Starting phenix.real_space_refine
on Tue Mar  3 15:26:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kmb_22922/03_2026/7kmb_22922.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kmb_22922/03_2026/7kmb_22922.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kmb_22922/03_2026/7kmb_22922.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kmb_22922/03_2026/7kmb_22922.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kmb_22922/03_2026/7kmb_22922.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kmb_22922/03_2026/7kmb_22922.map"
  }
  resolution = 3.39
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4159      2.51       5
     N    1067      2.21       5
     O    1246      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6509
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "F"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    Chain: "G"
      Number of atoms: 1521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1521
          Classifications: {'peptide': 192}
          Link IDs: {'PTRANS': 10, 'TRANS': 181}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 1.24, per 1000 atoms: 0.19
  Number of scatterers: 6509
  At special positions: 0
  Unit cell: (99.452, 75.118, 111.09, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1246      8.00
     N    1067      7.00
     C    4159      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS F 133 " - pdb=" SG  CYS F 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 344 " - pdb=" SG  CYS F 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 530 " - pdb=" SG  CYS F 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 336 " - pdb=" SG  CYS G 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 379 " - pdb=" SG  CYS G 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 391 " - pdb=" SG  CYS G 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 480 " - pdb=" SG  CYS G 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG A   1 " - " ASN F 546 "
      " NAG B   1 " - " ASN G 343 "
      " NAG F 701 " - " ASN F 322 "
      " NAG F 702 " - " ASN F 432 "
      " NAG F 703 " - " ASN F 103 "
      " NAG F 704 " - " ASN F  90 "
      " NAG F 705 " - " ASN F  53 "
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 232.7 milliseconds
  

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1482

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 4 sheets defined
      52.8% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'F' and resid 20 through 51
      removed outlier: 3.788A  pdb=" N   HIS F  34 " --> pdb=" O   ASP F  30 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ASP F  38 " --> pdb=" O   HIS F  34 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 55 through 82
      removed outlier: 3.796A  pdb=" N   VAL F  59 " --> pdb=" O   THR F  55 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   GLN F  60 " --> pdb=" O   GLU F  56 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA F  65 " --> pdb=" O   ASN F  61 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   THR F  78 " --> pdb=" O   LYS F  74 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   MET F  82 " --> pdb=" O   THR F  78 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 91 through 101
      removed outlier: 3.714A  pdb=" N   GLN F  96 " --> pdb=" O   THR F  92 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 109 through 128
      removed outlier: 4.551A  pdb=" N   ARG F 115 " --> pdb=" O   ASP F 111 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   LEU F 116 " --> pdb=" O   LYS F 112 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   ASN F 117 " --> pdb=" O   SER F 113 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   THR F 118 " --> pdb=" O   LYS F 114 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ILE F 119 " --> pdb=" O   ARG F 115 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 143 through 154
      removed outlier: 4.223A  pdb=" N   ASN F 149 " --> pdb=" O   GLU F 145 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   GLU F 150 " --> pdb=" O   PRO F 146 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ILE F 151 " --> pdb=" O   GLY F 147 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   MET F 152 " --> pdb=" O   LEU F 148 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 157 through 170
      removed outlier: 3.751A  pdb=" N   TRP F 168 " --> pdb=" O   ALA F 164 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   SER F 170 " --> pdb=" O   GLU F 166 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 172 through 175
      removed outlier: 3.608A  pdb=" N   GLN F 175 " --> pdb=" O   VAL F 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 172 through 175'
    Processing helix  chain 'F' and resid 176 through 194
      removed outlier: 3.607A  pdb=" N   GLU F 181 " --> pdb=" O   ARG F 177 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLU F 182 " --> pdb=" O   PRO F 178 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LEU F 186 " --> pdb=" O   GLU F 182 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ASN F 188 " --> pdb=" O   VAL F 184 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   GLU F 189 " --> pdb=" O   VAL F 185 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ALA F 191 " --> pdb=" O   LYS F 187 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   ARG F 192 " --> pdb=" O   ASN F 188 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA F 193 " --> pdb=" O   GLU F 189 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 198 through 204
      removed outlier: 3.569A  pdb=" N   ARG F 204 " --> pdb=" O   GLY F 200 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 220 through 249
