Starting phenix.real_space_refine
on Mon May  4 03:30:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9zdx_74076/05_2026/9zdx_74076.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9zdx_74076/05_2026/9zdx_74076.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9zdx_74076/05_2026/9zdx_74076.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9zdx_74076/05_2026/9zdx_74076.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9zdx_74076/05_2026/9zdx_74076.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9zdx_74076/05_2026/9zdx_74076.cif"
  }
  resolution = 2.95
  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=  -0.000 sd=   0.059
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: 7
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      23      5.16       5
     C    5583      2.51       5
     N    1512      2.21       5
     O    1728      1.98       5
     H    8438      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17292
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 8617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 550, 8617
          Classifications: {'peptide': 550}
          Link IDs: {'PTRANS': 11, 'TRANS': 538}
    Chain: "A"
      Number of atoms: 8607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 544, 8607
          Classifications: {'peptide': 544}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 532}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 3.32, per 1000 atoms: 0.19
  Number of scatterers: 17292
  At special positions: 0
  Unit cell: (79.662, 96.492, 131.274, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      23     16.00
     P       6     15.00
     Mg      2     11.99
     O    1728      8.00
     N    1512      7.00
     C    5583      6.00
     H    8438      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.55
  Conformation dependent library (CDL) restraints added in 538.3 milliseconds
  

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2064

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 6 sheets defined
      63.6% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'C' and resid 25 through 35
    Processing helix  chain 'C' and resid 39 through 53
      removed outlier: 3.977A  pdb=" N   LYS C  44 " --> pdb=" O   ASN C  40 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   HIS C  45 " --> pdb=" O   GLU C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 65
      removed outlier: 4.192A  pdb=" N   ALA C  63 " --> pdb=" O   PRO C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 77 through 91
    Processing helix  chain 'C' and resid 104 through 108
      removed outlier: 3.621A  pdb=" N   PHE C 108 " --> pdb=" O   ALA C 104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 104 through 108'
    Processing helix  chain 'C' and resid 115 through 129
      removed outlier: 4.089A  pdb=" N   HIS C 129 " --> pdb=" O   ALA C 125 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 141
    Processing helix  chain 'C' and resid 148 through 163
    Processing helix  chain 'C' and resid 168 through 182
      removed outlier: 3.701A  pdb=" N   MET C 174 " --> pdb=" O   HIS C 170 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 196
    Processing helix  chain 'C' and resid 198 through 203
    Processing helix  chain 'C' and resid 204 through 208
      removed outlier: 5.557A  pdb=" N   GLN C 207 " --> pdb=" O   ASP C 204 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 222
    Processing helix  chain 'C' and resid 224 through 235
    Processing helix  chain 'C' and resid 242 through 258
    Processing helix  chain 'C' and resid 269 through 275
      removed outlier: 3.965A  pdb=" N   PHE C 273 " --> pdb=" O   GLN C 269 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 277 through 296
      removed outlier: 3.575A  pdb=" N   GLY C 292 " --> pdb=" O   THR C 288 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 313
    Processing helix  chain 'C' and resid 319 through 325
    Processing helix  chain 'C' and resid 341 through 350
    Processing helix  chain 'C' and resid 354 through 375
      removed outlier: 6.471A  pdb=" N   ASP C 370 " --> pdb=" O   GLU C 366 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   ILE C 371 " --> pdb=" O   GLN C 367 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 390 through 396
      removed outlier: 3.591A  pdb=" N   PHE C 394 " --> pdb=" O   GLY C 390 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 403 through 416
      removed outlier: 3.613A  pdb=" N   ARG C 416 " --> pdb=" O   PHE C 412 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 428 through 443
      removed outlier: 3.679A  pdb=" N   GLN C 437 " --> pdb=" O   LEU C 433 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ILE C 443 " --> pdb=" O   ALA C 439 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 454 through 461
    Processing helix  chain 'C' and resid 466 through 476
      removed outlier: 3.840A  pdb=" N   THR C 472 " --> pdb=" O   ALA C 468 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 477 through 479
      No H-bonds generated for 'chain 'C' and resid 477 through 479'
    Processing helix  chain 'C' and resid 484 through 496
    Processing helix  chain 'C' and resid 505 through 512
      removed outlier: 3.580A  pdb=" N   THR C 511 " --> pdb=" O   ASP C 507 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 520 through 538
      removed outlier: 3.567A  pdb=" N   GLU C 538 " --> pdb=" O   ARG C 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3 through 7
      removed outlier: 3.960A  pdb=" N   PHE A   7 " --> pdb=" O   LYS A   4 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 35
    Processing helix  chain 'A' and resid 39 through 53
      removed outlier: 3.815A  pdb=" N   LYS A  44 " --> pdb=" O   ASN A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 65
      removed outlier: 3.828A  pdb=" N   ALA A  63 " --> pdb=" O   PRO A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 91
    Processing helix  chain 'A' and resid 104 through 108
    Processing helix  chain 'A' and resid 115 through 128
      removed outlier: 3.566A  pdb=" N   HIS A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 141
    Processing helix  chain 'A' and resid 148 through 163
    Processing helix  chain 'A' and resid 168 through 182
    Processing helix  chain 'A' and resid 183 through 196
    Processing helix  chain 'A' and resid 198 through 203
    Processing helix  chain 'A' and resid 204 through 206
      No H-bonds generated for 'chain 'A' and resid 204 through 206'
    Processing helix  chain 'A' and resid 209 through 222
