Starting phenix.real_space_refine
on Wed Feb  4 06:02:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zv2_60505/02_2026/8zv2_60505.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zv2_60505/02_2026/8zv2_60505.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zv2_60505/02_2026/8zv2_60505.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zv2_60505/02_2026/8zv2_60505.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zv2_60505/02_2026/8zv2_60505.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zv2_60505/02_2026/8zv2_60505.map"
  }
  resolution = 2.94
  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=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      50      5.16       5
     C    5547      2.51       5
     N    1544      2.21       5
     O    1679      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8824
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 673, 5190
          Classifications: {'peptide': 673}
          Link IDs: {'PTRANS': 24, 'TRANS': 648}
    Chain: "B"
      Number of atoms: 1713
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1713
          Classifications: {'peptide': 222}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 206}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1874
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 1874
          Classifications: {'peptide': 248}
          Link IDs: {'PTRANS': 10, 'TRANS': 237}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 47
          Unusual residues: {' MG': 1, 'ATP': 1, 'BTN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'BTN:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 2.44, per 1000 atoms: 0.28
  Number of scatterers: 8824
  At special positions: 0
  Unit cell: (95.76, 97.44, 135.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      50     16.00
     P       3     15.00
     Mg      1     11.99
     O    1679      8.00
     N    1544      7.00
     C    5547      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 352.4 milliseconds
  

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2106

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 12 sheets defined
      38.9% alpha, 23.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 72 through 84
    Processing helix  chain 'A' and resid 95 through 99
      removed outlier: 3.571A  pdb=" N   ALA A  98 " --> pdb=" O   ASP A  95 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   SER A  99 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 95 through 99'
    Processing helix  chain 'A' and resid 100 through 106
    Processing helix  chain 'A' and resid 116 through 121
    Processing helix  chain 'A' and resid 123 through 135
    Processing helix  chain 'A' and resid 149 through 159
      removed outlier: 3.823A  pdb=" N   GLU A 159 " --> pdb=" O   CYS A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 176
      removed outlier: 4.423A  pdb=" N   ASP A 176 " --> pdb=" O   GLN A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 187
    Processing helix  chain 'A' and resid 201 through 212
      removed outlier: 3.908A  pdb=" N   GLU A 211 " --> pdb=" O   ARG A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 253
      removed outlier: 4.173A  pdb=" N   ALA A 250 " --> pdb=" O   SER A 246 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   SER A 251 " --> pdb=" O   GLN A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 328
    Processing helix  chain 'A' and resid 357 through 366
      removed outlier: 4.377A  pdb=" N   THR A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE A 364 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 379
    Processing helix  chain 'A' and resid 458 through 472
    Processing helix  chain 'A' and resid 481 through 491
    Processing helix  chain 'A' and resid 491 through 497
    Processing helix  chain 'A' and resid 502 through 508
    Processing helix  chain 'A' and resid 518 through 540
    Processing helix  chain 'A' and resid 641 through 648
      removed outlier: 3.706A  pdb=" N   LYS A 648 " --> pdb=" O   ALA A 644 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 303
    Processing helix  chain 'B' and resid 315 through 324
      removed outlier: 3.863A  pdb=" N   ILE B 319 " --> pdb=" O   ASN B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 328
    Processing helix  chain 'B' and resid 361 through 365
    Processing helix  chain 'B' and resid 367 through 384
      removed outlier: 3.508A  pdb=" N   ARG B 376 " --> pdb=" O   VAL B 372 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   PHE B 377 " --> pdb=" O   LYS B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 407
      removed outlier: 3.594A  pdb=" N   GLU B 404 " --> pdb=" O   GLY B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 422
      removed outlier: 3.672A  pdb=" N   ALA B 422 " --> pdb=" O   ALA B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 442
      removed outlier: 3.799A  pdb=" N   ASP B 440 " --> pdb=" O   GLY B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 448
    Processing helix  chain 'B' and resid 493 through 499
      removed outlier: 3.569A  pdb=" N   ARG B 499 " --> pdb=" O   PRO B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 509
      No H-bonds generated for 'chain 'B' and resid 507 through 509'
    Processing helix  chain 'B' and resid 510 through 522
    Processing helix  chain 'B' and resid 523 through 525
      No H-bonds generated for 'chain 'B' and resid 523 through 525'
    Processing helix  chain 'F' and resid 34 through 49
    Processing helix  chain 'F' and resid 51 through 61
    Processing helix  chain 'F' and resid 65 through 74
    Processing helix  chain 'F' and resid 135 through 152