      removed outlier: 3.707A  pdb=" N   GLU F 224 " --> pdb=" O   GLY F 220 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   GLU F 231 " --> pdb=" O   GLU F 227 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   GLU F 232 " --> pdb=" O   HIS F 228 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ILE F 233 " --> pdb=" O   THR F 229 " (cutoff:3.500A)
      Proline residue:  F 235  - end of helix
      removed outlier: 3.778A  pdb=" N   HIS F 239 " --> pdb=" O   PRO F 235 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA F 246 " --> pdb=" O   ALA F 242 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   MET F 249 " --> pdb=" O   ARG F 245 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 265 through 267
      No H-bonds generated for 'chain 'F' and resid 265 through 267'
    Processing helix  chain 'F' and resid 275 through 279
    Processing helix  chain 'F' and resid 293 through 300
      removed outlier: 3.967A  pdb=" N   VAL F 298 " --> pdb=" O   THR F 294 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ASP F 299 " --> pdb=" O   ASP F 295 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLN F 300 " --> pdb=" O   ALA F 296 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 303 through 319
      removed outlier: 3.543A  pdb=" N   PHE F 308 " --> pdb=" O   ALA F 304 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ALA F 311 " --> pdb=" O   ILE F 307 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 324 through 329
      removed outlier: 4.140A  pdb=" N   TRP F 328 " --> pdb=" O   THR F 324 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   GLU F 329 " --> pdb=" O   GLN F 325 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 324 through 329'
    Processing helix  chain 'F' and resid 365 through 383
      removed outlier: 3.925A  pdb=" N   HIS F 378 " --> pdb=" O   HIS F 374 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ILE F 379 " --> pdb=" O   GLU F 375 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 399 through 413
      removed outlier: 4.040A  pdb=" N   GLY F 405 " --> pdb=" O   HIS F 401 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLU F 406 " --> pdb=" O   GLU F 402 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   MET F 408 " --> pdb=" O   VAL F 404 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   SER F 409 " --> pdb=" O   GLY F 405 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 414 through 422
    Processing helix  chain 'F' and resid 432 through 447
      removed outlier: 4.082A  pdb=" N   PHE F 438 " --> pdb=" O   THR F 434 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   THR F 445 " --> pdb=" O   LYS F 441 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 449 through 466
    Processing helix  chain 'F' and resid 469 through 471
      No H-bonds generated for 'chain 'F' and resid 469 through 471'
    Processing helix  chain 'F' and resid 472 through 484
      removed outlier: 3.703A  pdb=" N   LYS F 476 " --> pdb=" O   GLN F 472 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLU F 479 " --> pdb=" O   LYS F 475 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 498 through 502
    Processing helix  chain 'F' and resid 503 through 508
    Processing helix  chain 'F' and resid 512 through 523
      removed outlier: 4.074A  pdb=" N   TYR F 516 " --> pdb=" O   PHE F 512 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   THR F 519 " --> pdb=" O   TYR F 515 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU F 520 " --> pdb=" O   TYR F 516 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 523 through 533
    Processing helix  chain 'F' and resid 547 through 559
      removed outlier: 3.966A  pdb=" N   MET F 557 " --> pdb=" O   LYS F 553 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 565 through 572
      removed outlier: 3.632A  pdb=" N   GLU F 571 " --> pdb=" O   THR F 567 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 581 through 586
      removed outlier: 4.132A  pdb=" N   LEU F 585 " --> pdb=" O   VAL F 581 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ASN F 586 " --> pdb=" O   ARG F 582 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 581 through 586'
    Processing helix  chain 'F' and resid 588 through 599
      removed outlier: 3.636A  pdb=" N   TRP F 594 " --> pdb=" O   PRO F 590 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 338 through 343
    Processing helix  chain 'G' and resid 365 through 370
      removed outlier: 3.675A  pdb=" N   TYR G 369 " --> pdb=" O   TYR G 365 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ASN G 370 " --> pdb=" O   SER G 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 365 through 370'
    Processing helix  chain 'G' and resid 385 through 390
      removed outlier: 3.978A  pdb=" N   ASP G 389 " --> pdb=" O   THR G 385 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 405 through 410
      removed outlier: 4.508A  pdb=" N   ARG G 408 " --> pdb=" O   ASP G 405 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 417 through 422
    Processing helix  chain 'G' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'F' and resid 262 through 263
      removed outlier: 5.664A  pdb=" N   LEU F 262 " --> pdb=" O   VAL F 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'F' and resid 347 through 352
      removed outlier: 6.023A  pdb=" N   ASP F 355 " --> pdb=" O   LEU F 351 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'G' and resid 354 through 356
      removed outlier: 3.604A  pdb=" N   ASN G 354 " --> pdb=" O   SER G 399 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL G 510 " --> pdb=" O   PHE G 400 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 452 through 454

    236 hydrogen bonds defined for protein.