    Processing helix  chain 'A' and resid 224 through 239
    Processing helix  chain 'A' and resid 242 through 258
      removed outlier: 3.651A  pdb=" N   LYS A 257 " --> pdb=" O   TYR A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 275
    Processing helix  chain 'A' and resid 277 through 294
    Processing helix  chain 'A' and resid 308 through 315
    Processing helix  chain 'A' and resid 324 through 329
    Processing helix  chain 'A' and resid 341 through 350
    Processing helix  chain 'A' and resid 354 through 367
    Processing helix  chain 'A' and resid 369 through 376
    Processing helix  chain 'A' and resid 390 through 396
    Processing helix  chain 'A' and resid 401 through 414
      removed outlier: 4.253A  pdb=" N   PHE A 405 " --> pdb=" O   ALA A 401 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   GLN A 406 " --> pdb=" O   PRO A 402 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLU A 414 " --> pdb=" O   LYS A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 443
      removed outlier: 3.506A  pdb=" N   MET A 432 " --> pdb=" O   GLY A 428 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ILE A 443 " --> pdb=" O   ALA A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 456
    Processing helix  chain 'A' and resid 457 through 462
      removed outlier: 3.671A  pdb=" N   VAL A 461 " --> pdb=" O   PHE A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 465
      No H-bonds generated for 'chain 'A' and resid 463 through 465'
    Processing helix  chain 'A' and resid 466 through 477
      removed outlier: 3.682A  pdb=" N   GLY A 477 " --> pdb=" O   ILE A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 496
    Processing helix  chain 'A' and resid 505 through 513
    Processing helix  chain 'A' and resid 520 through 538
    Processing sheet with id=AA1, first strand: chain 'C' and resid 131 through 136
      removed outlier: 6.454A  pdb=" N   ASP C 131 " --> pdb=" O   LEU C 264 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   LEU C 266 " --> pdb=" O   ASP C 131 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   ILE C 133 " --> pdb=" O   LEU C 266 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   ASP C 268 " --> pdb=" O   ILE C 133 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   PHE C 135 " --> pdb=" O   ASP C 268 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   MET C 263 " --> pdb=" O   TRP C 300 " (cutoff:3.500A)
      removed outlier: 7.700A  pdb=" N   ILE C 302 " --> pdb=" O   MET C 263 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   PHE C 265 " --> pdb=" O   ILE C 302 " (cutoff:3.500A)
      removed outlier: 7.723A  pdb=" N   THR C 304 " --> pdb=" O   PHE C 265 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   VAL C 267 " --> pdb=" O   THR C 304 " (cutoff:3.500A)
      removed outlier: 9.319A  pdb=" N   GLN C 306 " --> pdb=" O   VAL C 267 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   GLY C  67 " --> pdb=" O   THR C 333 " (cutoff:3.500A)
      removed outlier: 7.850A  pdb=" N   LEU C 335 " --> pdb=" O   GLY C  67 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   TRP C  69 " --> pdb=" O   LEU C 335 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   LEU C 337 " --> pdb=" O   TRP C  69 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   SER C  71 " --> pdb=" O   LEU C 337 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 93 through 95
    Processing sheet with id=AA3, first strand: chain 'C' and resid 542 through 543
    Processing sheet with id=AA4, first strand: chain 'A' and resid 131 through 136
      removed outlier: 6.459A  pdb=" N   ASP A 131 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
      removed outlier: 7.385A  pdb=" N   LEU A 266 " --> pdb=" O   ASP A 131 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   ILE A 133 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   ASP A 268 " --> pdb=" O   ILE A 133 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   PHE A 135 " --> pdb=" O   ASP A 268 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   MET A 263 " --> pdb=" O   TRP A 300 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   ILE A 302 " --> pdb=" O   MET A 263 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   PHE A 265 " --> pdb=" O   ILE A 302 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   THR A 304 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 7.388A  pdb=" N   VAL A 267 " --> pdb=" O   THR A 304 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLY A  67 " --> pdb=" O   THR A 333 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   LEU A 335 " --> pdb=" O   GLY A  67 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   TRP A  69 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 93 through 95
    Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 544

    441 hydrogen bonds defined for protein.
    1275 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.86

  Time building geometry restraints manager: 2.22 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8434
        1.03 -     1.23: 29
        1.23 -     1.42: 3886
        1.42 -     1.62: 5072
        1.62 -     1.81: 42
  Bond restraints: 17463
  Sorted by residual:
  bond pdb=" N   ASN A   2 "
       pdb=" CA  ASN A   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.90e-02 2.77e+03 2.43e+00
  bond pdb=" N   ASN A   2 "
       pdb=" H   ASN A   2 "
    ideal  model  delta    sigma   weight residual
    0.860  0.891 -0.031 2.00e-02 2.50e+03 2.40e+00
  bond pdb=" CG  PRO A 399 "
       pdb=" CD  PRO A 399 "
    ideal  model  delta    sigma   weight residual
    1.512  1.485  0.027 2.70e-02 1.37e+03 9.93e-01
  bond pdb=" CB  THR C 304 "
       pdb=" CG2 THR C 304 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.99e-01
  bond pdb=" O3B ATP A1301 "
       pdb=" PB  ATP A1301 "
    ideal  model  delta    sigma   weight residual
    1.592  1.566  0.026 3.00e-02 1.11e+03 7.26e-01
  ... (remaining 17458 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    10.30: 31349
       10.30 -    20.59: 2
       20.59 -    30.89: 0
       30.89 -    41.18: 3
       41.18 -    51.48: 4
  Bond angle restraints: 31358
  Sorted by residual:
  angle pdb=" C   VAL C 312 "
        pdb=" N   LEU C 313 "
        pdb=" H   LEU C 313 "
      ideal   model   delta    sigma   weight residual
     123.97   72.49   51.48 3.00e+00 1.11e-01 2.94e+02
  angle pdb=" CA  LEU C 313 "
        pdb=" N   LEU C 313 "
        pdb=" H   LEU C 313 "
      ideal   model   delta    sigma   weight residual
