Starting phenix.real_space_refine
on Tue Mar  3 22:58:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zwa_14995/03_2026/7zwa_14995.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zwa_14995/03_2026/7zwa_14995.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zwa_14995/03_2026/7zwa_14995.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zwa_14995/03_2026/7zwa_14995.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zwa_14995/03_2026/7zwa_14995.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zwa_14995/03_2026/7zwa_14995.map"
  }
  resolution = 2.8
  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=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      32      5.49       5
     S      42      5.16       5
     C    5678      2.51       5
     N    1532      2.21       5
     O    1754      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  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: 9038
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4009
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 503, 4009
          Classifications: {'peptide': 503}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 27, 'TRANS': 475}
          Unresolved non-hydrogen bonds: 58
          Unresolved non-hydrogen angles: 68
          Unresolved non-hydrogen dihedrals: 51
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "B"
      Number of atoms: 4222
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 529, 4222
          Classifications: {'peptide': 529}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 26, 'TRANS': 502}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 165
          Classifications: {'peptide': 23}
          Link IDs: {'PTRANS': 3, 'TRANS': 19}
    Chain: "D"
      Number of atoms: 304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 304
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "E"
      Number of atoms: 333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 333
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'PO4': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.20, per 1000 atoms: 0.24
  Number of scatterers: 9038
  At special positions: 0
  Unit cell: (92.95, 87.75, 141.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      42     16.00
     P      32     15.00
     O    1754      8.00
     N    1532      7.00
     C    5678      6.00
    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: 0.80
  Conformation dependent library (CDL) restraints added in 318.1 milliseconds
  

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2010

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 10 sheets defined
      37.5% alpha, 20.9% beta
      6 base pairs and 24 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 3.801A  pdb=" N   GLU A  50 " --> pdb=" O   ALA A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 78
    Processing helix  chain 'A' and resid 112 through 121
    Processing helix  chain 'A' and resid 123 through 135
      removed outlier: 3.974A  pdb=" N   GLY A 127 " --> pdb=" O   LYS A 123 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   LYS A 129 " --> pdb=" O   GLN A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 157
      removed outlier: 4.074A  pdb=" N   VAL A 157 " --> pdb=" O   LEU A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 178
      removed outlier: 3.613A  pdb=" N   GLY A 177 " --> pdb=" O   ASP A 173 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ASN A 178 " --> pdb=" O   ASN A 174 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 173 through 178'
    Processing helix  chain 'A' and resid 179 through 197
    Processing helix  chain 'A' and resid 238 through 244
    Processing helix  chain 'A' and resid 312 through 314
      No H-bonds generated for 'chain 'A' and resid 312 through 314'
    Processing helix  chain 'A' and resid 330 through 337
    Processing helix  chain 'A' and resid 354 through 356
      No H-bonds generated for 'chain 'A' and resid 354 through 356'
    Processing helix  chain 'A' and resid 377 through 393
    Processing helix  chain 'A' and resid 439 through 443
      removed outlier: 3.586A  pdb=" N   LYS A 443 " --> pdb=" O   ALA A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 469
    Processing helix  chain 'A' and resid 480 through 496
    Processing helix  chain 'A' and resid 510 through 519
    Processing helix  chain 'A' and resid 520 through 530
    Processing helix  chain 'B' and resid 17 through 22
    Processing helix  chain 'B' and resid 29 through 48
    Processing helix  chain 'B' and resid 87 through 96
    Processing helix  chain 'B' and resid 106 through 123
      removed outlier: 4.041A  pdb=" N   ILE B 123 " --> pdb=" O   GLN B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 158
    Processing helix  chain 'B' and resid 198 through 217
    Processing helix  chain 'B' and resid 218 through 222
      removed outlier: 3.755A  pdb=" N   LEU B 221 " --> pdb=" O   GLU B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 231
    Processing helix  chain 'B' and resid 232 through 233
      No H-bonds generated for 'chain 'B' and resid 232 through 233'
    Processing helix  chain 'B' and resid 234 through 238
    Processing helix  chain 'B' and resid 306 through 308
      No H-bonds generated for 'chain 'B' and resid 306 through 308'
    Processing helix  chain 'B' and resid 324 through 332
    Processing helix  chain 'B' and resid 349 through 351
      No H-bonds generated for 'chain 'B' and resid 349 through 351'
    Processing helix  chain 'B' and resid 352 through 356