    675 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.88

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2068
        1.35 -     1.47: 1771
        1.47 -     1.59: 2792
        1.59 -     1.72: 0
        1.72 -     1.84: 58
  Bond restraints: 6689
  Sorted by residual:
  bond pdb=" C1  NAG A   1 "
       pdb=" O5  NAG A   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.17e+00
  bond pdb=" C1  NAG F 705 "
       pdb=" O5  NAG F 705 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 4.07e+00
  bond pdb=" C1  NAG F 703 "
       pdb=" O5  NAG F 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.445 -0.039 2.00e-02 2.50e+03 3.81e+00
  bond pdb=" C1  NAG F 702 "
       pdb=" O5  NAG F 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.445 -0.039 2.00e-02 2.50e+03 3.74e+00
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.57e+00
  ... (remaining 6684 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 8914
        2.29 -     4.57: 143
        4.57 -     6.86: 19
        6.86 -     9.14: 13
        9.14 -    11.43: 2
  Bond angle restraints: 9091
  Sorted by residual:
  angle pdb=" CB  MET F 152 "
        pdb=" CG  MET F 152 "
        pdb=" SD  MET F 152 "
      ideal   model   delta    sigma   weight residual
     112.70  124.13  -11.43 3.00e+00 1.11e-01 1.45e+01
  angle pdb=" CA  MET F 557 "
        pdb=" CB  MET F 557 "
        pdb=" CG  MET F 557 "
      ideal   model   delta    sigma   weight residual
     114.10  121.21   -7.11 2.00e+00 2.50e-01 1.27e+01
  angle pdb=" CB  MET F 557 "
        pdb=" CG  MET F 557 "
        pdb=" SD  MET F 557 "
      ideal   model   delta    sigma   weight residual
     112.70  123.33  -10.63 3.00e+00 1.11e-01 1.26e+01
  angle pdb=" N   ASP F 499 "
        pdb=" CA  ASP F 499 "
        pdb=" C   ASP F 499 "
      ideal   model   delta    sigma   weight residual
     109.81  117.51   -7.70 2.21e+00 2.05e-01 1.21e+01
  angle pdb=" CB  GLU F 238 "
        pdb=" CG  GLU F 238 "
        pdb=" CD  GLU F 238 "
      ideal   model   delta    sigma   weight residual
     112.60  118.18   -5.58 1.70e+00 3.46e-01 1.08e+01
  ... (remaining 9086 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 3596
       17.56 -    35.12: 373
       35.12 -    52.68: 70
       52.68 -    70.24: 17
       70.24 -    87.80: 5
  Dihedral angle restraints: 4061
    sinusoidal: 1750
      harmonic: 2311
  Sorted by residual:
  dihedral pdb=" CB  CYS G 336 "
           pdb=" SG  CYS G 336 "
           pdb=" SG  CYS G 361 "
           pdb=" CB  CYS G 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   26.69   66.31     1      1.00e+01 1.00e-02 5.74e+01
  dihedral pdb=" CB  CYS F 530 "
           pdb=" SG  CYS F 530 "
           pdb=" SG  CYS F 542 "
           pdb=" CB  CYS F 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -122.53   36.53     1      1.00e+01 1.00e-02 1.89e+01
  dihedral pdb=" SG  CYS G 391 "
           pdb=" CB  CYS G 525 "
           pdb=" SG  CYS G 525 "
           pdb=" CA  CYS G 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   16.22   62.78     1      2.00e+01 2.50e-03 1.30e+01
  ... (remaining 4058 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 594
       0.036 -    0.072: 267
       0.072 -    0.108: 84
       0.108 -    0.144: 25
       0.144 -    0.180: 7
  Chirality restraints: 977
  Sorted by residual:
  chirality pdb=" CB  VAL F 364 "
            pdb=" CA  VAL F 364 "
            pdb=" CG1 VAL F 364 "
            pdb=" CG2 VAL F 364 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.81    0.18 2.00e-01 2.50e+01 8.07e-01
  chirality pdb=" CA  ASP F 499 "
            pdb=" N   ASP F 499 "
            pdb=" C   ASP F 499 "
            pdb=" CB  ASP F 499 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.82e-01
  chirality pdb=" CA  ILE F 468 "
            pdb=" N   ILE F 468 "
            pdb=" C   ILE F 468 "
            pdb=" CB  ILE F 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.81e-01
  ... (remaining 974 not shown)

  Planarity restraints: 1174
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL G 395 "   -0.012 2.00e-02 2.50e+03   2.42e-02 5.85e+00
        pdb=" C   VAL G 395 "    0.042 2.00e-02 2.50e+03
        pdb=" O   VAL G 395 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   TYR G 396 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F 491 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.67e+00
        pdb=" C   VAL F 491 "    0.028 2.00e-02 2.50e+03
        pdb=" O   VAL F 491 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   PRO F 492 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL F 491 "   -0.026 5.00e-02 4.00e+02   3.95e-02 2.49e+00
        pdb=" N   PRO F 492 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO F 492 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO F 492 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1171 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2005
        2.82 -     3.34: 5801
        3.34 -     3.86: 10775
        3.86 -     4.38: 12487