     113.67   62.32   51.35 3.00e+00 1.11e-01 2.93e+02
  angle pdb=" C   ASP C 323 "
        pdb=" N   PHE C 324 "
        pdb=" H   PHE C 324 "
      ideal   model   delta    sigma   weight residual
     124.33   73.93   50.40 3.00e+00 1.11e-01 2.82e+02
  angle pdb=" CA  PHE C 324 "
        pdb=" N   PHE C 324 "
        pdb=" H   PHE C 324 "
      ideal   model   delta    sigma   weight residual
     114.03   64.30   49.73 3.00e+00 1.11e-01 2.75e+02
  angle pdb=" CB  ALA C 468 "
        pdb=" CA  ALA C 468 "
        pdb=" HA  ALA C 468 "
      ideal   model   delta    sigma   weight residual
     109.00   74.06   34.94 3.00e+00 1.11e-01 1.36e+02
  ... (remaining 31353 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 7285
       17.97 -    35.95: 660
       35.95 -    53.92: 229
       53.92 -    71.89: 50
       71.89 -    89.87: 26
  Dihedral angle restraints: 8250
    sinusoidal: 4424
      harmonic: 3826
  Sorted by residual:
  dihedral pdb=" CA  GLN A 207 "
           pdb=" C   GLN A 207 "
           pdb=" N   PHE A 208 "
           pdb=" CA  PHE A 208 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.51   17.49     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" CA  ASP A 145 "
           pdb=" C   ASP A 145 "
           pdb=" N   ASP A 146 "
           pdb=" CA  ASP A 146 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.52   17.48     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" C   ALA C 468 "
           pdb=" N   ALA C 468 "
           pdb=" CA  ALA C 468 "
           pdb=" CB  ALA C 468 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.32    8.72     0      2.50e+00 1.60e-01 1.22e+01
  ... (remaining 8247 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1205
       0.061 -    0.123: 111
       0.123 -    0.184: 7
       0.184 -    0.246: 0
       0.246 -    0.307: 1
  Chirality restraints: 1324
  Sorted by residual:
  chirality pdb=" CA  ALA C 468 "
            pdb=" N   ALA C 468 "
            pdb=" C   ALA C 468 "
            pdb=" CB  ALA C 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.18    0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CA  VAL C 452 "
            pdb=" N   VAL C 452 "
            pdb=" C   VAL C 452 "
            pdb=" CB  VAL C 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.59e-01
  chirality pdb=" CA  PRO A 402 "
            pdb=" N   PRO A 402 "
            pdb=" C   PRO A 402 "
            pdb=" CB  PRO A 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 3.99e-01
  ... (remaining 1321 not shown)

  Planarity restraints: 2645
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 148 "   -0.024 5.00e-02 4.00e+02   3.60e-02 2.08e+00
        pdb=" N   PRO A 149 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A 149 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 149 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 168 "    0.020 5.00e-02 4.00e+02   3.02e-02 1.46e+00
        pdb=" N   PRO A 169 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 169 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 169 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 382 "   -0.019 5.00e-02 4.00e+02   2.84e-02 1.29e+00
        pdb=" N   PRO A 383 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 383 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 383 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 2642 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.12: 375
        2.12 -     2.74: 30527
        2.74 -     3.36: 49302
        3.36 -     3.98: 63944
        3.98 -     4.60: 102518
  Nonbonded interactions: 246666
  Sorted by model distance:
  nonbonded pdb=" H   PHE C 324 "
            pdb=" HA  PHE C 324 "
     model   vdw
     1.495 1.816
  nonbonded pdb=" OD1 ASP C 131 "
            pdb="HE21 GLN C 261 "
     model   vdw
     1.570 2.450
  nonbonded pdb=" O   LEU A 313 "
            pdb=" H   SER A 317 "
     model   vdw
     1.581 2.450
  nonbonded pdb=" OD1 ASP C  96 "
            pdb=" H   ALA C  97 "
     model   vdw
     1.598 2.450
  nonbonded pdb=" HA  ALA C 468 "
            pdb=" HB2 ALA C 468 "
     model   vdw
     1.605 1.952
  ... (remaining 246661 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ 
r name CG or name OD1 or name ND2)) or (resid 3 and (name N or name CA or name C \ 
 or name O or name CB or name CG1 or name CG2 or name CD1)) or resid 4 through 4 \ 
16 or (resid 424 and (name N or name CA or name C or name O or name CB or name C \ 
G or name ND1 or name CD2 or name CE1 or name NE2)) or resid 425 through 470 or  \ 
(resid 471 and (name N or name CA or name C or name O or name CB or name CG or n \ 
ame CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA )) or  \ 
resid 472 through 550 or resid 1301 through 1302))
  selection = (chain 'C' and (resid 2 through 319 or (resid 320 and (name N or name CA or name \ 
 C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid  \ 
321 through 397 or (resid 398 and (name N or name CA or name C or name O or name \ 
 CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or nam \ 
e OH )) or (resid 399 and (name N or name CA or name C or name O or name CB or n \ 
ame CG or name CD )) or resid 400 through 416 or resid 424 through 1302))
}

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:             4.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.110
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     18.110
  Find NCS groups from input model:        0.220
  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:6.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
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   0.031   9025  Z= 0.186
  Angle     :  0.540  16.594  12189  Z= 0.305
  Chirality :  0.039   0.307   1324
  Planarity :  0.003   0.036   1587
  Dihedral  : 17.788  89.868   3367
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 18.76 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole: -0.20 (0.26), residues: 1088
  helix:  0.32 (0.21), residues: 660
  sheet:  0.24 (0.67), residues: 54
  loop : -0.84 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 330 
 TYR   0.011   0.002   TYR A 398 
 PHE   0.014   0.002   PHE C  49 
 TRP   0.009   0.001   TRP C 231 
 HIS   0.006   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 9025)
  covalent geometry    : angle       0.53998 (12189)
  hydrogen bonds       : bond        0.15933 (  441)
  hydrogen bonds       : angle       6.13523 ( 1275)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   79 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue LYS  320 is missing expected H atoms. Skipping.