    Processing helix  chain 'B' and resid 370 through 388
    Processing helix  chain 'B' and resid 447 through 461
    Processing helix  chain 'B' and resid 478 through 482
    Processing helix  chain 'B' and resid 484 through 500
      removed outlier: 4.013A  pdb=" N   GLN B 488 " --> pdb=" O   ASN B 484 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 509 through 517
    Processing helix  chain 'B' and resid 519 through 526
    Processing helix  chain 'B' and resid 526 through 537
      removed outlier: 3.555A  pdb=" N   LEU B 530 " --> pdb=" O   SER B 526 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 104
      removed outlier: 6.902A  pdb=" N   ARG A  35 " --> pdb=" O   SER A 162 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   LYS A 164 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 7.382A  pdb=" N   SER A  37 " --> pdb=" O   LYS A 164 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   ILE A 166 " --> pdb=" O   SER A  37 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   ILE A  39 " --> pdb=" O   ILE A 166 " (cutoff:3.500A)
      removed outlier: 5.420A  pdb=" N   LEU A 168 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   LEU A  41 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
      removed outlier: 5.365A  pdb=" N   THR A 170 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   ASP A  43 " --> pdb=" O   THR A 170 " (cutoff:3.500A)
      removed outlier: 8.655A  pdb=" N   PHE A 199 " --> pdb=" O   SER A 162 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   LYS A 164 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   ASP A 201 " --> pdb=" O   LYS A 164 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ILE A 166 " --> pdb=" O   ASP A 201 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   MET A 203 " --> pdb=" O   ILE A 166 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   LEU A 168 " --> pdb=" O   MET A 203 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 262
      removed outlier: 3.689A  pdb=" N   SER A 257 " --> pdb=" O   ILE A 273 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   VAL A 394 " --> pdb=" O   PRO A 415 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ARG A 399 " --> pdb=" O   LEU A 347 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   LEU A 347 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   THR A 401 " --> pdb=" O   LEU A 345 " (cutoff:3.500A)
      removed outlier: 5.676A  pdb=" N   LEU A 345 " --> pdb=" O   THR A 401 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 289
    Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 304
      removed outlier: 3.797A  pdb=" N   PHE A 303 " --> pdb=" O   GLN B 290 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLN B 290 " --> pdb=" O   PHE A 303 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 329
    Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 376
    Processing sheet with id=AA7, first strand: chain 'A' and resid 419 through 420
      removed outlier: 6.652A  pdb=" N   GLU A 419 " --> pdb=" O   VAL A 427 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 84
      removed outlier: 6.339A  pdb=" N   LEU B  56 " --> pdb=" O   HIS B  80 " (cutoff:3.500A)
      removed outlier: 5.172A  pdb=" N   HIS B  82 " --> pdb=" O   ILE B  54 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   ILE B  54 " --> pdb=" O   HIS B  82 " (cutoff:3.500A)
      removed outlier: 8.486A  pdb=" N   GLN B 162 " --> pdb=" O   ARG B 130 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ILE B 132 " --> pdb=" O   GLN B 162 " (cutoff:3.500A)
      removed outlier: 8.224A  pdb=" N   PHE B 164 " --> pdb=" O   ILE B 132 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   ILE B 134 " --> pdb=" O   PHE B 164 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   PHE B 163 " --> pdb=" O   TYR B 225 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 247 through 253
      removed outlier: 3.554A  pdb=" N   LEU B 257 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   VAL B 361 " --> pdb=" O   SER B 266 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   LEU B 268 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 9.945A  pdb=" N   ASN B 359 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
      removed outlier: 8.288A  pdb=" N   GLN B 360 " --> pdb=" O   GLN B 423 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   GLN B 423 " --> pdb=" O   GLN B 360 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   ALA B 366 " --> pdb=" O   GLU B 417 " (cutoff:3.500A)
      removed outlier: 9.814A  pdb=" N   GLU B 417 " --> pdb=" O   ALA B 366 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   VAL B 405 " --> pdb=" O   LEU B 424 " (cutoff:3.500A)
      removed outlier: 9.078A  pdb=" N   MET B 389 " --> pdb=" O   PRO B 410 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   VAL B 390 " --> pdb=" O   PHE B 345 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   PHE B 345 " --> pdb=" O   VAL B 390 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ILE B 392 " --> pdb=" O   LEU B 343 " (cutoff:3.500A)
      removed outlier: 8.077A  pdb=" N   PHE B 340 " --> pdb=" O   PRO B 248 " (cutoff:3.500A)
      removed outlier: 5.628A  pdb=" N   ARG B 250 " --> pdb=" O   PHE B 340 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   VAL B 342 " --> pdb=" O   ARG B 250 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   THR B 252 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   GLY B 344 " --> pdb=" O   THR B 252 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 466

    367 hydrogen bonds defined for protein.