      removed outlier: 3.567A  pdb=" N   GLN F 139 " --> pdb=" O   GLY F 135 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 170 through 187
    Processing helix  chain 'F' and resid 205 through 211
      removed outlier: 3.876A  pdb=" N   ALA F 209 " --> pdb=" O   VAL F 205 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 227 through 236
    Processing helix  chain 'F' and resid 240 through 246
    Processing helix  chain 'F' and resid 246 through 253
    Processing helix  chain 'F' and resid 263 through 276
    Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111
      removed outlier: 3.593A  pdb=" N   GLU A 108 " --> pdb=" O   THR A  89 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL A 110 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ILE A  92 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   LYS A  65 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   HIS A 140 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   LEU A  67 " --> pdb=" O   HIS A 140 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 229 through 232
    Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 351
      removed outlier: 3.948A  pdb=" N   GLU A 336 " --> pdb=" O   LEU A 348 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   MET A 350 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   THR A 334 " --> pdb=" O   MET A 350 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   HIS A 269 " --> pdb=" O   CYS A 290 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   GLN A 273 " --> pdb=" O   ASN A 286 " (cutoff:3.500A)
      removed outlier: 5.200A  pdb=" N   ASN A 286 " --> pdb=" O   GLN A 273 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   LEU A 275 " --> pdb=" O   TRP A 284 " (cutoff:3.500A)
      removed outlier: 5.472A  pdb=" N   TRP A 284 " --> pdb=" O   LEU A 275 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   SER A 291 " --> pdb=" O   VAL A 300 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   VAL A 300 " --> pdb=" O   SER A 291 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   GLN A 293 " --> pdb=" O   LYS A 298 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LYS A 298 " --> pdb=" O   GLN A 293 " (cutoff:3.500A)
      removed outlier: 14.572A  pdb=" N   GLN A 297 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 10.847A  pdb=" N   TYR A 401 " --> pdb=" O   GLN A 297 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   VAL A 299 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 415 through 416
    Processing sheet with id=AA5, first strand: chain 'A' and resid 419 through 421
    Processing sheet with id=AA6, first strand: chain 'A' and resid 558 through 565
      removed outlier: 6.425A  pdb=" N   SER A 626 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   ARG A 619 " --> pdb=" O   ASN A 624 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   ASN A 624 " --> pdb=" O   ARG A 619 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 696 through 700
      removed outlier: 3.791A  pdb=" N   MET A 699 " --> pdb=" O   CYS A 688 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   CYS A 688 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
      removed outlier: 7.838A  pdb=" N   ILE A 687 " --> pdb=" O   VAL A 673 " (cutoff:3.500A)
      removed outlier: 5.350A  pdb=" N   VAL A 673 " --> pdb=" O   ILE A 687 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   VAL A 689 " --> pdb=" O   VAL A 671 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 707 through 710
      removed outlier: 3.693A  pdb=" N   SER A 709 " --> pdb=" O   GLU A 726 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 330 through 332
      removed outlier: 4.583A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   ASP B 393 " --> pdb=" O   ASN B 357 " (cutoff:3.500A)
      removed outlier: 9.011A  pdb=" N   VAL B 394 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   LYS B 433 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   GLU B 459 " --> pdb=" O   ILE B 430 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   ARG B 432 " --> pdb=" O   GLU B 459 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   ALA B 461 " --> pdb=" O   ARG B 432 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   ALA B 434 " --> pdb=" O   ALA B 461 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 330 through 332
      removed outlier: 4.583A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   ASP B 393 " --> pdb=" O   ASN B 357 " (cutoff:3.500A)
      removed outlier: 9.011A  pdb=" N   VAL B 394 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   LYS B 433 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   THR B 451 " --> pdb=" O   LYS B 426 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ASP B 504 " --> pdb=" O   ASN B 452 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 80 through 82
      removed outlier: 4.749A  pdb=" N   THR F 109 " --> pdb=" O   SER F  82 " (cutoff:3.500A)
      removed outlier: 8.559A  pdb=" N   ILE F 156 " --> pdb=" O   LEU F 118 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   TYR F 120 " --> pdb=" O   ILE F 156 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   LEU F 158 " --> pdb=" O   TYR F 120 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   PHE F 122 " --> pdb=" O   LEU F 158 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   VAL F 155 " --> pdb=" O   ILE F 193 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   LEU F 195 " --> pdb=" O   VAL F 155 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   GLY F 157 " --> pdb=" O   LEU F 195 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ARG F 259 " --> pdb=" O   THR F 214 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 199 through 201

    427 hydrogen bonds defined for protein.