Evaluate side-chains
  120 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   31 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7521 (mp10)
REVERT: C   95 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.6664 (mtm110)
REVERT: C  253 TYR cc_start: 0.8235 (t80) cc_final: 0.7965 (t80)
REVERT: C  497 ARG cc_start: 0.7118 (mtp180) cc_final: 0.6701 (ttp80)
REVERT: A   51 GLN cc_start: 0.7695 (pt0) cc_final: 0.7381 (tt0)
REVERT: A   95 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7349 (mtt90)
REVERT: A  181 LYS cc_start: 0.7529 (mmtt) cc_final: 0.7277 (mttt)
REVERT: A  248 GLN cc_start: 0.7295 (tp40) cc_final: 0.6839 (tt0)
REVERT: A  251 LYS cc_start: 0.7622 (tttm) cc_final: 0.6811 (tttp)
  outliers start: 14
  outliers final: 10
  residues processed: 116
  average time/residue: 1.5709
  time to fit residues: 192.0458
Evaluate side-chains
  113 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 ASN
Chi-restraints excluded: chain C residue   31 GLN
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  319 SER
Chi-restraints excluded: chain C residue  348 LYS
Chi-restraints excluded: chain C residue  443 ILE
Chi-restraints excluded: chain C residue  465 LEU
Chi-restraints excluded: chain C residue  509 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  304 THR
Chi-restraints excluded: chain A residue  507 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
C 136 ASN
C 397 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.128811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.103245 restraints weight = 27183.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 1.65
r_work: 0.2892 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.2764 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.0561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9025  Z= 0.202
  Angle     :  0.556  17.842  12189  Z= 0.309
  Chirality :  0.040   0.311   1324
  Planarity :  0.004   0.030   1587
  Dihedral  :  9.968  83.071   1277
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.60 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole: -0.17 (0.26), residues: 1088
  helix:  0.38 (0.21), residues: 663
  sheet: -0.33 (0.63), residues: 56
  loop : -0.81 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 298 
 TYR   0.018   0.002   TYR A 398 
 PHE   0.014   0.002   PHE C  49 
 TRP   0.011   0.002   TRP C 231 
 HIS   0.007   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 9025)
  covalent geometry    : angle       0.55576 (12189)
  hydrogen bonds       : bond        0.04872 (  441)
  hydrogen bonds       : angle       4.92225 ( 1275)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   79 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue LYS  320 is missing expected H atoms. Skipping.
Evaluate side-chains
  129 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   31 GLN cc_start: 0.7723 (mt0) cc_final: 0.7501 (mp10)
REVERT: C   95 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.6415 (mtm110)
REVERT: C  253 TYR cc_start: 0.8263 (t80) cc_final: 0.7971 (t80)
REVERT: C  410 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7097 (mmtp)
REVERT: C  497 ARG cc_start: 0.6899 (mtp180) cc_final: 0.6443 (ttp80)
REVERT: A   51 GLN cc_start: 0.7718 (pt0) cc_final: 0.7387 (tt0)
REVERT: A   95 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7442 (mtt90)
REVERT: A  180 GLN cc_start: 0.6972 (mt0) cc_final: 0.6710 (mt0)
REVERT: A  248 GLN cc_start: 0.7301 (tp40) cc_final: 0.6906 (tt0)
REVERT: A  251 LYS cc_start: 0.7612 (tttm) cc_final: 0.6797 (tttp)
  outliers start: 23
  outliers final: 10
  residues processed: 124
  average time/residue: 1.4775
  time to fit residues: 193.4523
Evaluate side-chains
  114 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 ASN
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  348 LYS
Chi-restraints excluded: chain C residue  410 LYS
Chi-restraints excluded: chain C residue  415 ILE
Chi-restraints excluded: chain C residue  509 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  304 THR
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  542 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0060
   chunk 7 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
C 397 ASN
A 219 GLN
A 222 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.129964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.104377 restraints weight = 27213.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 1.67
r_work: 0.2893 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.2765 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.0770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9025  Z= 0.148
  Angle     :  0.512  18.675  12189  Z= 0.283
  Chirality :  0.038   0.312   1324
  Planarity :  0.003   0.030   1587
  Dihedral  :  9.431  78.377   1267
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 18.34 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole:  0.15 (0.26), residues: 1088
  helix:  0.67 (0.21), residues: 652
  sheet: -0.57 (0.62), residues: 56
  loop : -0.65 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 298 
 TYR   0.014   0.002   TYR A 398 
 PHE   0.012   0.001   PHE A  49 
 TRP   0.009   0.001   TRP C 231 
 HIS   0.005   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 9025)
  covalent geometry    : angle       0.51216 (12189)
  hydrogen bonds       : bond        0.04087 (  441)
  hydrogen bonds       : angle       4.55523 ( 1275)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   79 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue LYS  320 is missing expected H atoms. Skipping.
