 ( 1287)
  Misc. bond           : bond        0.00005 (    1)
  link_ALPHA1-2        : bond        0.00433 (    2)
  link_ALPHA1-2        : angle       2.14228 (    6)
  link_ALPHA1-3        : bond        0.00693 (    2)
  link_ALPHA1-3        : angle       1.56054 (    6)
  link_BETA1-4         : bond        0.00211 (    2)
  link_BETA1-4         : angle       2.14823 (    6)
  link_NAG-ASN         : bond        0.00600 (    1)
  link_NAG-ASN         : angle       3.38536 (    3)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A  181 ASN cc_start: 0.8910 (m-40) cc_final: 0.8523 (m-40)
REVERT: B   79 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7752 (mt-10)
REVERT: B  254 ARG cc_start: 0.8297 (mtp85) cc_final: 0.8023 (mtp85)
REVERT: B  258 MET cc_start: 0.8185 (mtp) cc_final: 0.7780 (mtp)
REVERT: B  285 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8552 (mp0)
REVERT: B  323 MET cc_start: 0.8457 (mmm) cc_final: 0.8134 (mmm)
REVERT: B  405 ARG cc_start: 0.7689 (tpt170) cc_final: 0.7269 (ttp80)
REVERT: C   98 LYS cc_start: 0.7240 (ptmt) cc_final: 0.6909 (ptmt)
REVERT: C  120 THR cc_start: 0.8359 (p) cc_final: 0.8109 (t)
REVERT: C  318 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7297 (pp)
REVERT: C  357 MET cc_start: 0.6315 (tpp) cc_final: 0.6103 (tpp)
  outliers start: 17
  outliers final: 14
  residues processed: 119
  average time/residue: 0.0958
  time to fit residues: 16.5681
Evaluate side-chains
  115 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain B residue    7 GLU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  459 HIS
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  201 ASP
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 94 optimal weight:   10.0000
   chunk 96 optimal weight:    0.0770
   chunk 18 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
B 459 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.193948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.123435 restraints weight = 9887.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.83
r_work: 0.3297 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8982  Z= 0.120
  Angle     :  0.516   6.706  12146  Z= 0.263
  Chirality :  0.041   0.163   1300
  Planarity :  0.004   0.041   1525
  Dihedral  :  7.168  67.727   1329
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.02 %
    Favored  : 85.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.26), residues: 1060
  helix:  2.77 (0.24), residues: 385
  sheet: -0.37 (0.38), residues: 189
  loop : -0.43 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 422 
 TYR   0.010   0.001   TYR B 177 
 PHE   0.015   0.001   PHE C 113 
 TRP   0.012   0.001   TRP B 481 
 HIS   0.004   0.001   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 8959)
  covalent geometry    : angle       0.50736 (12095)
  SS BOND              : bond        0.00276 (   15)
  SS BOND              : angle       0.84960 (   30)
  hydrogen bonds       : bond        0.03783 (  437)
  hydrogen bonds       : angle       4.17771 ( 1287)
  Misc. bond           : bond        0.00005 (    1)
  link_ALPHA1-2        : bond        0.00420 (    2)
  link_ALPHA1-2        : angle       2.13656 (    6)
  link_ALPHA1-3        : bond        0.00636 (    2)
  link_ALPHA1-3        : angle       1.54863 (    6)
  link_BETA1-4         : bond        0.00215 (    2)
  link_BETA1-4         : angle       2.09696 (    6)
  link_NAG-ASN         : bond        0.00623 (    1)
  link_NAG-ASN         : angle       3.48490 (    3)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  181 ASN cc_start: 0.8887 (m-40) cc_final: 0.8497 (m-40)
REVERT: B  254 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7972 (mtp85)
REVERT: B  258 MET cc_start: 0.8205 (mtp) cc_final: 0.7803 (mtp)
REVERT: B  285 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8539 (mp0)
REVERT: B  323 MET cc_start: 0.8412 (mmm) cc_final: 0.8085 (mmm)
REVERT: B  405 ARG cc_start: 0.7667 (tpt170) cc_final: 0.7216 (ttp80)
REVERT: C   98 LYS cc_start: 0.7225 (ptmt) cc_final: 0.6887 (ptmt)
REVERT: C  120 THR cc_start: 0.8362 (p) cc_final: 0.8113 (t)
REVERT: C  318 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7230 (pp)
REVERT: C  357 MET cc_start: 0.6276 (tpp) cc_final: 0.6063 (tpp)
  outliers start: 17
  outliers final: 15
  residues processed: 115
  average time/residue: 0.0648
  time to fit residues: 10.7378
Evaluate side-chains
  115 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain B residue    7 GLU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  459 HIS
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  201 ASP
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0010
   chunk 22 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0980
   chunk 38 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