    1206 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.67

  Time building geometry restraints manager: 1.06 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1503
        1.32 -     1.44: 2237
        1.44 -     1.56: 5156
        1.56 -     1.69: 8
        1.69 -     1.81: 80
  Bond restraints: 8984
  Sorted by residual:
  bond pdb=" C2  BTN A 801 "
       pdb=" S1  BTN A 801 "
    ideal  model  delta    sigma   weight residual
    1.824  1.437  0.387 2.00e-02 2.50e+03 3.74e+02
  bond pdb=" C3  BTN A 801 "
       pdb=" N2  BTN A 801 "
    ideal  model  delta    sigma   weight residual
    1.362  1.556 -0.194 2.00e-02 2.50e+03 9.42e+01
  bond pdb=" C3  BTN A 801 "
       pdb=" N1  BTN A 801 "
    ideal  model  delta    sigma   weight residual
    1.358  1.506 -0.148 2.00e-02 2.50e+03 5.51e+01
  bond pdb=" C2  BTN A 801 "
       pdb=" C4  BTN A 801 "
    ideal  model  delta    sigma   weight residual
    1.534  1.682 -0.148 2.00e-02 2.50e+03 5.49e+01
  bond pdb=" C2  BTN A 801 "
       pdb=" C7  BTN A 801 "
    ideal  model  delta    sigma   weight residual
    1.517  1.637 -0.120 2.00e-02 2.50e+03 3.57e+01
  ... (remaining 8979 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.20: 12122
        3.20 -     6.41: 35
        6.41 -     9.61: 4
        9.61 -    12.82: 0
       12.82 -    16.02: 1
  Bond angle restraints: 12162
  Sorted by residual:
  angle pdb=" C2  BTN A 801 "
        pdb=" S1  BTN A 801 "
        pdb=" C6  BTN A 801 "
      ideal   model   delta    sigma   weight residual
      88.98  105.00  -16.02 3.00e+00 1.11e-01 2.85e+01
  angle pdb=" CA  LYS F  60 "
        pdb=" CB  LYS F  60 "
        pdb=" CG  LYS F  60 "
      ideal   model   delta    sigma   weight residual
     114.10  122.30   -8.20 2.00e+00 2.50e-01 1.68e+01
  angle pdb=" N   VAL A 112 "
        pdb=" CA  VAL A 112 "
        pdb=" C   VAL A 112 "
      ideal   model   delta    sigma   weight residual
     113.47  109.76    3.71 1.01e+00 9.80e-01 1.35e+01
  angle pdb=" C   ILE A 171 "
        pdb=" N   GLN A 172 "
        pdb=" CA  GLN A 172 "
      ideal   model   delta    sigma   weight residual
     121.58  115.03    6.55 1.95e+00 2.63e-01 1.13e+01
  angle pdb=" N   ILE F 166 "
        pdb=" CA  ILE F 166 "
        pdb=" C   ILE F 166 "
      ideal   model   delta    sigma   weight residual
     112.80  109.43    3.37 1.15e+00 7.56e-01 8.61e+00
  ... (remaining 12157 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 5046
       17.74 -    35.48: 339
       35.48 -    53.22: 53
       53.22 -    70.95: 21
       70.95 -    88.69: 10
  Dihedral angle restraints: 5469
    sinusoidal: 2197
      harmonic: 3272
  Sorted by residual:
  dihedral pdb=" CA  ARG B 432 "
           pdb=" C   ARG B 432 "
           pdb=" N   LYS B 433 "
           pdb=" CA  LYS B 433 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.29  -16.71     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CB  GLU A 302 "
           pdb=" CG  GLU A 302 "
           pdb=" CD  GLU A 302 "
           pdb=" OE1 GLU A 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.69  -88.69     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" C6  BTN A 801 "
           pdb=" C2  BTN A 801 "
           pdb=" S1  BTN A 801 "
           pdb=" C7  BTN A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     169.29   84.67   84.62     1      3.00e+01 1.11e-03 9.67e+00
  ... (remaining 5466 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 840
       0.030 -    0.061: 315
       0.061 -    0.091: 122
       0.091 -    0.121: 94
       0.121 -    0.152: 12
  Chirality restraints: 1383
  Sorted by residual:
  chirality pdb=" C4  BTN A 801 "
            pdb=" C2  BTN A 801 "
            pdb=" C5  BTN A 801 "
            pdb=" N2  BTN A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.76    2.91   -0.15 2.00e-01 2.50e+01 5.74e-01
  chirality pdb=" CA  ILE A 453 "
            pdb=" N   ILE A 453 "
            pdb=" C   ILE A 453 "
            pdb=" CB  ILE A 453 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.12e-01
  chirality pdb=" CA  ILE B 537 "
            pdb=" N   ILE B 537 "
            pdb=" C   ILE B 537 "
            pdb=" CB  ILE B 537 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.58e-01
  ... (remaining 1380 not shown)

  Planarity restraints: 1580
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 125 "    0.009 2.00e-02 2.50e+03   1.77e-02 3.15e+00
        pdb=" C   ASP A 125 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   ASP A 125 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ALA A 126 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 537 "   -0.027 5.00e-02 4.00e+02   4.14e-02 2.74e+00
        pdb=" N   PRO B 538 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 538 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 538 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 394 "    0.025 5.00e-02 4.00e+02   3.77e-02 2.27e+00
        pdb=" N   PRO B 395 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO B 395 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 395 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1577 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 80
        2.60 -     3.17: 7502
