Starting phenix.real_space_refine
on Wed Feb  4 04:58:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zuz_60502/02_2026/8zuz_60502.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zuz_60502/02_2026/8zuz_60502.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zuz_60502/02_2026/8zuz_60502.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zuz_60502/02_2026/8zuz_60502.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zuz_60502/02_2026/8zuz_60502.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zuz_60502/02_2026/8zuz_60502.cif"
  }
  resolution = 2.73
  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=   0.015
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      49      5.16       5
     C    5431      2.51       5
     N    1509      2.21       5
     O    1644      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: 8637
  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: 1693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1693
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 203}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1718
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 10, 'TRANS': 218}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "A"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 36
          Unusual residues: {' MG': 1, 'ATP': 1, 'BCT': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.98, per 1000 atoms: 0.23
  Number of scatterers: 8637
  At special positions: 0
  Unit cell: (96.6, 100.8, 134.4, 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      49     16.00
     P       3     15.00
     Mg      1     11.99
     O    1644      8.00
     N    1509      7.00
     C    5431      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: 0.67
  Conformation dependent library (CDL) restraints added in 338.0 milliseconds
  

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2070

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 11 sheets defined
      38.3% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 72 through 85
    Processing helix  chain 'A' and resid 95 through 99
      removed outlier: 4.082A  pdb=" N   SER A  99 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 106
      removed outlier: 3.976A  pdb=" N   LYS A 104 " --> pdb=" O   SER A 100 " (cutoff:3.500A)
    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
    Processing helix  chain 'A' and resid 167 through 176
      removed outlier: 4.038A  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
    Processing helix  chain 'A' and resid 236 through 253
      removed outlier: 3.591A  pdb=" N   ASP A 240 " --> pdb=" O   GLU A 236 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   PHE A 242 " --> pdb=" O   THR A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 328
    Processing helix  chain 'A' and resid 357 through 366
      removed outlier: 4.384A  pdb=" N   THR A 361 " --> pdb=" O   GLU A 357 " (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 541
    Processing helix  chain 'A' and resid 641 through 648
    Processing helix  chain 'B' and resid 299 through 303
    Processing helix  chain 'B' and resid 315 through 324
      removed outlier: 3.931A  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
    Processing helix  chain 'B' and resid 400 through 406
    Processing helix  chain 'B' and resid 407 through 422
      removed outlier: 3.691A  pdb=" N   LEU B 415 " --> pdb=" O   HIS B 411 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ALA B 422 " --> pdb=" O   ALA B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 437 through 442
    Processing helix  chain 'B' and resid 493 through 500
    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
      removed outlier: 3.570A  pdb=" N   CYS B 517 " --> pdb=" O   ALA B 513 " (cutoff:3.500A)
    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 52 through 61
    Processing helix  chain 'F' and resid 65 through 74
    Processing helix  chain 'F' and resid 125 through 130
      removed outlier: 3.912A  pdb=" N   PHE F 129 " --> pdb=" O   ASP F 125 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   GLY F 130 " --> pdb=" O   PHE F 126 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 125 through 130'
    Processing helix  chain 'F' and resid 134 through 152
      removed outlier: 3.607A  pdb=" N   ALA F 138 " --> pdb=" O   SER F 134 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 169 through 187
      removed outlier: 3.732A  pdb=" N   LEU F 173 " --> pdb=" O   GLY F 169 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ALA F 174 " --> pdb=" O   VAL F 170 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 205 through 211
      removed outlier: 3.613A  pdb=" N   ALA F 209 " --> pdb=" O   VAL F 205 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 227 through 235
    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: 6.634A  pdb=" N   THR A  89 " --> pdb=" O   GLU A 108 " (cutoff:3.500A)