B 459 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.193895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.122000 restraints weight = 9910.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.43
r_work: 0.3307 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8982  Z= 0.126
  Angle     :  0.524   6.640  12146  Z= 0.268
  Chirality :  0.041   0.154   1300
  Planarity :  0.004   0.041   1525
  Dihedral  :  7.042  67.679   1329
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.24 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.26), residues: 1060
  helix:  2.77 (0.24), residues: 385
  sheet: -0.38 (0.38), residues: 189
  loop : -0.44 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 422 
 TYR   0.010   0.001   TYR A 232 
 PHE   0.015   0.001   PHE C 113 
 TRP   0.012   0.001   TRP B 481 
 HIS   0.007   0.001   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8959)
  covalent geometry    : angle       0.51384 (12095)
  SS BOND              : bond        0.00279 (   15)
  SS BOND              : angle       0.86960 (   30)
  hydrogen bonds       : bond        0.03795 (  437)
  hydrogen bonds       : angle       4.17338 ( 1287)
  Misc. bond           : bond        0.00007 (    1)
  link_ALPHA1-2        : bond        0.00415 (    2)
  link_ALPHA1-2        : angle       2.13382 (    6)
  link_ALPHA1-3        : bond        0.00645 (    2)
  link_ALPHA1-3        : angle       1.54898 (    6)
  link_BETA1-4         : bond        0.00446 (    2)
  link_BETA1-4         : angle       2.10212 (    6)
  link_NAG-ASN         : bond        0.00337 (    1)
  link_NAG-ASN         : angle       3.95314 (    3)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.255 
Fit side-chains
REVERT: B   79 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7719 (mt-10)
REVERT: B  254 ARG cc_start: 0.8262 (mtp85) cc_final: 0.7991 (mtp85)
REVERT: B  258 MET cc_start: 0.8201 (mtp) cc_final: 0.7802 (mtp)
REVERT: B  285 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8543 (mp0)
REVERT: B  323 MET cc_start: 0.8432 (mmm) cc_final: 0.8130 (mmm)
REVERT: B  405 ARG cc_start: 0.7676 (tpt170) cc_final: 0.7247 (ttp80)
REVERT: C   98 LYS cc_start: 0.7220 (ptmt) cc_final: 0.6878 (ptmt)
REVERT: C  120 THR cc_start: 0.8365 (p) cc_final: 0.8118 (t)
REVERT: C  318 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7241 (pp)
REVERT: C  357 MET cc_start: 0.6281 (tpp) cc_final: 0.6068 (tpp)
  outliers start: 17
  outliers final: 14
  residues processed: 114
  average time/residue: 0.0678
  time to fit residues: 11.0778
Evaluate side-chains
  113 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain B residue    7 GLU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  459 HIS
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  201 ASP
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 105 optimal weight:   20.0000
   chunk 44 optimal weight:    0.0170
   chunk 88 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0670
   chunk 52 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 26 optimal weight:    9.9990
   chunk 71 optimal weight:    9.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
B 459 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.194709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.123256 restraints weight = 9817.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.41
r_work: 0.3323 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8982  Z= 0.111
  Angle     :  0.512   6.821  12146  Z= 0.263
  Chirality :  0.040   0.167   1300
  Planarity :  0.004   0.040   1525
  Dihedral  :  6.828  66.679   1329
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.02 %
    Favored  : 85.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.26), residues: 1060
  helix:  2.84 (0.25), residues: 385
  sheet: -0.37 (0.38), residues: 189
  loop : -0.44 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 422 
 TYR   0.010   0.001   TYR B 308 
 PHE   0.015   0.001   PHE C 113 
 TRP   0.013   0.001   TRP B 481 
 HIS   0.011   0.001   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 8959)
  covalent geometry    : angle       0.50158 (12095)
  SS BOND              : bond        0.00339 (   15)
  SS BOND              : angle       1.15695 (   30)
  hydrogen bonds       : bond        0.03656 (  437)
  hydrogen bonds       : angle       4.13371 ( 1287)
  Misc. bond           : bond        0.00000 (    1)
  link_ALPHA1-2        : bond        0.00435 (    2)
  link_ALPHA1-2        : angle       2.14664 (    6)
  link_ALPHA1-3        : bond        0.00683 (    2)
  link_ALPHA1-3        : angle       1.50828 (    6)
  link_BETA1-4         : bond        0.00467 (    2)
  link_BETA1-4         : angle       2.02831 (    6)
  link_NAG-ASN         : bond        0.00486 (    1)
  link_NAG-ASN         : angle       3.16541 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3076.32 seconds
wall clock time: 53 minutes 16.17 seconds (3196.17 seconds total)