        3.17 -     3.75: 13290
        3.75 -     4.32: 18714
        4.32 -     4.90: 31624
  Nonbonded interactions: 71210
  Sorted by model distance:
  nonbonded pdb=" O3B ATP A 802 "
            pdb="MG    MG A 803 "
     model   vdw
     2.024 2.170
  nonbonded pdb=" O1A ATP A 802 "
            pdb="MG    MG A 803 "
     model   vdw
     2.065 2.170
  nonbonded pdb=" OE1 GLU A 349 "
            pdb="MG    MG A 803 "
     model   vdw
     2.085 2.170
  nonbonded pdb=" O2G ATP A 802 "
            pdb="MG    MG A 803 "
     model   vdw
     2.087 2.170
  nonbonded pdb=" NH2 ARG A 268 "
            pdb=" O   GLY A 497 "
     model   vdw
     2.255 3.120
  ... (remaining 71205 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:             3.760
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     10.410
  Find NCS groups from input model:        0.040
  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:6.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.387   8985  Z= 0.343
  Angle     :  0.560  16.021  12162  Z= 0.292
  Chirality :  0.044   0.152   1383
  Planarity :  0.003   0.041   1580
  Dihedral  : 13.233  88.693   3363
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  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:  0.46 (0.25), residues: 1133
  helix:  1.11 (0.27), residues: 399
  sheet:  0.68 (0.31), residues: 257
  loop : -0.54 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 154 
 TYR   0.024   0.001   TYR A 473 
 PHE   0.011   0.001   PHE F 122 
 TRP   0.022   0.002   TRP A 394 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00641 ( 8984)
  covalent geometry    : angle       0.55960 (12162)
  hydrogen bonds       : bond        0.15197 (  407)
  hydrogen bonds       : angle       6.41942 ( 1206)
  Misc. bond           : bond        0.12954 (    1)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.7475
  time to fit residues: 72.4961
Evaluate side-chains
  74 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    0.9980
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 286 ASN
F 147 GLN
F 165 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.130685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.075613 restraints weight = 14757.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 2.78
r_work: 0.2724 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2584 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9006
moved from start:          0.0935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8985  Z= 0.206
  Angle     :  0.567   7.179  12162  Z= 0.295
  Chirality :  0.046   0.152   1383
  Planarity :  0.004   0.041   1580
  Dihedral  :  8.015  68.734   1285
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  6.41 %
    Favored  : 92.54 %
  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:  0.53 (0.25), residues: 1133
  helix:  1.21 (0.26), residues: 412
  sheet:  0.70 (0.32), residues: 249
  loop : -0.56 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 135 
 TYR   0.016   0.001   TYR A 473 
 PHE   0.014   0.001   PHE A 307 
 TRP   0.014   0.002   TRP A 394 
 HIS   0.006   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 8984)
  covalent geometry    : angle       0.56660 (12162)
  hydrogen bonds       : bond        0.04580 (  407)
  hydrogen bonds       : angle       5.09288 ( 1206)
  Misc. bond           : bond        0.00034 (    1)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  693 MET cc_start: 0.7716 (ttt) cc_final: 0.7173 (tmm)
REVERT: B  459 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7575 (pp20)
REVERT: F   84 MET cc_start: 0.6775 (OUTLIER) cc_final: 0.6293 (ttt)
  outliers start: 10
  outliers final: 2
  residues processed: 83
  average time/residue: 0.7310
  time to fit residues: 64.0070
Evaluate side-chains
  75 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain F residue  235 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 83 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 96 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 63 optimal weight:   30.0000
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
F 147 GLN
F 165 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.132117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.077127 restraints weight = 14582.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.2904 rms_B_bonded: 2.81
r_work: 0.2762 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2622 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8983
moved from start:          0.1074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8985  Z= 0.120
  Angle     :  0.513   7.283  12162  Z= 0.265
  Chirality :  0.044   0.148   1383
  Planarity :  0.004   0.042   1580
  Dihedral  :  7.141  61.709   1285
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  8.82 %
    Favored  : 90.44 %
  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:  0.65 (0.25), residues: 1133
  helix:  1.39 (0.26), residues: 412
  sheet:  0.73 (0.32), residues: 252
  loop : -0.54 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 135 
 TYR   0.008   0.001   TYR A 473 
 PHE   0.010   0.001   PHE F 122 
 TRP   0.011   0.001   TRP A 233 
 HIS   0.006   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8984)