        4.38 -     4.90: 21006
  Nonbonded interactions: 52074
  Sorted by model distance:
  nonbonded pdb=" O   ALA F 501 "
            pdb=" OG  SER F 507 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   ILE F 544 "
            pdb=" OG  SER F 547 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   THR F 118 "
            pdb=" OG1 THR F 122 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OG  SER G 438 "
            pdb=" O   PRO G 507 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   GLU F 406 "
            pdb=" OG  SER F 409 "
     model   vdw
     2.342 3.040
  ... (remaining 52069 not shown)

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

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:             5.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.130
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
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   0.041   6705  Z= 0.174
  Angle     :  0.751  11.430   9132  Z= 0.370
  Chirality :  0.047   0.180    977
  Planarity :  0.005   0.039   1167
  Dihedral  : 14.633  87.805   2558
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.57 (0.24), residues: 784
  helix: -3.19 (0.17), residues: 348
  sheet: -0.40 (0.79), residues: 41
  loop : -1.70 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G 466 
 TYR   0.018   0.001   TYR G 396 
 PHE   0.009   0.001   PHE G 486 
 TRP   0.011   0.001   TRP F 478 
 HIS   0.006   0.001   HIS F 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 6689)
  covalent geometry    : angle       0.74145 ( 9091)
  SS BOND              : bond        0.00214 (    7)
  SS BOND              : angle       1.70651 (   14)
  hydrogen bonds       : bond        0.30483 (  236)
  hydrogen bonds       : angle       9.17138 (  675)
  link_BETA1-4         : bond        0.00548 (    2)
  link_BETA1-4         : angle       0.75241 (    6)
  link_NAG-ASN         : bond        0.00363 (    7)
  link_NAG-ASN         : angle       2.22106 (   21)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  121 ASN cc_start: 0.8003 (m110) cc_final: 0.7788 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.0689
  time to fit residues: 8.3362
Evaluate side-chains
  66 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.2980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0870
   overall best weight:    0.7760

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

Flipped N/Q/H residues before XYZ refinement:
F 188 ASN
F 373 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.094372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.082810 restraints weight = 17727.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 2.96
r_work: 0.3309 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6705  Z= 0.147
  Angle     :  0.609   8.334   9132  Z= 0.310
  Chirality :  0.042   0.148    977
  Planarity :  0.004   0.030   1167
  Dihedral  :  4.964  46.235   1045
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 10.13 %
    Favored  : 89.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.06 (0.27), residues: 784
  helix: -1.15 (0.25), residues: 342
  sheet: -0.32 (0.70), residues: 42
  loop : -1.64 (0.28), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G 466 
 TYR   0.022   0.001   TYR F 183 
 PHE   0.012   0.001   PHE F 369 
 TRP   0.012   0.001   TRP F 165 
 HIS   0.011   0.001   HIS F 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6689)
  covalent geometry    : angle       0.60113 ( 9091)
  SS BOND              : bond        0.00498 (    7)
  SS BOND              : angle       1.08833 (   14)
  hydrogen bonds       : bond        0.06140 (  236)
  hydrogen bonds       : angle       5.40600 (  675)
  link_BETA1-4         : bond        0.00300 (    2)
  link_BETA1-4         : angle       0.79150 (    6)
  link_NAG-ASN         : bond        0.00251 (    7)
  link_NAG-ASN         : angle       1.92750 (   21)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  441 LYS cc_start: 0.8699 (tmtt) cc_final: 0.8457 (tmtt)
  outliers start: 4
  outliers final: 2
  residues processed: 74
  average time/residue: 0.0682
  time to fit residues: 7.1652
Evaluate side-chains
  69 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   82 MET
Chi-restraints excluded: chain F residue   91 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 27 optimal weight:    0.4980
   chunk 71 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0570
   chunk 41 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 40 optimal weight:    0.4980
   chunk 11 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.5298

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.094347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.082881 restraints weight = 17498.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 2.96
r_work: 0.3312 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6705  Z= 0.115
  Angle     :  0.541   6.527   9132  Z= 0.273
  Chirality :  0.041   0.146    977
  Planarity :  0.003   0.029   1167