      removed outlier: 8.156A  pdb=" N   VAL A 110 " --> pdb=" O   THR A  89 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   ALA A  91 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   ILE A  66 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 7.600A  pdb=" N   ILE A  92 " --> pdb=" O   ILE A  66 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   VAL A  68 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 229 through 232
      removed outlier: 3.698A  pdb=" N   GLU A 261 " --> pdb=" O   MET A 217 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 351
      removed outlier: 7.050A  pdb=" N   PHE A 347 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   LEU A 338 " --> pdb=" O   PHE A 347 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   GLU A 349 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   VAL A 339 " --> pdb=" O   ARG A 268 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   HIS A 269 " --> pdb=" O   CYS A 290 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   GLN A 273 " --> pdb=" O   ASN A 286 " (cutoff:3.500A)
      removed outlier: 5.508A  pdb=" N   ASN A 286 " --> pdb=" O   GLN A 273 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   LEU A 275 " --> pdb=" O   TRP A 284 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   TRP A 284 " --> pdb=" O   LEU A 275 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   SER A 291 " --> pdb=" O   VAL A 300 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   VAL A 300 " --> pdb=" O   SER A 291 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   GLN A 293 " --> pdb=" O   LYS A 298 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   LYS A 298 " --> pdb=" O   GLN A 293 " (cutoff:3.500A)
      removed outlier: 14.550A  pdb=" N   GLN A 297 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 11.324A  pdb=" N   TYR A 401 " --> pdb=" O   GLN A 297 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   VAL A 299 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 404
    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 588 through 593
      removed outlier: 6.901A  pdb=" N   ASN A 624 " --> pdb=" O   ARG A 619 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   ARG A 619 " --> pdb=" O   ASN A 624 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   SER A 626 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 695 through 700
      removed outlier: 6.320A  pdb=" N   MET A 695 " --> pdb=" O   GLU A 691 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   GLU A 691 " --> pdb=" O   MET A 695 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ASN A 697 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   VAL A 689 " --> pdb=" O   ASN A 697 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   MET A 699 " --> pdb=" O   ILE A 687 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   GLU A 691 " --> pdb=" O   VAL A 670 " (cutoff:3.500A)
      removed outlier: 5.281A  pdb=" N   VAL A 670 " --> pdb=" O   GLU A 691 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 680 through 681
    Processing sheet with id=AA9, first strand: chain 'B' and resid 330 through 332
      removed outlier: 4.559A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
      removed outlier: 8.268A  pdb=" N   ILE B 389 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   GLY B 353 " --> pdb=" O   ILE B 389 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   PHE B 391 " --> pdb=" O   GLY B 353 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   VAL B 355 " --> pdb=" O   PHE B 391 " (cutoff:3.500A)
      removed outlier: 7.948A  pdb=" N   ASP B 393 " --> pdb=" O   VAL B 355 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   ASN B 357 " --> pdb=" O   ASP B 393 " (cutoff:3.500A)
      removed outlier: 8.897A  pdb=" N   VAL B 394 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
      removed outlier: 5.468A  pdb=" N   LYS B 433 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   THR B 451 " --> pdb=" O   LYS B 426 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ASP B 504 " --> pdb=" O   ASN B 452 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 80 through 81
      removed outlier: 8.477A  pdb=" N   ILE F 156 " --> pdb=" O   LEU F 118 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   TYR F 120 " --> pdb=" O   ILE F 156 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   LEU F 158 " --> pdb=" O   TYR F 120 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   PHE F 122 " --> pdb=" O   LEU F 158 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   VAL F 155 " --> pdb=" O   ILE F 193 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   LEU F 195 " --> pdb=" O   VAL F 155 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   GLY F 157 " --> pdb=" O   LEU F 195 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ARG F 259 " --> pdb=" O   THR F 214 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 199 through 201