  covalent geometry    : angle       0.51253 (12162)
  hydrogen bonds       : bond        0.03694 (  407)
  hydrogen bonds       : angle       4.74441 ( 1206)
  Misc. bond           : bond        0.00010 (    1)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8912 (mm-30)
REVERT: A  693 MET cc_start: 0.7706 (ttt) cc_final: 0.7181 (tmm)
REVERT: B  459 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7629 (pp20)
REVERT: B  463 MET cc_start: 0.7008 (mmm) cc_final: 0.6570 (mpm)
REVERT: F   84 MET cc_start: 0.6825 (pmt) cc_final: 0.6279 (ttt)
REVERT: F  165 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8563 (mp10)
  outliers start: 7
  outliers final: 3
  residues processed: 81
  average time/residue: 0.7017
  time to fit residues: 60.0607
Evaluate side-chains
  78 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain F residue  235 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   chunk 36 optimal weight:    0.0980
   chunk 81 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   chunk 85 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
F 147 GLN
F 183 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.131960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.076937 restraints weight = 14843.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 2.80
r_work: 0.2763 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2620 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8990
moved from start:          0.1253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8985  Z= 0.124
  Angle     :  0.509   8.666  12162  Z= 0.261
  Chirality :  0.044   0.150   1383
  Planarity :  0.004   0.041   1580
  Dihedral  :  6.324  57.965   1285
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 10.61 %
    Favored  : 88.13 %
  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:  0.72 (0.25), residues: 1133
  helix:  1.52 (0.26), residues: 413
  sheet:  0.59 (0.32), residues: 257
  loop : -0.48 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 135 
 TYR   0.006   0.001   TYR A 473 
 PHE   0.015   0.001   PHE A 307 
 TRP   0.007   0.001   TRP A 394 
 HIS   0.005   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8984)
  covalent geometry    : angle       0.50897 (12162)
  hydrogen bonds       : bond        0.03525 (  407)
  hydrogen bonds       : angle       4.55377 ( 1206)
  Misc. bond           : bond        0.00004 (    1)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8889 (mm-30)
REVERT: A  301 GLU cc_start: 0.7830 (mp0) cc_final: 0.7530 (mp0)
REVERT: A  693 MET cc_start: 0.7759 (ttt) cc_final: 0.7214 (tmm)
REVERT: B  459 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7570 (pp20)
REVERT: B  463 MET cc_start: 0.7220 (mmm) cc_final: 0.6821 (mpm)
REVERT: F   84 MET cc_start: 0.6835 (pmt) cc_final: 0.6357 (ttt)
REVERT: F  165 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8575 (mp10)
  outliers start: 12
  outliers final: 4
  residues processed: 81
  average time/residue: 0.7227
  time to fit residues: 61.8716
Evaluate side-chains
  79 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain B residue  520 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 99 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0570
   chunk 97 optimal weight:    0.9980
   chunk 10 optimal weight:    0.4980
   chunk 54 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   chunk 48 optimal weight:    0.4980
   chunk 77 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    1.0100

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

Flipped N/Q/H residues before XYZ refinement:
F 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.131845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.076857 restraints weight = 14670.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 2.80
r_work: 0.2760 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2619 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8985
moved from start:          0.1340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8985  Z= 0.127
  Angle     :  0.489   6.684  12162  Z= 0.255
  Chirality :  0.044   0.129   1383
  Planarity :  0.003   0.048   1580
  Dihedral  :  5.595  58.284   1285
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 11.87 %
    Favored  : 87.08 %
  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:  0.82 (0.25), residues: 1133
  helix:  1.62 (0.26), residues: 412
  sheet:  0.63 (0.32), residues: 259
  loop : -0.44 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 135 
 TYR   0.006   0.001   TYR A 401 
 PHE   0.011   0.001   PHE F 122 
 TRP   0.013   0.001   TRP A 233 
 HIS   0.005   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8984)
  covalent geometry    : angle       0.48887 (12162)
  hydrogen bonds       : bond        0.03460 (  407)
  hydrogen bonds       : angle       4.45196 ( 1206)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 MET cc_start: 0.8953 (mmm) cc_final: 0.8749 (mmm)
REVERT: A  129 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8874 (mm-30)
REVERT: A  155 CYS cc_start: 0.9483 (t) cc_final: 0.9198 (t)
REVERT: A  233 TRP cc_start: 0.8050 (m100) cc_final: 0.7818 (m100)
REVERT: A  301 GLU cc_start: 0.7873 (mp0) cc_final: 0.7642 (mp0)