Evaluate side-chains
  127 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   31 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7333 (mp10)
REVERT: C   91 ASN cc_start: 0.8580 (t0) cc_final: 0.8211 (t0)
REVERT: C   95 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.6472 (mtm110)
REVERT: C  253 TYR cc_start: 0.8230 (t80) cc_final: 0.7926 (t80)
REVERT: C  348 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8602 (mmmt)
REVERT: C  376 ILE cc_start: 0.7499 (mt) cc_final: 0.7287 (mp)
REVERT: C  410 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7011 (mmtp)
REVERT: C  497 ARG cc_start: 0.6838 (mtp180) cc_final: 0.6413 (ttp80)
REVERT: A   51 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7430 (tt0)
REVERT: A   95 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7439 (mtt90)
REVERT: A  145 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7506 (m-30)
REVERT: A  180 GLN cc_start: 0.6859 (mt0) cc_final: 0.6576 (mt0)
REVERT: A  248 GLN cc_start: 0.7290 (tp40) cc_final: 0.7056 (tt0)
REVERT: A  251 LYS cc_start: 0.7495 (tttm) cc_final: 0.7065 (tttm)
  outliers start: 20
  outliers final: 10
  residues processed: 120
  average time/residue: 1.5166
  time to fit residues: 191.8536
Evaluate side-chains
  119 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 ASN
Chi-restraints excluded: chain C residue   31 GLN
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  276 SER
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  318 SER
Chi-restraints excluded: chain C residue  348 LYS
Chi-restraints excluded: chain C residue  410 LYS
Chi-restraints excluded: chain C residue  443 ILE
Chi-restraints excluded: chain C residue  509 LEU
Chi-restraints excluded: chain A residue   51 GLN
Chi-restraints excluded: chain A residue  145 ASP
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  304 THR
Chi-restraints excluded: chain A residue  542 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 99 optimal weight:    0.0870
   chunk 102 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 98 optimal weight:    0.5980
   chunk 105 optimal weight:    0.0870
   chunk 94 optimal weight:    0.8980
   overall best weight:    0.5336

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

Flipped N/Q/H residues before XYZ refinement:
C 397 ASN
A 219 GLN
A 397 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.130841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.105064 restraints weight = 27106.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 1.69
r_work: 0.2900 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2771 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.0926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9025  Z= 0.124
  Angle     :  0.491  18.901  12189  Z= 0.271
  Chirality :  0.038   0.313   1324
  Planarity :  0.003   0.029   1587
  Dihedral  :  9.224  77.336   1267
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 18.23 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole:  0.31 (0.26), residues: 1088
  helix:  0.84 (0.21), residues: 655
  sheet: -0.68 (0.61), residues: 56
  loop : -0.64 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 298 
 TYR   0.012   0.001   TYR A 398 
 PHE   0.011   0.001   PHE A  49 
 TRP   0.008   0.001   TRP C 231 
 HIS   0.004   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9025)
  covalent geometry    : angle       0.49069 (12189)
  hydrogen bonds       : bond        0.03615 (  441)
  hydrogen bonds       : angle       4.32411 ( 1275)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   79 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue LYS  320 is missing expected H atoms. Skipping.
Evaluate side-chains
  133 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   31 GLN cc_start: 0.7608 (mt0) cc_final: 0.7364 (mp10)
REVERT: C   91 ASN cc_start: 0.8587 (t0) cc_final: 0.8189 (t0)
REVERT: C  253 TYR cc_start: 0.8257 (t80) cc_final: 0.8004 (t80)
REVERT: C  332 LYS cc_start: 0.8052 (tttp) cc_final: 0.6999 (mmtp)
REVERT: C  410 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7079 (mmtp)
REVERT: C  497 ARG cc_start: 0.6811 (mtp180) cc_final: 0.6470 (ttp80)
REVERT: A   51 GLN cc_start: 0.7716 (pt0) cc_final: 0.7434 (tt0)
REVERT: A   95 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7464 (mtt90)
REVERT: A  180 GLN cc_start: 0.6983 (mt0) cc_final: 0.6743 (mt0)
REVERT: A  248 GLN cc_start: 0.7371 (tp40) cc_final: 0.7124 (tt0)
REVERT: A  251 LYS cc_start: 0.7611 (tttm) cc_final: 0.7187 (tttm)
REVERT: A  373 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7401 (mptm)
  outliers start: 20
  outliers final: 11
  residues processed: 128
  average time/residue: 1.4753
  time to fit residues: 199.9076
Evaluate side-chains
  118 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 ASN
Chi-restraints excluded: chain C residue  276 SER
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  318 SER
Chi-restraints excluded: chain C residue  410 LYS
Chi-restraints excluded: chain C residue  443 ILE
Chi-restraints excluded: chain C residue  509 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  304 THR
Chi-restraints excluded: chain A residue  373 LYS
Chi-restraints excluded: chain A residue  377 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 80 optimal weight:    0.0040
   chunk 106 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0970
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
C 341 ASN
C 397 ASN
A  26 ASN
A 222 ASN
A 397 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.130683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.105300 restraints weight = 27034.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 1.63
r_work: 0.2927 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2798 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.1042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9025  Z= 0.135
  Angle     :  0.491  18.879  12189  Z= 0.272
  Chirality :  0.038   0.313   1324
  Planarity :  0.003   0.029   1587
  Dihedral  :  8.947  79.107   1259
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.23 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole:  0.34 (0.26), residues: 1088
  helix:  0.87 (0.21), residues: 657
  sheet: -0.63 (0.63), residues: 55
  loop : -0.67 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 298 
 TYR   0.013   0.001   TYR A 398 
 PHE   0.012   0.001   PHE C  49 
 TRP   0.008   0.001   TRP C 231 
 HIS   0.005   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 9025)
  covalent geometry    : angle       0.49147 (12189)
  hydrogen bonds       : bond        0.03640 (  441)
  hydrogen bonds       : angle       4.27143 ( 1275)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   79 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue LYS  320 is missing expected H atoms. Skipping.