    1023 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      16 hydrogen bonds
      32 hydrogen bond angles
      0 basepair planarities
      6 basepair parallelities
      24 stacking parallelities
  Total time for adding SS restraints: 1.49

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2463
        1.33 -     1.45: 1551
        1.45 -     1.57: 5139
        1.57 -     1.69: 60
        1.69 -     1.81: 70
  Bond restraints: 9283
  Sorted by residual:
  bond pdb=" O3  PO4 A 701 "
       pdb=" P   PO4 A 701 "
    ideal  model  delta    sigma   weight residual
    1.569  1.510  0.059 2.00e-02 2.50e+03 8.84e+00
  bond pdb=" O4  PO4 A 701 "
       pdb=" P   PO4 A 701 "
    ideal  model  delta    sigma   weight residual
    1.568  1.510  0.058 2.00e-02 2.50e+03 8.48e+00
  bond pdb=" O2  PO4 A 701 "
       pdb=" P   PO4 A 701 "
    ideal  model  delta    sigma   weight residual
    1.567  1.509  0.058 2.00e-02 2.50e+03 8.31e+00
  bond pdb=" O1  PO4 A 701 "
       pdb=" P   PO4 A 701 "
    ideal  model  delta    sigma   weight residual
    1.565  1.510  0.055 2.00e-02 2.50e+03 7.70e+00
  bond pdb=" C3'  DT E   4 "
       pdb=" O3'  DT E   4 "
    ideal  model  delta    sigma   weight residual
    1.422  1.456 -0.034 3.00e-02 1.11e+03 1.27e+00
  ... (remaining 9278 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 12338
        1.37 -     2.73: 262
        2.73 -     4.10: 47
        4.10 -     5.47: 12
        5.47 -     6.84: 1
  Bond angle restraints: 12660
  Sorted by residual:
  angle pdb=" N   GLY A 127 "
        pdb=" CA  GLY A 127 "
        pdb=" C   GLY A 127 "
      ideal   model   delta    sigma   weight residual
     112.77  108.96    3.81 1.28e+00 6.10e-01 8.85e+00
  angle pdb=" C   LEU B 215 "
        pdb=" N   GLU B 216 "
        pdb=" CA  GLU B 216 "
      ideal   model   delta    sigma   weight residual
     122.79  117.67    5.12 1.78e+00 3.16e-01 8.27e+00
  angle pdb=" C   GLN A 125 "
        pdb=" N   GLN A 126 "
        pdb=" CA  GLN A 126 "
      ideal   model   delta    sigma   weight residual
     121.54  126.57   -5.03 1.91e+00 2.74e-01 6.95e+00
  angle pdb=" C   ASN B 514 "
        pdb=" N   MET B 515 "
        pdb=" CA  MET B 515 "
      ideal   model   delta    sigma   weight residual
     120.31  117.13    3.18 1.52e+00 4.33e-01 4.37e+00
  angle pdb=" N   PHE B 107 "
        pdb=" CA  PHE B 107 "
        pdb=" C   PHE B 107 "
      ideal   model   delta    sigma   weight residual
     113.01  110.50    2.51 1.20e+00 6.94e-01 4.36e+00
  ... (remaining 12655 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.58: 5407
       35.58 -    71.16: 204
       71.16 -   106.74: 9
      106.74 -   142.32: 0
      142.32 -   177.90: 1
  Dihedral angle restraints: 5621
    sinusoidal: 2533
      harmonic: 3088
  Sorted by residual:
  dihedral pdb=" C4'  DT E   4 "
           pdb=" C3'  DT E   4 "
           pdb=" O3'  DT E   4 "
           pdb=" P    DC E   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   42.10  177.90     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  ASP B 398 "
           pdb=" CB  ASP B 398 "
           pdb=" CG  ASP B 398 "
           pdb=" OD1 ASP B 398 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.85   58.85     1      2.00e+01 2.50e-03 1.16e+01
  dihedral pdb=" CA  ASP B  72 "
           pdb=" C   ASP B  72 "
           pdb=" N   GLN B  73 "
           pdb=" CA  GLN B  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.66   16.34     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 5618 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 853
       0.028 -    0.057: 358
       0.057 -    0.085: 117
       0.085 -    0.113: 77
       0.113 -    0.141: 14
  Chirality restraints: 1419
  Sorted by residual:
  chirality pdb=" CA  GLU B 216 "
            pdb=" N   GLU B 216 "
            pdb=" C   GLU B 216 "
            pdb=" CB  GLU B 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.00e-01
  chirality pdb=" CA  ILE B  24 "
            pdb=" N   ILE B  24 "
            pdb=" C   ILE B  24 "
            pdb=" CB  ILE B  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.97e-01
  chirality pdb=" CA  ILE A 213 "
            pdb=" N   ILE A 213 "
            pdb=" C   ILE A 213 "
            pdb=" CB  ILE A 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.82e-01
  ... (remaining 1416 not shown)

  Planarity restraints: 1523
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 126 "    0.010 2.00e-02 2.50e+03   2.07e-02 4.28e+00
        pdb=" C   GLN A 126 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   GLN A 126 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLY A 127 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 211 "    0.013 2.00e-02 2.50e+03   1.39e-02 3.37e+00
        pdb=" CG  PHE A 211 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 211 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 211 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 211 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 211 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 211 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 518 "    0.021 5.00e-02 4.00e+02   3.18e-02 1.62e+00