REVERT: A  693 MET cc_start: 0.7886 (ttt) cc_final: 0.7520 (tmm)
REVERT: A  695 MET cc_start: 0.8050 (mmt) cc_final: 0.7577 (mmp)
REVERT: B  459 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7505 (pp20)
REVERT: F   84 MET cc_start: 0.6681 (OUTLIER) cc_final: 0.6305 (ttt)
REVERT: F  165 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8636 (mp10)
  outliers start: 10
  outliers final: 5
  residues processed: 81
  average time/residue: 0.7730
  time to fit residues: 66.0910
Evaluate side-chains
  82 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain B residue  520 ASP
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain F residue  226 THR
Chi-restraints excluded: chain F residue  238 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 108 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 90 optimal weight:   30.0000
   chunk 43 optimal weight:    0.6980
   chunk 39 optimal weight:    7.9990
   chunk 76 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0670
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.7320

-------------------------------------------------------------------------------
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 = 0.3814 r_free = 0.3814 target = 0.132120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.077156 restraints weight = 14848.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 2.83
r_work: 0.2761 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.2621 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8975
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8985  Z= 0.108
  Angle     :  0.506  11.027  12162  Z= 0.258
  Chirality :  0.043   0.140   1383
  Planarity :  0.003   0.050   1580
  Dihedral  :  5.341  53.964   1285
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 12.39 %
    Favored  : 86.24 %
  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 (0.25), residues: 1133
  helix:  1.68 (0.26), residues: 412
  sheet:  0.63 (0.32), residues: 257
  loop : -0.43 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 135 
 TYR   0.006   0.001   TYR A 401 
 PHE   0.018   0.001   PHE A 307 
 TRP   0.011   0.001   TRP A 233 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8984)
  covalent geometry    : angle       0.50567 (12162)
  hydrogen bonds       : bond        0.03221 (  407)
  hydrogen bonds       : angle       4.37245 ( 1206)
  Misc. bond           : bond        0.00006 (    1)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8848 (mm-30)
REVERT: A  233 TRP cc_start: 0.8047 (m100) cc_final: 0.7841 (m100)
REVERT: A  301 GLU cc_start: 0.7940 (mp0) cc_final: 0.7599 (mp0)
REVERT: A  397 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8887 (tm-30)
REVERT: A  666 MET cc_start: 0.8282 (ppp) cc_final: 0.8045 (mtp)
REVERT: A  693 MET cc_start: 0.7799 (ttt) cc_final: 0.7427 (tmm)
REVERT: A  695 MET cc_start: 0.7911 (mmt) cc_final: 0.7484 (mmp)
REVERT: B  463 MET cc_start: 0.6965 (mmm) cc_final: 0.6732 (mmm)
REVERT: F   84 MET cc_start: 0.6745 (pmt) cc_final: 0.6362 (ttt)
REVERT: F  165 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8637 (mp10)
  outliers start: 13
  outliers final: 6
  residues processed: 91
  average time/residue: 0.6935
  time to fit residues: 66.8802
Evaluate side-chains
  84 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain B residue  520 ASP
Chi-restraints excluded: chain F residue  226 THR
Chi-restraints excluded: chain F residue  238 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 60 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0070
   chunk 25 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 84 optimal weight:    9.9990
   chunk 108 optimal weight:    0.0670
   chunk 78 optimal weight:    2.9990
   chunk 103 optimal weight:    0.7980
   overall best weight:    1.1740

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

Flipped N/Q/H residues before XYZ refinement:
F 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.131399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.076351 restraints weight = 14722.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 2.79
r_work: 0.2754 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.2612 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9000
moved from start:          0.1487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8985  Z= 0.142
  Angle     :  0.525   8.527  12162  Z= 0.269
  Chirality :  0.044   0.147   1383
  Planarity :  0.004   0.054   1580
  Dihedral  :  5.326  54.795   1285
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 13.13 %
    Favored  : 85.40 %
  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:  0.86 (0.25), residues: 1133
  helix:  1.66 (0.26), residues: 412
  sheet:  0.71 (0.32), residues: 255
  loop : -0.46 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 135 
 TYR   0.006   0.001   TYR A 401 
 PHE   0.013   0.001   PHE F 122 
 TRP   0.011   0.001   TRP A 233 
 HIS   0.005   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8984)
  covalent geometry    : angle       0.52467 (12162)
  hydrogen bonds       : bond        0.03532 (  407)
  hydrogen bonds       : angle       4.39664 ( 1206)
  Misc. bond           : bond        0.00007 (    1)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8831 (mm-30)