  Dihedral  :  4.471  39.084   1045
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 13.60 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.28), residues: 784
  helix: -0.40 (0.27), residues: 342
  sheet: -0.56 (0.69), residues: 42
  loop : -1.50 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G 466 
 TYR   0.018   0.001   TYR F 183 
 PHE   0.010   0.001   PHE F 523 
 TRP   0.010   0.001   TRP F  69 
 HIS   0.012   0.001   HIS F 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 6689)
  covalent geometry    : angle       0.53405 ( 9091)
  SS BOND              : bond        0.00191 (    7)
  SS BOND              : angle       0.92210 (   14)
  hydrogen bonds       : bond        0.04977 (  236)
  hydrogen bonds       : angle       4.76747 (  675)
  link_BETA1-4         : bond        0.00505 (    2)
  link_BETA1-4         : angle       0.76351 (    6)
  link_NAG-ASN         : bond        0.00232 (    7)
  link_NAG-ASN         : angle       1.80797 (   21)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  332 MET cc_start: 0.6989 (ppp) cc_final: 0.6607 (ptt)
REVERT: F  441 LYS cc_start: 0.8715 (tmtt) cc_final: 0.8483 (tmtt)
  outliers start: 4
  outliers final: 3
  residues processed: 69
  average time/residue: 0.0698
  time to fit residues: 6.7964
Evaluate side-chains
  65 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   82 MET
Chi-restraints excluded: chain F residue  276 THR
Chi-restraints excluded: chain F residue  450 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
F 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.092280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.080999 restraints weight = 17606.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.85
r_work: 0.3290 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6705  Z= 0.149
  Angle     :  0.560   6.812   9132  Z= 0.284
  Chirality :  0.043   0.146    977
  Planarity :  0.003   0.028   1167
  Dihedral  :  4.390  28.825   1045
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 14.91 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.17 (0.29), residues: 784
  helix: -0.07 (0.27), residues: 351
  sheet: -0.68 (0.71), residues: 42
  loop : -1.42 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G 466 
 TYR   0.020   0.001   TYR G 396 
 PHE   0.010   0.001   PHE F 523 
 TRP   0.011   0.001   TRP F 610 
 HIS   0.010   0.001   HIS F 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6689)
  covalent geometry    : angle       0.55095 ( 9091)
  SS BOND              : bond        0.00314 (    7)
  SS BOND              : angle       1.07138 (   14)
  hydrogen bonds       : bond        0.04436 (  236)
  hydrogen bonds       : angle       4.51438 (  675)
  link_BETA1-4         : bond        0.00253 (    2)
  link_BETA1-4         : angle       0.83013 (    6)
  link_NAG-ASN         : bond        0.00287 (    7)
  link_NAG-ASN         : angle       1.94228 (   21)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.191 
Fit side-chains
REVERT: F  332 MET cc_start: 0.7244 (ppp) cc_final: 0.6934 (ptt)
REVERT: G  355 ARG cc_start: 0.8250 (ttt90) cc_final: 0.7777 (ptm160)
  outliers start: 6
  outliers final: 3
  residues processed: 70
  average time/residue: 0.0668
  time to fit residues: 6.6287
Evaluate side-chains
  64 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   82 MET
Chi-restraints excluded: chain F residue  276 THR
Chi-restraints excluded: chain F residue  408 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.093564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.082383 restraints weight = 17833.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 2.94
r_work: 0.3270 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6705  Z= 0.136
  Angle     :  0.565   6.424   9132  Z= 0.284
  Chirality :  0.042   0.149    977
  Planarity :  0.003   0.029   1167
  Dihedral  :  4.314  24.556   1045
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.77 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.29), residues: 784
  helix:  0.15 (0.28), residues: 351
  sheet: -0.54 (0.73), residues: 41
  loop : -1.40 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 466 
 TYR   0.018   0.001   TYR F 183 
 PHE   0.012   0.001   PHE F 504 
 TRP   0.019   0.001   TRP F 610 
 HIS   0.010   0.001   HIS F 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6689)
  covalent geometry    : angle       0.55680 ( 9091)
  SS BOND              : bond        0.00277 (    7)
  SS BOND              : angle       1.04513 (   14)
  hydrogen bonds       : bond        0.04264 (  236)
  hydrogen bonds       : angle       4.38720 (  675)
  link_BETA1-4         : bond        0.00364 (    2)
  link_BETA1-4         : angle       0.84404 (    6)
  link_NAG-ASN         : bond        0.00244 (    7)
  link_NAG-ASN         : angle       1.96479 (   21)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.233 
Fit side-chains
REVERT: F  288 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6602 (ptpt)
REVERT: G  355 ARG cc_start: 0.8340 (ttt90) cc_final: 0.7653 (ptm160)