Evaluate side-chains
  134 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   31 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7265 (mp10)
REVERT: C   91 ASN cc_start: 0.8561 (t0) cc_final: 0.8172 (t0)
REVERT: C   95 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6241 (mtm180)
REVERT: C  253 TYR cc_start: 0.8201 (t80) cc_final: 0.7933 (t80)
REVERT: C  332 LYS cc_start: 0.8080 (tttp) cc_final: 0.7058 (mmtp)
REVERT: C  410 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7091 (mmtp)
REVERT: C  497 ARG cc_start: 0.6745 (mtp180) cc_final: 0.6400 (ttp80)
REVERT: A   51 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7307 (tt0)
REVERT: A   95 ARG cc_start: 0.7883 (mtm-85) cc_final: 0.7502 (mtt90)
REVERT: A  145 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7274 (m-30)
REVERT: A  180 GLN cc_start: 0.6922 (mt0) cc_final: 0.6672 (mt0)
REVERT: A  248 GLN cc_start: 0.7279 (tp40) cc_final: 0.7036 (tt0)
REVERT: A  251 LYS cc_start: 0.7492 (tttm) cc_final: 0.7049 (tttm)
REVERT: A  373 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7294 (mptm)
  outliers start: 25
  outliers final: 11
  residues processed: 127
  average time/residue: 1.5136
  time to fit residues: 203.1189
Evaluate side-chains
  119 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 ASN
Chi-restraints excluded: chain C residue   31 GLN
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  276 SER
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  318 SER
Chi-restraints excluded: chain C residue  410 LYS
Chi-restraints excluded: chain C residue  443 ILE
Chi-restraints excluded: chain C residue  509 LEU
Chi-restraints excluded: chain A residue   51 GLN
Chi-restraints excluded: chain A residue  145 ASP
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  304 THR
Chi-restraints excluded: chain A residue  373 LYS
Chi-restraints excluded: chain A residue  377 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 102 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0970
   chunk 53 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.8178

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

Flipped N/Q/H residues before XYZ refinement:
C 397 ASN
A  26 ASN
A 219 GLN
A 397 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.129523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.104296 restraints weight = 27100.859|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 1.63
r_work: 0.2892 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2763 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9025  Z= 0.170
  Angle     :  0.516  18.705  12189  Z= 0.285
  Chirality :  0.039   0.311   1324
  Planarity :  0.003   0.031   1587
  Dihedral  :  9.119  79.875   1259
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 18.86 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole:  0.19 (0.26), residues: 1088
  helix:  0.76 (0.21), residues: 657
  sheet: -0.69 (0.61), residues: 55
  loop : -0.74 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 471 
 TYR   0.015   0.002   TYR A 398 
 PHE   0.014   0.001   PHE C  49 
 TRP   0.009   0.001   TRP C 231 
 HIS   0.006   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 9025)
  covalent geometry    : angle       0.51582 (12189)
  hydrogen bonds       : bond        0.03938 (  441)
  hydrogen bonds       : angle       4.33456 ( 1275)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   79 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue LYS  320 is missing expected H atoms. Skipping.
Evaluate side-chains
  128 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   31 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7319 (mp10)
REVERT: C   91 ASN cc_start: 0.8584 (t0) cc_final: 0.8197 (t0)
REVERT: C   95 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6124 (mtm180)
REVERT: C  253 TYR cc_start: 0.8226 (t80) cc_final: 0.7955 (t80)
REVERT: C  332 LYS cc_start: 0.8120 (tttp) cc_final: 0.7063 (mmtp)
REVERT: C  410 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7074 (mmtp)
REVERT: C  497 ARG cc_start: 0.6750 (mtp180) cc_final: 0.6392 (ttp80)
REVERT: A   51 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7317 (tt0)
REVERT: A   95 ARG cc_start: 0.7865 (mtm-85) cc_final: 0.7514 (mtt90)
REVERT: A  145 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7349 (m-30)
REVERT: A  180 GLN cc_start: 0.6918 (mt0) cc_final: 0.6608 (mt0)
REVERT: A  248 GLN cc_start: 0.7295 (tp40) cc_final: 0.7053 (tt0)
REVERT: A  251 LYS cc_start: 0.7518 (tttm) cc_final: 0.7073 (tttm)
REVERT: A  373 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7318 (mptm)
  outliers start: 23
  outliers final: 11
  residues processed: 121
  average time/residue: 1.5117
  time to fit residues: 193.4307
Evaluate side-chains
  120 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 ASN
Chi-restraints excluded: chain C residue   31 GLN
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  276 SER
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  318 SER
Chi-restraints excluded: chain C residue  410 LYS
Chi-restraints excluded: chain C residue  443 ILE
Chi-restraints excluded: chain C residue  509 LEU
Chi-restraints excluded: chain A residue   51 GLN
Chi-restraints excluded: chain A residue  145 ASP
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  304 THR
Chi-restraints excluded: chain A residue  373 LYS
Chi-restraints excluded: chain A residue  377 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0570
   chunk 62 optimal weight:    0.4980
   chunk 107 optimal weight:    0.9990
   chunk 40 optimal weight:    0.3980
   chunk 81 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
C 397 ASN
A  26 ASN
A 177 HIS
A 219 GLN
A 222 ASN
A 397 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.131016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.105348 restraints weight = 27087.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 1.67
r_work: 0.2907 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.1157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9025  Z= 0.119
  Angle     :  0.483  18.897  12189  Z= 0.266
  Chirality :  0.037   0.312   1324
  Planarity :  0.003   0.030   1587
  Dihedral  :  8.834  77.100   1259
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 19.70 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole:  0.40 (0.26), residues: 1088
  helix:  0.93 (0.21), residues: 658
  sheet: -0.80 (0.64), residues: 52
  loop : -0.63 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 298 
 TYR   0.015   0.001   TYR C 398 
 PHE   0.011   0.001   PHE A  49 
 TRP   0.008   0.001   TRP C 231 
 HIS   0.004   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9025)
  covalent geometry    : angle       0.48253 (12189)
  hydrogen bonds       : bond        0.03454 (  441)
  hydrogen bonds       : angle       4.17266 ( 1275)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   79 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue LYS  320 is missing expected H atoms. Skipping.