        pdb=" N   PRO B 519 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO B 519 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 519 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1520 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1188
        2.76 -     3.29: 8601
        3.29 -     3.83: 15153
        3.83 -     4.36: 17888
        4.36 -     4.90: 30091
  Nonbonded interactions: 72921
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 409 "
            pdb=" OE1 GLN B 269 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" ND2 ASN A 171 "
            pdb=" O   LYS A 206 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" OG  SER A  78 "
            pdb=" OD2 ASP A  81 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OE1 GLU B 223 "
            pdb=" OH  TYR B 225 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   ILE B 118 "
            pdb=" OG1 THR B 122 "
     model   vdw
     2.254 3.040
  ... (remaining 72916 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.900
  Find NCS groups from input model:        0.050
  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:6.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9283  Z= 0.131
  Angle     :  0.512   6.835  12660  Z= 0.280
  Chirality :  0.040   0.141   1419
  Planarity :  0.003   0.032   1523
  Dihedral  : 16.751 177.899   3611
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  0.85 (0.26), residues: 1047
  helix:  1.93 (0.29), residues: 336
  sheet:  0.39 (0.41), residues: 164
  loop : -0.21 (0.26), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 271 
 TYR   0.010   0.001   TYR A 103 
 PHE   0.032   0.001   PHE A 211 
 TRP   0.004   0.001   TRP B 247 
 HIS   0.002   0.000   HIS A 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9283)
  covalent geometry    : angle       0.51249 (12660)
  hydrogen bonds       : bond        0.15424 (  383)
  hydrogen bonds       : angle       6.18194 ( 1055)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A  128 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8299 (pm20)
REVERT: A  129 LYS cc_start: 0.9077 (mppt) cc_final: 0.8755 (mptt)
REVERT: A  216 PHE cc_start: 0.8415 (t80) cc_final: 0.8174 (t80)
REVERT: A  265 LYS cc_start: 0.8929 (pttp) cc_final: 0.8656 (pptt)
REVERT: C  184 SER cc_start: 0.9008 (t) cc_final: 0.8794 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.7166
  time to fit residues: 104.2897
Evaluate side-chains
  91 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 204 HIS
A 304 ASN
B 269 GLN
B 312 GLN
B 440 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.108990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.070375 restraints weight = 15465.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 3.09
r_work: 0.2652 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.1063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9283  Z= 0.163
  Angle     :  0.556   6.597  12660  Z= 0.291
  Chirality :  0.042   0.139   1419
  Planarity :  0.004   0.031   1523
  Dihedral  : 17.662 177.766   1467
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 10.49 %
    Favored  : 88.33 %
  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:  0.91 (0.26), residues: 1047
  helix:  2.03 (0.29), residues: 336
  sheet:  0.15 (0.39), residues: 164
  loop : -0.10 (0.26), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 315 
 TYR   0.012   0.001   TYR A 409 
 PHE   0.013   0.001   PHE B  18 
 TRP   0.005   0.001   TRP B 247 
 HIS   0.003   0.001   HIS B 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 9283)
  covalent geometry    : angle       0.55621 (12660)
  hydrogen bonds       : bond        0.04015 (  383)
  hydrogen bonds       : angle       4.81508 ( 1055)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A   48 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8368 (mtp)
REVERT: A   99 PHE cc_start: 0.7711 (m-10) cc_final: 0.7509 (m-10)
REVERT: A  128 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8341 (pm20)
REVERT: A  129 LYS cc_start: 0.9149 (mppt) cc_final: 0.8845 (mptt)
REVERT: A  265 LYS cc_start: 0.9065 (pttp) cc_final: 0.8789 (pptt)
REVERT: A  299 LYS cc_start: 0.8863 (mtmm) cc_final: 0.8601 (mtmm)
REVERT: B  270 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8653 (tt0)
REVERT: C  184 SER cc_start: 0.8968 (t) cc_final: 0.8763 (t)
  outliers start: 11
  outliers final: 3
  residues processed: 114
  average time/residue: 0.6331
  time to fit residues: 76.7976
Evaluate side-chains
  104 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 MET
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  270 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 98 optimal weight:    0.0670
   chunk 101 optimal weight:    0.9980
   chunk 84 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.7122

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

Flipped N/Q/H residues before XYZ refinement:
B 432 GLN