  outliers start: 12
  outliers final: 6
  residues processed: 72
  average time/residue: 0.0675
  time to fit residues: 6.9017
Evaluate side-chains
  63 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   82 MET
Chi-restraints excluded: chain F residue  276 THR
Chi-restraints excluded: chain F residue  288 LYS
Chi-restraints excluded: chain F residue  408 MET
Chi-restraints excluded: chain F residue  570 LEU
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  510 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0000
   chunk 70 optimal weight:    3.9990
   chunk 32 optimal weight:    0.4980
   chunk 69 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 71 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
F 134 ASN
F 524 GLN
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 460 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.093066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.081815 restraints weight = 17585.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.86
r_work: 0.3303 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6705  Z= 0.114
  Angle     :  0.575   7.474   9132  Z= 0.287
  Chirality :  0.042   0.150    977
  Planarity :  0.003   0.029   1167
  Dihedral  :  4.187  21.532   1045
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 15.92 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.29), residues: 784
  helix:  0.30 (0.28), residues: 351
  sheet: -0.56 (0.75), residues: 41
  loop : -1.40 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 192 
 TYR   0.018   0.001   TYR F 183 
 PHE   0.012   0.001   PHE F 504 
 TRP   0.012   0.001   TRP F 610 
 HIS   0.009   0.001   HIS F 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6689)
  covalent geometry    : angle       0.56414 ( 9091)
  SS BOND              : bond        0.00488 (    7)
  SS BOND              : angle       1.76017 (   14)
  hydrogen bonds       : bond        0.04059 (  236)
  hydrogen bonds       : angle       4.23820 (  675)
  link_BETA1-4         : bond        0.00414 (    2)
  link_BETA1-4         : angle       0.84340 (    6)
  link_NAG-ASN         : bond        0.00223 (    7)
  link_NAG-ASN         : angle       1.99137 (   21)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: F  116 LEU cc_start: 0.7918 (tt) cc_final: 0.7662 (mt)
REVERT: F  261 CYS cc_start: 0.7655 (m) cc_final: 0.7356 (m)
REVERT: F  288 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6795 (ptpt)
REVERT: F  366 MET cc_start: 0.8422 (mmm) cc_final: 0.8179 (mmm)
REVERT: F  593 THR cc_start: 0.8562 (m) cc_final: 0.8345 (p)
REVERT: G  355 ARG cc_start: 0.8193 (ttt90) cc_final: 0.7603 (ptm160)
  outliers start: 11
  outliers final: 9
  residues processed: 76
  average time/residue: 0.0716
  time to fit residues: 7.5502
Evaluate side-chains
  72 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain F residue   82 MET
Chi-restraints excluded: chain F residue  271 TRP
Chi-restraints excluded: chain F residue  276 THR
Chi-restraints excluded: chain F residue  288 LYS
Chi-restraints excluded: chain F residue  364 VAL
Chi-restraints excluded: chain F residue  408 MET
Chi-restraints excluded: chain F residue  570 LEU
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  510 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 43 optimal weight:    0.1980
   chunk 32 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.092561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.081322 restraints weight = 17545.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 2.89
r_work: 0.3288 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6705  Z= 0.120
  Angle     :  0.568   6.812   9132  Z= 0.283
  Chirality :  0.042   0.151    977
  Planarity :  0.003   0.029   1167
  Dihedral  :  4.099  17.576   1045
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 16.21 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.29), residues: 784
  helix:  0.34 (0.28), residues: 351
  sheet: -0.56 (0.75), residues: 41
  loop : -1.35 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 192 
 TYR   0.018   0.001   TYR F 183 
 PHE   0.013   0.001   PHE F 504 
 TRP   0.010   0.001   TRP F 610 
 HIS   0.008   0.001   HIS F 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6689)
  covalent geometry    : angle       0.55840 ( 9091)
  SS BOND              : bond        0.00529 (    7)
  SS BOND              : angle       1.32753 (   14)
  hydrogen bonds       : bond        0.04005 (  236)
  hydrogen bonds       : angle       4.22201 (  675)
  link_BETA1-4         : bond        0.00379 (    2)
  link_BETA1-4         : angle       0.84977 (    6)
  link_NAG-ASN         : bond        0.00230 (    7)
  link_NAG-ASN         : angle       2.00555 (   21)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: F  116 LEU cc_start: 0.7948 (tt) cc_final: 0.7731 (mt)
REVERT: F  261 CYS cc_start: 0.7696 (m) cc_final: 0.7384 (m)
REVERT: F  288 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6765 (ptpt)