Evaluate side-chains
  123 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   31 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7289 (mp10)
REVERT: C   91 ASN cc_start: 0.8565 (t0) cc_final: 0.8189 (t0)
REVERT: C   95 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6124 (mtm180)
REVERT: C  253 TYR cc_start: 0.8209 (t80) cc_final: 0.7936 (t80)
REVERT: C  332 LYS cc_start: 0.8085 (tttp) cc_final: 0.7143 (mmtp)
REVERT: C  410 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7074 (mmtp)
REVERT: C  497 ARG cc_start: 0.6672 (mtp180) cc_final: 0.6321 (ttp80)
REVERT: A   51 GLN cc_start: 0.7584 (pt0) cc_final: 0.7307 (tt0)
REVERT: A   95 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7600 (mtt90)
REVERT: A  180 GLN cc_start: 0.6903 (mt0) cc_final: 0.6596 (mt0)
REVERT: A  248 GLN cc_start: 0.7310 (tp40) cc_final: 0.7040 (tt0)
REVERT: A  251 LYS cc_start: 0.7512 (tttm) cc_final: 0.7063 (tttm)
REVERT: A  373 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7323 (mptm)
  outliers start: 17
  outliers final: 11
  residues processed: 118
  average time/residue: 1.5481
  time to fit residues: 193.1322
Evaluate side-chains
  119 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 ASN
Chi-restraints excluded: chain C residue   31 GLN
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  276 SER
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  318 SER
Chi-restraints excluded: chain C residue  410 LYS
Chi-restraints excluded: chain C residue  443 ILE
Chi-restraints excluded: chain C residue  509 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  304 THR
Chi-restraints excluded: chain A residue  373 LYS
Chi-restraints excluded: chain A residue  377 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 22 optimal weight:    0.4980
   chunk 43 optimal weight:    0.0670
   chunk 20 optimal weight:    0.6980
   chunk 107 optimal weight:    0.9990
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
C 397 ASN
A 397 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.130621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.105210 restraints weight = 27022.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 1.63
r_work: 0.2892 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2761 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9025  Z= 0.135
  Angle     :  0.490  18.843  12189  Z= 0.271
  Chirality :  0.038   0.311   1324
  Planarity :  0.003   0.030   1587
  Dihedral  :  8.921  79.027   1259
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 19.60 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole:  0.38 (0.26), residues: 1088
  helix:  0.92 (0.21), residues: 659
  sheet: -0.83 (0.64), residues: 52
  loop : -0.65 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 114 
 TYR   0.013   0.001   TYR A 398 
 PHE   0.012   0.001   PHE C  49 
 TRP   0.009   0.001   TRP C 231 
 HIS   0.005   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 9025)
  covalent geometry    : angle       0.48970 (12189)
  hydrogen bonds       : bond        0.03559 (  441)
  hydrogen bonds       : angle       4.18578 ( 1275)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   79 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue LYS  320 is missing expected H atoms. Skipping.
Evaluate side-chains
  123 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   31 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.7179 (mp10)
REVERT: C   91 ASN cc_start: 0.8495 (t0) cc_final: 0.8120 (t0)
REVERT: C   95 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.6013 (mtm180)
REVERT: C  253 TYR cc_start: 0.8120 (t80) cc_final: 0.7838 (t80)
REVERT: C  332 LYS cc_start: 0.7965 (tttp) cc_final: 0.7025 (mmtp)
REVERT: C  410 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6868 (mmtp)
REVERT: C  497 ARG cc_start: 0.6567 (mtp180) cc_final: 0.6205 (ttp80)
REVERT: A   51 GLN cc_start: 0.7454 (pt0) cc_final: 0.7183 (tt0)
REVERT: A   95 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7498 (mtt90)
REVERT: A  180 GLN cc_start: 0.6768 (mt0) cc_final: 0.6458 (mt0)
REVERT: A  248 GLN cc_start: 0.7165 (tp40) cc_final: 0.6864 (tt0)
REVERT: A  251 LYS cc_start: 0.7328 (tttm) cc_final: 0.6859 (tttm)
REVERT: A  373 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7147 (mptm)
  outliers start: 19
  outliers final: 12
  residues processed: 118
  average time/residue: 1.5396
  time to fit residues: 191.9810
Evaluate side-chains
  119 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 ASN
Chi-restraints excluded: chain C residue   31 GLN
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  276 SER
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  318 SER
Chi-restraints excluded: chain C residue  398 TYR
Chi-restraints excluded: chain C residue  410 LYS
Chi-restraints excluded: chain C residue  443 ILE
Chi-restraints excluded: chain C residue  509 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  304 THR
Chi-restraints excluded: chain A residue  373 LYS
Chi-restraints excluded: chain A residue  377 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 85 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
C 397 ASN
A  26 ASN
A 219 GLN
A 222 ASN
A 347 GLN
A 397 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.129197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.103722 restraints weight = 27255.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 1.64
r_work: 0.2884 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2755 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9025  Z= 0.183
  Angle     :  0.527  18.689  12189  Z= 0.291
  Chirality :  0.039   0.309   1324
  Planarity :  0.003   0.031   1587
  Dihedral  :  9.177  80.054   1259
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 19.81 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole:  0.20 (0.26), residues: 1088
  helix:  0.76 (0.21), residues: 657
  sheet: -0.77 (0.62), residues: 55
  loop : -0.71 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 203 
 TYR   0.015   0.002   TYR A 398 
 PHE   0.015   0.002   PHE C  49 
 TRP   0.010   0.001   TRP C 231 
 HIS   0.006   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 9025)
  covalent geometry    : angle       0.52746 (12189)
  hydrogen bonds       : bond        0.04019 (  441)
  hydrogen bonds       : angle       4.32656 ( 1275)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   79 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue LYS  320 is missing expected H atoms. Skipping.