B 440 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.109410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.070876 restraints weight = 15191.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 3.07
r_work: 0.2657 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.1293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9283  Z= 0.128
  Angle     :  0.516   5.918  12660  Z= 0.273
  Chirality :  0.040   0.138   1419
  Planarity :  0.003   0.030   1523
  Dihedral  : 17.588 177.896   1467
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.31 %
    Favored  : 86.08 %
  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:  0.95 (0.26), residues: 1047
  helix:  2.10 (0.29), residues: 336
  sheet:  0.20 (0.41), residues: 155
  loop : -0.11 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 502 
 TYR   0.013   0.001   TYR A 289 
 PHE   0.011   0.001   PHE B  18 
 TRP   0.003   0.001   TRP B 247 
 HIS   0.003   0.000   HIS B 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9283)
  covalent geometry    : angle       0.51627 (12660)
  hydrogen bonds       : bond        0.03510 (  383)
  hydrogen bonds       : angle       4.58418 ( 1055)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8330 (mtp)
REVERT: A   99 PHE cc_start: 0.7858 (m-10) cc_final: 0.7649 (m-80)
REVERT: A  128 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8166 (pm20)
REVERT: B  328 GLU cc_start: 0.9426 (OUTLIER) cc_final: 0.9218 (tt0)
  outliers start: 15
  outliers final: 6
  residues processed: 111
  average time/residue: 0.5741
  time to fit residues: 68.1747
Evaluate side-chains
  103 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 MET
Chi-restraints excluded: chain A residue  161 MET
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  448 PHE
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  296 CYS
Chi-restraints excluded: chain B residue  328 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 47 optimal weight:    0.1980
   chunk 87 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0980
   chunk 31 optimal weight:    2.9990
   chunk 4 optimal weight:    0.4980
   chunk 15 optimal weight:    5.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B  43 GLN
B 432 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.110677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.072326 restraints weight = 15566.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 3.13
r_work: 0.2674 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.1446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9283  Z= 0.112
  Angle     :  0.519   6.695  12660  Z= 0.271
  Chirality :  0.040   0.138   1419
  Planarity :  0.003   0.031   1523
  Dihedral  : 17.544 178.278   1467
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 14.88 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.26), residues: 1047
  helix:  2.00 (0.29), residues: 342
  sheet:  0.18 (0.41), residues: 155
  loop : -0.12 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 502 
 TYR   0.009   0.001   TYR A 289 
 PHE   0.012   0.001   PHE B  18 
 TRP   0.003   0.001   TRP B 247 
 HIS   0.002   0.000   HIS B 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 9283)
  covalent geometry    : angle       0.51854 (12660)
  hydrogen bonds       : bond        0.03272 (  383)
  hydrogen bonds       : angle       4.47984 ( 1055)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8246 (mtp)
REVERT: A  128 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8288 (pm20)
REVERT: B  242 ARG cc_start: 0.7990 (mtp85) cc_final: 0.7565 (ttm-80)
  outliers start: 9
  outliers final: 6
  residues processed: 107
  average time/residue: 0.5999
  time to fit residues: 68.5595
Evaluate side-chains
  103 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 MET
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain B residue   40 MET
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  296 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 43 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 100 optimal weight:    6.9990
   chunk 96 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 19 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
B 104 GLN
** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 382 HIS
B 432 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.107313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.068332 restraints weight = 15379.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.2778 rms_B_bonded: 3.10
r_work: 0.2607 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9283  Z= 0.211
  Angle     :  0.560   7.365  12660  Z= 0.291
  Chirality :  0.042   0.149   1419
  Planarity :  0.003   0.034   1523
  Dihedral  : 17.653 176.197   1467
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.52 %
    Favored  : 82.44 %
  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:  0.89 (0.26), residues: 1047
  helix:  2.03 (0.29), residues: 335
  sheet:  0.18 (0.40), residues: 153
  loop : -0.13 (0.26), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 502 
 TYR   0.010   0.001   TYR A 409 
 PHE   0.025   0.001   PHE A 216 
 TRP   0.003   0.001   TRP B 276 
 HIS   0.005   0.001   HIS B 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 9283)