REVERT: F  593 THR cc_start: 0.8619 (m) cc_final: 0.8383 (p)
REVERT: G  355 ARG cc_start: 0.8232 (ttt90) cc_final: 0.7587 (ptm160)
  outliers start: 12
  outliers final: 9
  residues processed: 76
  average time/residue: 0.0723
  time to fit residues: 7.8911
Evaluate side-chains
  72 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain F residue   82 MET
Chi-restraints excluded: chain F residue  271 TRP
Chi-restraints excluded: chain F residue  276 THR
Chi-restraints excluded: chain F residue  288 LYS
Chi-restraints excluded: chain F residue  364 VAL
Chi-restraints excluded: chain F residue  408 MET
Chi-restraints excluded: chain F residue  570 LEU
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  510 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0870
   chunk 2 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.7762

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

Flipped N/Q/H residues before XYZ refinement:
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.091713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.080735 restraints weight = 17652.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 2.81
r_work: 0.3279 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6705  Z= 0.139
  Angle     :  0.611  11.366   9132  Z= 0.301
  Chirality :  0.043   0.151    977
  Planarity :  0.003   0.031   1167
  Dihedral  :  4.208  17.601   1045
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 17.22 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.29), residues: 784
  helix:  0.27 (0.28), residues: 358
  sheet: -0.58 (0.76), residues: 41
  loop : -1.24 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 460 
 TYR   0.018   0.001   TYR F 183 
 PHE   0.013   0.001   PHE F 504 
 TRP   0.009   0.001   TRP F 610 
 HIS   0.009   0.001   HIS F 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6689)
  covalent geometry    : angle       0.59860 ( 9091)
  SS BOND              : bond        0.00514 (    7)
  SS BOND              : angle       2.13472 (   14)
  hydrogen bonds       : bond        0.03996 (  236)
  hydrogen bonds       : angle       4.31131 (  675)
  link_BETA1-4         : bond        0.00378 (    2)
  link_BETA1-4         : angle       0.90938 (    6)
  link_NAG-ASN         : bond        0.00259 (    7)
  link_NAG-ASN         : angle       2.03968 (   21)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: F  116 LEU cc_start: 0.8004 (tt) cc_final: 0.7804 (mt)
REVERT: F  261 CYS cc_start: 0.7704 (m) cc_final: 0.7430 (m)
REVERT: F  288 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6795 (ptpt)
REVERT: F  593 THR cc_start: 0.8615 (m) cc_final: 0.8383 (p)
REVERT: G  355 ARG cc_start: 0.8257 (ttt90) cc_final: 0.7617 (ptm160)
  outliers start: 12
  outliers final: 10
  residues processed: 71
  average time/residue: 0.0750
  time to fit residues: 7.5074
Evaluate side-chains
  73 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain F residue   82 MET
Chi-restraints excluded: chain F residue  271 TRP
Chi-restraints excluded: chain F residue  276 THR
Chi-restraints excluded: chain F residue  288 LYS
Chi-restraints excluded: chain F residue  364 VAL
Chi-restraints excluded: chain F residue  408 MET
Chi-restraints excluded: chain F residue  570 LEU
Chi-restraints excluded: chain G residue  392 PHE
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  510 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0040
   chunk 57 optimal weight:    0.9990
   chunk 22 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0770
   chunk 44 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0470
   chunk 13 optimal weight:    0.3980
   overall best weight:    0.1648

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

Flipped N/Q/H residues before XYZ refinement:
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.095453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.084274 restraints weight = 17736.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 2.92
r_work: 0.3320 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.067   6705  Z= 0.104
  Angle     :  0.576   7.254   9132  Z= 0.283
  Chirality :  0.041   0.155    977
  Planarity :  0.003   0.030   1167
  Dihedral  :  3.836  16.503   1045
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 17.22 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.29), residues: 784
  helix:  0.30 (0.29), residues: 359
  sheet: -0.60 (0.74), residues: 41
  loop : -1.28 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 192 
 TYR   0.018   0.001   TYR F 183 
 PHE   0.013   0.001   PHE F 504 
 TRP   0.010   0.001   TRP F 610 
 HIS   0.009   0.001   HIS F 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6689)
  covalent geometry    : angle       0.56533 ( 9091)
  SS BOND              : bond        0.00376 (    7)
  SS BOND              : angle       1.54505 (   14)
  hydrogen bonds       : bond        0.03806 (  236)
  hydrogen bonds       : angle       4.14226 (  675)
  link_BETA1-4         : bond        0.00551 (    2)
  link_BETA1-4         : angle       0.83554 (    6)