REVERT: A  301 GLU cc_start: 0.7951 (mp0) cc_final: 0.7739 (mp0)
REVERT: A  693 MET cc_start: 0.7699 (ttt) cc_final: 0.7461 (tmm)
REVERT: A  695 MET cc_start: 0.7856 (mmt) cc_final: 0.7472 (mmp)
REVERT: B  463 MET cc_start: 0.7025 (mmm) cc_final: 0.6443 (mpm)
REVERT: B  526 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8724 (mtpt)
REVERT: F   84 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.6414 (ttt)
REVERT: F  165 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8649 (mp10)
  outliers start: 14
  outliers final: 5
  residues processed: 88
  average time/residue: 0.7385
  time to fit residues: 68.6985
Evaluate side-chains
  84 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain B residue  520 ASP
Chi-restraints excluded: chain B residue  526 LYS
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain F residue  226 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 84 optimal weight:    8.9990
   chunk 101 optimal weight:    0.6980
   chunk 108 optimal weight:    5.9990
   chunk 112 optimal weight:    0.6980
   chunk 61 optimal weight:    7.9990
   chunk 96 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3814 r_free = 0.3814 target = 0.132026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.077104 restraints weight = 14729.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.2894 rms_B_bonded: 2.80
r_work: 0.2755 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2614 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8980
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8985  Z= 0.119
  Angle     :  0.509   8.557  12162  Z= 0.263
  Chirality :  0.044   0.174   1383
  Planarity :  0.003   0.057   1580
  Dihedral  :  5.259  55.713   1285
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 13.13 %
    Favored  : 85.50 %
  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 (0.25), residues: 1133
  helix:  1.70 (0.26), residues: 412
  sheet:  0.85 (0.33), residues: 249
  loop : -0.47 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 135 
 TYR   0.006   0.001   TYR A 401 
 PHE   0.020   0.001   PHE A 307 
 TRP   0.013   0.001   TRP A 233 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8984)
  covalent geometry    : angle       0.50909 (12162)
  hydrogen bonds       : bond        0.03295 (  407)
  hydrogen bonds       : angle       4.35975 ( 1206)
  Misc. bond           : bond        0.00004 (    1)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8839 (mm-30)
REVERT: A  233 TRP cc_start: 0.8002 (m100) cc_final: 0.7801 (m100)
REVERT: A  301 GLU cc_start: 0.7891 (mp0) cc_final: 0.7686 (mp0)
REVERT: A  397 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8929 (tm-30)
REVERT: A  693 MET cc_start: 0.7557 (ttt) cc_final: 0.7357 (tmm)
REVERT: A  695 MET cc_start: 0.7801 (mmt) cc_final: 0.7491 (mmp)
REVERT: B  463 MET cc_start: 0.7203 (mmm) cc_final: 0.6636 (mpm)
REVERT: B  526 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8748 (mtpt)
REVERT: F   84 MET cc_start: 0.6748 (pmt) cc_final: 0.6400 (ttt)
REVERT: F  165 GLN cc_start: 0.9076 (mm-40) cc_final: 0.8646 (mp10)
  outliers start: 13
  outliers final: 7
  residues processed: 87
  average time/residue: 0.7031
  time to fit residues: 64.6354
Evaluate side-chains
  86 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  520 ASP
Chi-restraints excluded: chain B residue  526 LYS
Chi-restraints excluded: chain F residue  226 THR
Chi-restraints excluded: chain F residue  239 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0020
   chunk 62 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    3.9990
   chunk 24 optimal weight:    0.2980
   chunk 29 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.6388

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

Flipped N/Q/H residues before XYZ refinement:
F 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.132495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.077696 restraints weight = 14686.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 2.77
r_work: 0.2769 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2627 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8974
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8985  Z= 0.108
  Angle     :  0.533  14.497  12162  Z= 0.270
  Chirality :  0.043   0.159   1383
  Planarity :  0.004   0.073   1580
  Dihedral  :  5.224  56.190   1285
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 13.34 %
    Favored  : 85.29 %
  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:  0.95 (0.26), residues: 1133
  helix:  1.73 (0.26), residues: 412
  sheet:  0.85 (0.33), residues: 249
  loop : -0.45 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.000   ARG A 154 
 TYR   0.006   0.001   TYR A 401 
 PHE   0.009   0.001   PHE F 122 
 TRP   0.012   0.001   TRP A 233 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8984)
  covalent geometry    : angle       0.53338 (12162)
  hydrogen bonds       : bond        0.03192 (  407)
  hydrogen bonds       : angle       4.32948 ( 1206)
  Misc. bond           : bond        0.00003 (    1)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8886 (mm-30)
REVERT: A  301 GLU cc_start: 0.7874 (mp0) cc_final: 0.7664 (mp0)
REVERT: A  307 PHE cc_start: 0.8628 (t80) cc_final: 0.8377 (t80)