  covalent geometry    : angle       0.55988 (12660)
  hydrogen bonds       : bond        0.03900 (  383)
  hydrogen bonds       : angle       4.58630 ( 1055)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A   48 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8347 (mtp)
REVERT: A   99 PHE cc_start: 0.8108 (m-80) cc_final: 0.7509 (m-10)
REVERT: A  128 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8368 (pm20)
REVERT: A  129 LYS cc_start: 0.9193 (mppt) cc_final: 0.8900 (mptt)
REVERT: A  199 PHE cc_start: 0.8511 (t80) cc_final: 0.8291 (t80)
REVERT: A  201 ASP cc_start: 0.8406 (m-30) cc_final: 0.8114 (m-30)
REVERT: B  242 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7635 (ttm-80)
  outliers start: 19
  outliers final: 7
  residues processed: 111
  average time/residue: 0.5545
  time to fit residues: 66.2001
Evaluate side-chains
  106 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 MET
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  448 PHE
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  296 CYS
Chi-restraints excluded: chain B residue  310 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 83 optimal weight:    0.3980
   chunk 104 optimal weight:    2.9990
   chunk 84 optimal weight:    0.6980
   chunk 89 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 94 optimal weight:    0.6980
   chunk 17 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 432 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.109791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.070975 restraints weight = 15356.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 3.14
r_work: 0.2653 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.1696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9283  Z= 0.124
  Angle     :  0.530   8.987  12660  Z= 0.278
  Chirality :  0.040   0.137   1419
  Planarity :  0.003   0.031   1523
  Dihedral  : 17.529 177.381   1467
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.74 %
    Favored  : 81.80 %
  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:  0.94 (0.26), residues: 1047
  helix:  2.07 (0.29), residues: 335
  sheet:  0.13 (0.40), residues: 155
  loop : -0.08 (0.26), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 502 
 TYR   0.009   0.001   TYR A  88 
 PHE   0.013   0.001   PHE B  59 
 TRP   0.003   0.001   TRP B 247 
 HIS   0.003   0.000   HIS A 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9283)
  covalent geometry    : angle       0.52987 (12660)
  hydrogen bonds       : bond        0.03309 (  383)
  hydrogen bonds       : angle       4.48263 ( 1055)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8383 (mtp)
REVERT: A   99 PHE cc_start: 0.8062 (m-80) cc_final: 0.7451 (m-10)
REVERT: A  128 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8167 (pm20)
REVERT: A  199 PHE cc_start: 0.8524 (t80) cc_final: 0.8308 (t80)
REVERT: A  201 ASP cc_start: 0.8388 (m-30) cc_final: 0.8098 (m-30)
REVERT: B  242 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7652 (ttm-80)
REVERT: B  328 GLU cc_start: 0.9445 (OUTLIER) cc_final: 0.9179 (tt0)
REVERT: B  368 ARG cc_start: 0.8667 (mtm110) cc_final: 0.8428 (mtp85)
  outliers start: 23
  outliers final: 9
  residues processed: 117
  average time/residue: 0.5455
  time to fit residues: 68.5013
Evaluate side-chains
  107 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 MET
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  161 MET
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  448 PHE
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  296 CYS
Chi-restraints excluded: chain B residue  328 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0570
   chunk 59 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9980
   chunk 78 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.1702

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

Flipped N/Q/H residues before XYZ refinement:
** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 432 GLN
B 440 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.108829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.069815 restraints weight = 15425.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.2793 rms_B_bonded: 3.15
r_work: 0.2619 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9283  Z= 0.163
  Angle     :  0.554   8.710  12660  Z= 0.287
  Chirality :  0.041   0.135   1419
  Planarity :  0.003   0.033   1523
  Dihedral  : 17.571 176.853   1467
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.45 %
    Favored  : 80.73 %
  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:  0.96 (0.26), residues: 1047
  helix:  2.06 (0.29), residues: 335
  sheet:  0.25 (0.40), residues: 153
  loop : -0.08 (0.26), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 502 
 TYR   0.010   0.001   TYR A 361 
 PHE   0.029   0.001   PHE A 216 
 TRP   0.003   0.001   TRP B 276 
 HIS   0.003   0.001   HIS B 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 9283)
  covalent geometry    : angle       0.55444 (12660)
  hydrogen bonds       : bond        0.03520 (  383)