  link_NAG-ASN         : bond        0.00233 (    7)
  link_NAG-ASN         : angle       1.97096 (   21)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
REVERT: F  261 CYS cc_start: 0.7856 (m) cc_final: 0.7494 (m)
REVERT: F  288 LYS cc_start: 0.6784 (OUTLIER) cc_final: 0.6543 (ptpt)
REVERT: F  366 MET cc_start: 0.8476 (mmm) cc_final: 0.8130 (tmm)
REVERT: F  593 THR cc_start: 0.8660 (m) cc_final: 0.8390 (p)
  outliers start: 11
  outliers final: 8
  residues processed: 78
  average time/residue: 0.0645
  time to fit residues: 7.2865
Evaluate side-chains
  73 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain F residue  271 TRP
Chi-restraints excluded: chain F residue  276 THR
Chi-restraints excluded: chain F residue  288 LYS
Chi-restraints excluded: chain F residue  364 VAL
Chi-restraints excluded: chain F residue  570 LEU
Chi-restraints excluded: chain G residue  392 PHE
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  510 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 60 optimal weight:    0.2980
   chunk 58 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.092637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.081520 restraints weight = 17691.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 2.87
r_work: 0.3295 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   6705  Z= 0.135
  Angle     :  0.604   7.337   9132  Z= 0.304
  Chirality :  0.043   0.150    977
  Planarity :  0.003   0.031   1167
  Dihedral  :  4.001  16.398   1045
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 17.51 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.30), residues: 784
  helix:  0.27 (0.28), residues: 361
  sheet: -0.58 (0.74), residues: 41
  loop : -1.22 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 460 
 TYR   0.045   0.001   TYR F  50 
 PHE   0.013   0.001   PHE F 504 
 TRP   0.013   0.001   TRP F 168 
 HIS   0.007   0.001   HIS F 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6689)
  covalent geometry    : angle       0.59494 ( 9091)
  SS BOND              : bond        0.00421 (    7)
  SS BOND              : angle       1.25635 (   14)
  hydrogen bonds       : bond        0.03950 (  236)
  hydrogen bonds       : angle       4.28151 (  675)
  link_BETA1-4         : bond        0.00400 (    2)
  link_BETA1-4         : angle       0.87392 (    6)
  link_NAG-ASN         : bond        0.00233 (    7)
  link_NAG-ASN         : angle       2.02989 (   21)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
REVERT: F  116 LEU cc_start: 0.7924 (mt) cc_final: 0.7655 (tt)
REVERT: F  261 CYS cc_start: 0.7669 (m) cc_final: 0.7362 (m)
REVERT: F  288 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6688 (ptpt)
REVERT: F  593 THR cc_start: 0.8634 (m) cc_final: 0.8387 (p)
REVERT: G  355 ARG cc_start: 0.8381 (ttt90) cc_final: 0.7707 (ptm160)
  outliers start: 10
  outliers final: 9
  residues processed: 75
  average time/residue: 0.0668
  time to fit residues: 7.2307
Evaluate side-chains
  75 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain F residue   82 MET
Chi-restraints excluded: chain F residue  132 VAL
Chi-restraints excluded: chain F residue  271 TRP
Chi-restraints excluded: chain F residue  276 THR
Chi-restraints excluded: chain F residue  288 LYS
Chi-restraints excluded: chain F residue  364 VAL
Chi-restraints excluded: chain F residue  570 LEU
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  510 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
F 194 ASN
** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.090967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.079846 restraints weight = 17882.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 2.91
r_work: 0.3264 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   6705  Z= 0.155
  Angle     :  0.627   9.478   9132  Z= 0.316
  Chirality :  0.044   0.149    977
  Planarity :  0.003   0.035   1167
  Dihedral  :  4.258  19.110   1045
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 17.66 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.30), residues: 784
  helix:  0.27 (0.28), residues: 360
  sheet: -0.58 (0.76), residues: 41
  loop : -1.23 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 466 
 TYR   0.046   0.001   TYR F  50 
 PHE   0.013   0.001   PHE F 504 
 TRP   0.011   0.001   TRP F 168 
 HIS   0.009   0.001   HIS F 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 6689)
  covalent geometry    : angle       0.61706 ( 9091)
  SS BOND              : bond        0.00437 (    7)
  SS BOND              : angle       1.47779 (   14)
  hydrogen bonds       : bond        0.04069 (  236)
  hydrogen bonds       : angle       4.33000 (  675)
  link_BETA1-4         : bond        0.00354 (    2)
  link_BETA1-4         : angle       0.98538 (    6)
  link_NAG-ASN         : bond        0.00274 (    7)
  link_NAG-ASN         : angle       2.13314 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1386.67 seconds
wall clock time: 24 minutes 34.13 seconds (1474.13 seconds total)