Evaluate side-chains
  123 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   31 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7354 (mp10)
REVERT: C   91 ASN cc_start: 0.8597 (t0) cc_final: 0.8211 (t0)
REVERT: C  253 TYR cc_start: 0.8247 (t80) cc_final: 0.8038 (t80)
REVERT: C  332 LYS cc_start: 0.8044 (tttp) cc_final: 0.7121 (mmtp)
REVERT: C  410 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.7017 (mmtp)
REVERT: C  497 ARG cc_start: 0.6799 (mtp180) cc_final: 0.6419 (ttp80)
REVERT: A   51 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7322 (tt0)
REVERT: A   95 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.7513 (mtt90)
REVERT: A  180 GLN cc_start: 0.6962 (mt0) cc_final: 0.6631 (mt0)
REVERT: A  248 GLN cc_start: 0.7321 (tp40) cc_final: 0.7083 (tt0)
REVERT: A  251 LYS cc_start: 0.7598 (tttm) cc_final: 0.7147 (tttm)
REVERT: A  373 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7348 (mptm)
  outliers start: 19
  outliers final: 12
  residues processed: 118
  average time/residue: 1.4893
  time to fit residues: 185.9277
Evaluate side-chains
  119 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 ASN
Chi-restraints excluded: chain C residue   31 GLN
Chi-restraints excluded: chain C residue  276 SER
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  318 SER
Chi-restraints excluded: chain C residue  398 TYR
Chi-restraints excluded: chain C residue  410 LYS
Chi-restraints excluded: chain C residue  443 ILE
Chi-restraints excluded: chain C residue  509 LEU
Chi-restraints excluded: chain A residue   51 GLN
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  304 THR
Chi-restraints excluded: chain A residue  373 LYS
Chi-restraints excluded: chain A residue  377 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 92 optimal weight:    0.7980
   chunk 99 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 98 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C 397 ASN
A 177 HIS
A 219 GLN
A 347 GLN
A 397 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.130268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.104861 restraints weight = 26922.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 1.63
r_work: 0.2902 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2773 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9025  Z= 0.138
  Angle     :  0.496  18.807  12189  Z= 0.274
  Chirality :  0.038   0.310   1324
  Planarity :  0.003   0.030   1587
  Dihedral  :  8.968  78.829   1259
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 20.13 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole:  0.31 (0.26), residues: 1088
  helix:  0.87 (0.21), residues: 658
  sheet: -0.85 (0.65), residues: 52
  loop : -0.69 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 114 
 TYR   0.014   0.002   TYR A 398 
 PHE   0.011   0.001   PHE C  49 
 TRP   0.008   0.001   TRP C 231 
 HIS   0.005   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9025)
  covalent geometry    : angle       0.49573 (12189)
  hydrogen bonds       : bond        0.03614 (  441)
  hydrogen bonds       : angle       4.20699 ( 1275)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   79 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue LYS  320 is missing expected H atoms. Skipping.
Evaluate side-chains
  119 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   31 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7289 (mp10)
REVERT: C   91 ASN cc_start: 0.8573 (t0) cc_final: 0.8188 (t0)
REVERT: C   95 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.6180 (mtm180)
REVERT: C  253 TYR cc_start: 0.8192 (t80) cc_final: 0.7912 (t80)
REVERT: C  332 LYS cc_start: 0.7944 (tttp) cc_final: 0.7070 (mmtp)
REVERT: C  410 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6957 (mmtp)
REVERT: C  497 ARG cc_start: 0.6777 (mtp180) cc_final: 0.6390 (ttp80)
REVERT: A   51 GLN cc_start: 0.7572 (pt0) cc_final: 0.7302 (tt0)
REVERT: A   95 ARG cc_start: 0.7921 (mtm-85) cc_final: 0.7572 (mtt90)
REVERT: A  180 GLN cc_start: 0.6910 (mt0) cc_final: 0.6601 (mt0)
REVERT: A  248 GLN cc_start: 0.7288 (tp40) cc_final: 0.7029 (tt0)
REVERT: A  251 LYS cc_start: 0.7500 (tttm) cc_final: 0.7049 (tttm)
REVERT: A  373 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7317 (mptm)
REVERT: A  459 THR cc_start: 0.8820 (m) cc_final: 0.8611 (p)
  outliers start: 16
  outliers final: 11
  residues processed: 115
  average time/residue: 1.6073
  time to fit residues: 194.9550
Evaluate side-chains
  119 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 ASN
Chi-restraints excluded: chain C residue   31 GLN
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  276 SER
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  318 SER
Chi-restraints excluded: chain C residue  410 LYS
Chi-restraints excluded: chain C residue  443 ILE
Chi-restraints excluded: chain C residue  509 LEU
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  304 THR
Chi-restraints excluded: chain A residue  373 LYS
Chi-restraints excluded: chain A residue  377 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 104 optimal weight:    0.9980
   chunk 106 optimal weight:    0.1980
   chunk 94 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   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 397 ASN
A  26 ASN
A 222 ASN
A 397 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.130039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.104700 restraints weight = 27148.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 1.63
r_work: 0.2883 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.1228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9025  Z= 0.149
  Angle     :  0.505  18.820  12189  Z= 0.278
  Chirality :  0.038   0.303   1324
  Planarity :  0.003   0.068   1587
  Dihedral  :  8.999  79.156   1259
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 20.02 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole:  0.28 (0.26), residues: 1088
  helix:  0.85 (0.21), residues: 661
  sheet: -0.90 (0.65), residues: 52
  loop : -0.72 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C 543 
 TYR   0.014   0.002   TYR A 398 
 PHE   0.013   0.001   PHE C  49 
 TRP   0.009   0.001   TRP C 231 
 HIS   0.006   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 9025)
  covalent geometry    : angle       0.50498 (12189)
  hydrogen bonds       : bond        0.03694 (  441)
  hydrogen bonds       : angle       4.22708 ( 1275)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 5879.27 seconds
wall clock time: 100 minutes 8.92 seconds (6008.92 seconds total)