  hydrogen bonds       : angle       4.49064 ( 1055)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8368 (mtp)
REVERT: A   99 PHE cc_start: 0.8084 (m-80) cc_final: 0.7497 (m-10)
REVERT: A  128 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8151 (pm20)
REVERT: A  199 PHE cc_start: 0.8512 (t80) cc_final: 0.8301 (t80)
REVERT: A  201 ASP cc_start: 0.8445 (m-30) cc_final: 0.8137 (m-30)
REVERT: A  265 LYS cc_start: 0.9193 (ptmm) cc_final: 0.8710 (pptt)
REVERT: B  242 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7658 (ttm-80)
REVERT: B  328 GLU cc_start: 0.9449 (OUTLIER) cc_final: 0.9197 (tt0)
REVERT: B  368 ARG cc_start: 0.8701 (mtm110) cc_final: 0.8452 (mtp85)
  outliers start: 17
  outliers final: 8
  residues processed: 108
  average time/residue: 0.5530
  time to fit residues: 64.3628
Evaluate side-chains
  104 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 MET
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  448 PHE
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  296 CYS
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  328 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 93 optimal weight:    3.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 432 GLN
B 440 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.109142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.070131 restraints weight = 15316.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.2786 rms_B_bonded: 3.13
r_work: 0.2610 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9283  Z= 0.158
  Angle     :  0.560   9.668  12660  Z= 0.289
  Chirality :  0.041   0.138   1419
  Planarity :  0.003   0.033   1523
  Dihedral  : 17.558 176.556   1467
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 18.20 %
    Favored  : 80.19 %
  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:  0.93 (0.26), residues: 1047
  helix:  2.01 (0.29), residues: 335
  sheet:  0.14 (0.39), residues: 159
  loop : -0.04 (0.26), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 502 
 TYR   0.009   0.001   TYR A  88 
 PHE   0.017   0.001   PHE C 190 
 TRP   0.004   0.001   TRP B 276 
 HIS   0.003   0.000   HIS B 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 9283)
  covalent geometry    : angle       0.55999 (12660)
  hydrogen bonds       : bond        0.03472 (  383)
  hydrogen bonds       : angle       4.51798 ( 1055)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8363 (mtp)
REVERT: A   99 PHE cc_start: 0.8056 (m-80) cc_final: 0.7498 (m-10)
REVERT: A  128 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8131 (pm20)
REVERT: A  199 PHE cc_start: 0.8493 (t80) cc_final: 0.8263 (t80)
REVERT: A  201 ASP cc_start: 0.8451 (m-30) cc_final: 0.8117 (m-30)
REVERT: A  250 GLU cc_start: 0.8604 (tp30) cc_final: 0.8375 (tp30)
REVERT: A  265 LYS cc_start: 0.9180 (ptmm) cc_final: 0.8702 (pptt)
REVERT: B  242 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7640 (ttm-80)
REVERT: B  328 GLU cc_start: 0.9448 (OUTLIER) cc_final: 0.9174 (tt0)
REVERT: B  368 ARG cc_start: 0.8706 (mtm110) cc_final: 0.8437 (mtp85)
  outliers start: 15
  outliers final: 8
  residues processed: 110
  average time/residue: 0.5711
  time to fit residues: 67.5771
Evaluate side-chains
  111 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 MET
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  448 PHE
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  296 CYS
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  328 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 74 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0970
   chunk 98 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0040
   chunk 90 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 105 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 312 GLN
B 432 GLN
B 440 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.110942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.072318 restraints weight = 15254.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 3.14
r_work: 0.2683 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9283  Z= 0.111
  Angle     :  0.547   9.209  12660  Z= 0.283
  Chirality :  0.040   0.137   1419
  Planarity :  0.003   0.032   1523
  Dihedral  : 17.471 178.142   1467
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 18.20 %
    Favored  : 80.19 %
  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:  1.00 (0.26), residues: 1047
  helix:  2.07 (0.29), residues: 335
  sheet:  0.20 (0.41), residues: 155
  loop : -0.01 (0.26), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG B 141 
 TYR   0.010   0.001   TYR A 103 
 PHE   0.031   0.001   PHE A 216 
 TRP   0.005   0.001   TRP B 247 
 HIS   0.002   0.000   HIS B 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 9283)
  covalent geometry    : angle       0.54679 (12660)
  hydrogen bonds       : bond        0.03094 (  383)
  hydrogen bonds       : angle       4.46768 ( 1055)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8361 (mtp)
REVERT: A   99 PHE cc_start: 0.8017 (m-80) cc_final: 0.7438 (m-10)
REVERT: A  128 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8122 (pm20)