REVERT: A  397 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8934 (tm-30)
REVERT: A  695 MET cc_start: 0.7714 (mmt) cc_final: 0.7498 (mmp)
REVERT: B  463 MET cc_start: 0.7340 (mmm) cc_final: 0.6807 (mpm)
REVERT: B  526 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8734 (mtpt)
REVERT: F   84 MET cc_start: 0.6759 (pmt) cc_final: 0.6412 (ttt)
REVERT: F  165 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8642 (mp10)
  outliers start: 13
  outliers final: 5
  residues processed: 86
  average time/residue: 0.7032
  time to fit residues: 64.0364
Evaluate side-chains
  87 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain B residue  520 ASP
Chi-restraints excluded: chain B residue  526 LYS
Chi-restraints excluded: chain F residue  226 THR
Chi-restraints excluded: chain F residue  239 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 19 optimal weight:   20.0000
   chunk 34 optimal weight:    6.9990
   chunk 106 optimal weight:    0.3980
   chunk 24 optimal weight:    0.0870
   chunk 6 optimal weight:    0.8980
   chunk 65 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 103 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 66 optimal weight:    8.9990
   overall best weight:    1.0762

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

Flipped N/Q/H residues before XYZ refinement:
F 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.131950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.076903 restraints weight = 14651.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 2.80
r_work: 0.2761 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2622 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8989
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8985  Z= 0.138
  Angle     :  0.572  17.044  12162  Z= 0.285
  Chirality :  0.044   0.160   1383
  Planarity :  0.004   0.078   1580
  Dihedral  :  5.216  55.177   1285
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 13.66 %
    Favored  : 85.40 %
  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:  0.90 (0.26), residues: 1133
  helix:  1.67 (0.26), residues: 412
  sheet:  0.74 (0.32), residues: 256
  loop : -0.41 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.000   ARG A 154 
 TYR   0.021   0.001   TYR B 435 
 PHE   0.012   0.001   PHE F 122 
 TRP   0.008   0.001   TRP A 233 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8984)
  covalent geometry    : angle       0.57212 (12162)
  hydrogen bonds       : bond        0.03442 (  407)
  hydrogen bonds       : angle       4.38864 ( 1206)
  Misc. bond           : bond        0.00027 (    1)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8853 (mm-30)
REVERT: A  301 GLU cc_start: 0.7881 (mp0) cc_final: 0.7664 (mp0)
REVERT: A  307 PHE cc_start: 0.8666 (t80) cc_final: 0.8423 (t80)
REVERT: A  397 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8935 (tm-30)
REVERT: A  695 MET cc_start: 0.7726 (mmt) cc_final: 0.7340 (mmp)
REVERT: B  463 MET cc_start: 0.7426 (mmm) cc_final: 0.6812 (mpm)
REVERT: B  526 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8737 (mtpt)
REVERT: F   84 MET cc_start: 0.6766 (pmt) cc_final: 0.6451 (ttt)
REVERT: F  165 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8642 (mp10)
  outliers start: 9
  outliers final: 5
  residues processed: 84
  average time/residue: 0.7922
  time to fit residues: 70.2543
Evaluate side-chains
  84 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain B residue  520 ASP
Chi-restraints excluded: chain B residue  526 LYS
Chi-restraints excluded: chain F residue  226 THR
Chi-restraints excluded: chain F residue  239 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 88 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 86 optimal weight:    0.6980
   chunk 107 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
F 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.132526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.077685 restraints weight = 14446.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.2906 rms_B_bonded: 2.76
r_work: 0.2768 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2628 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8982
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8985  Z= 0.116
  Angle     :  0.550  14.719  12162  Z= 0.278
  Chirality :  0.044   0.162   1383
  Planarity :  0.004   0.065   1580
  Dihedral  :  5.182  58.203   1285
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 14.08 %
    Favored  : 84.87 %
  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: 1133
  helix:  1.68 (0.27), residues: 412
  sheet:  0.80 (0.33), residues: 252
  loop : -0.40 (0.29), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.000   ARG A 154 
 TYR   0.008   0.001   TYR B 435 
 PHE   0.009   0.001   PHE F 122 
 TRP   0.007   0.001   TRP A 233 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8984)
  covalent geometry    : angle       0.55008 (12162)
  hydrogen bonds       : bond        0.03251 (  407)
  hydrogen bonds       : angle       4.35114 ( 1206)
  Misc. bond           : bond        0.00024 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3703.41 seconds
wall clock time: 63 minutes 43.62 seconds (3823.62 seconds total)