REVERT: A  199 PHE cc_start: 0.8515 (t80) cc_final: 0.8272 (t80)
REVERT: A  201 ASP cc_start: 0.8471 (m-30) cc_final: 0.8111 (m-30)
REVERT: A  265 LYS cc_start: 0.9169 (ptmm) cc_final: 0.8687 (pptt)
REVERT: B  238 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8698 (ttmt)
REVERT: B  242 ARG cc_start: 0.8059 (mtp85) cc_final: 0.7644 (ttm-80)
REVERT: B  368 ARG cc_start: 0.8654 (mtm110) cc_final: 0.8423 (mtp85)
  outliers start: 15
  outliers final: 7
  residues processed: 112
  average time/residue: 0.5974
  time to fit residues: 71.6578
Evaluate side-chains
  106 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 MET
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  296 CYS
Chi-restraints excluded: chain B residue  310 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 78 optimal weight:    0.1980
   chunk 20 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0030
   chunk 42 optimal weight:    4.9990
   chunk 104 optimal weight:    3.9990
   chunk 56 optimal weight:    8.9990
   chunk 97 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 432 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.110668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.071874 restraints weight = 15329.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.2840 rms_B_bonded: 3.13
r_work: 0.2673 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9283  Z= 0.127
  Angle     :  0.579   9.832  12660  Z= 0.297
  Chirality :  0.041   0.160   1419
  Planarity :  0.004   0.066   1523
  Dihedral  : 17.506 177.823   1467
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 19.16 %
    Favored  : 79.66 %
  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:  0.99 (0.26), residues: 1047
  helix:  2.08 (0.29), residues: 335
  sheet:  0.28 (0.41), residues: 149
  loop : -0.06 (0.26), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG B 141 
 TYR   0.025   0.001   TYR A 103 
 PHE   0.022   0.001   PHE A 211 
 TRP   0.003   0.000   TRP B 247 
 HIS   0.003   0.000   HIS B 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9283)
  covalent geometry    : angle       0.57869 (12660)
  hydrogen bonds       : bond        0.03206 (  383)
  hydrogen bonds       : angle       4.43945 ( 1055)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A   48 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8341 (mtp)
REVERT: A   99 PHE cc_start: 0.8004 (m-80) cc_final: 0.7459 (m-10)
REVERT: A  128 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8129 (pm20)
REVERT: A  129 LYS cc_start: 0.9126 (mppt) cc_final: 0.8806 (mptt)
REVERT: A  134 MET cc_start: 0.9173 (ptm) cc_final: 0.8912 (tmm)
REVERT: A  199 PHE cc_start: 0.8532 (t80) cc_final: 0.8295 (t80)
REVERT: A  201 ASP cc_start: 0.8501 (m-30) cc_final: 0.8160 (m-30)
REVERT: A  265 LYS cc_start: 0.9155 (ptmm) cc_final: 0.8688 (pptt)
REVERT: B  141 ARG cc_start: 0.8260 (mmm160) cc_final: 0.7784 (tpm170)
REVERT: B  242 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7633 (ttm-80)
REVERT: B  368 ARG cc_start: 0.8691 (mtm110) cc_final: 0.8436 (mtp85)
  outliers start: 11
  outliers final: 8
  residues processed: 104
  average time/residue: 0.5420
  time to fit residues: 60.6652
Evaluate side-chains
  108 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 MET
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  296 CYS
Chi-restraints excluded: chain B residue  310 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 37 optimal weight:    0.0980
   chunk 42 optimal weight:    0.0570
   chunk 57 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 100 optimal weight:    0.0010
   chunk 32 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 80 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.3904

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

Flipped N/Q/H residues before XYZ refinement:
B 432 GLN
B 440 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.110895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.072008 restraints weight = 15212.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 3.10
r_work: 0.2695 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9283  Z= 0.114
  Angle     :  0.580  10.409  12660  Z= 0.297
  Chirality :  0.040   0.178   1419
  Planarity :  0.004   0.063   1523
  Dihedral  : 17.483 178.148   1467
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 19.38 %
    Favored  : 79.55 %
  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:  1.02 (0.26), residues: 1047
  helix:  2.13 (0.29), residues: 335
  sheet:  0.20 (0.41), residues: 155
  loop : -0.02 (0.26), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG B 141 
 TYR   0.019   0.001   TYR A 103 
 PHE   0.032   0.001   PHE A 216 
 TRP   0.004   0.000   TRP B 247 
 HIS   0.002   0.000   HIS B 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9283)
  covalent geometry    : angle       0.58022 (12660)
  hydrogen bonds       : bond        0.03092 (  383)
  hydrogen bonds       : angle       4.39957 ( 1055)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3053.08 seconds
wall clock time: 52 minutes 50.39 seconds (3170.39 seconds total)