    387 hydrogen bonds defined for protein.
    1080 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: 1.43

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2881
        1.34 -     1.45: 1053
        1.45 -     1.57: 4776
        1.57 -     1.69: 5
        1.69 -     1.81: 79
  Bond restraints: 8794
  Sorted by residual:
  bond pdb=" C   BCT A 803 "
       pdb=" O3  BCT A 803 "
    ideal  model  delta    sigma   weight residual
    1.389  1.435 -0.046 2.00e-02 2.50e+03 5.36e+00
  bond pdb=" CG  GLU A 487 "
       pdb=" CD  GLU A 487 "
    ideal  model  delta    sigma   weight residual
    1.516  1.488  0.028 2.50e-02 1.60e+03 1.24e+00
  bond pdb=" C   BCT A 803 "
       pdb=" O2  BCT A 803 "
    ideal  model  delta    sigma   weight residual
    1.241  1.219  0.022 2.00e-02 2.50e+03 1.23e+00
  bond pdb=" C   PHE B 494 "
       pdb=" N   PRO B 495 "
    ideal  model  delta    sigma   weight residual
    1.335  1.350 -0.015 1.36e-02 5.41e+03 1.22e+00
  bond pdb=" CA  MET B 333 "
       pdb=" C   MET B 333 "
    ideal  model  delta    sigma   weight residual
    1.531  1.524  0.008 7.40e-03 1.83e+04 1.06e+00
  ... (remaining 8789 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 11636
        1.55 -     3.10: 224
        3.10 -     4.65: 34
        4.65 -     6.20: 11
        6.20 -     7.75: 3
  Bond angle restraints: 11908
  Sorted by residual:
  angle pdb=" N   GLU A 487 "
        pdb=" CA  GLU A 487 "
        pdb=" CB  GLU A 487 "
      ideal   model   delta    sigma   weight residual
     110.28  115.14   -4.86 1.55e+00 4.16e-01 9.83e+00
  angle pdb=" C   LEU B 447 "
        pdb=" N   CYS B 448 "
        pdb=" CA  CYS B 448 "
      ideal   model   delta    sigma   weight residual
     123.47  128.20   -4.73 1.53e+00 4.27e-01 9.56e+00
  angle pdb=" C   ASP A 265 "
        pdb=" N   ASN A 266 "
        pdb=" CA  ASN A 266 "
      ideal   model   delta    sigma   weight residual
     121.80  129.09   -7.29 2.44e+00 1.68e-01 8.92e+00
  angle pdb=" C   ALA B 420 "
        pdb=" N   GLU B 421 "
        pdb=" CA  GLU B 421 "
      ideal   model   delta    sigma   weight residual
     121.58  116.04    5.54 1.95e+00 2.63e-01 8.06e+00
  angle pdb=" N   TYR A 445 "
        pdb=" CA  TYR A 445 "
        pdb=" C   TYR A 445 "
      ideal   model   delta    sigma   weight residual
     108.86  112.71   -3.85 1.41e+00 5.03e-01 7.47e+00
  ... (remaining 11903 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 4850
       17.71 -    35.42: 391
       35.42 -    53.12: 71
       53.12 -    70.83: 19
       70.83 -    88.54: 11
  Dihedral angle restraints: 5342
    sinusoidal: 2128
      harmonic: 3214
  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 -159.16  -20.84     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  ASP A 309 "
           pdb=" C   ASP A 309 "
           pdb=" N   ALA A 310 "
           pdb=" CA  ALA A 310 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.55  -18.45     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  ASP B 450 "
           pdb=" CB  ASP B 450 "
           pdb=" CG  ASP B 450 "
           pdb=" OD1 ASP B 450 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.15   57.15     1      2.00e+01 2.50e-03 1.10e+01
  ... (remaining 5339 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1173
       0.066 -    0.131: 176
       0.131 -    0.197: 4
       0.197 -    0.263: 0
       0.263 -    0.328: 1
  Chirality restraints: 1354
  Sorted by residual:
  chirality pdb=" CB  ILE A 218 "
            pdb=" CA  ILE A 218 "
            pdb=" CG1 ILE A 218 "
            pdb=" CG2 ILE A 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.33 2.00e-01 2.50e+01 2.69e+00
  chirality pdb=" CG  LEU F 133 "
            pdb=" CB  LEU F 133 "
            pdb=" CD1 LEU F 133 "
            pdb=" CD2 LEU F 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 5.17e-01
  chirality pdb=" CA  ILE B 505 "
            pdb=" N   ILE B 505 "
            pdb=" C   ILE B 505 "
            pdb=" CB  ILE B 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.11e-01
  ... (remaining 1351 not shown)

  Planarity restraints: 1548
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   BCT A 803 "    0.031 2.00e-02 2.50e+03   1.82e-02 3.31e+00
        pdb=" O1  BCT A 803 "   -0.012 2.00e-02 2.50e+03
        pdb=" O2  BCT A 803 "   -0.012 2.00e-02 2.50e+03
        pdb=" O3  BCT A 803 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 483 "    0.008 2.00e-02 2.50e+03   1.54e-02 2.39e+00
        pdb=" C   ALA A 483 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   ALA A 483 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LEU A 484 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 473 "    0.013 2.00e-02 2.50e+03   1.07e-02 2.29e+00
        pdb=" CG  TYR A 473 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 473 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 473 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 473 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 473 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 473 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 473 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1545 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 108
        2.64 -     3.20: 7893
        3.20 -     3.77: 13403
        3.77 -     4.33: 18654
        4.33 -     4.90: 30851
  Nonbonded interactions: 70909
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A  73 "
            pdb=" OH  TYR A 143 "
     model   vdw
     2.072 3.040
  nonbonded pdb=" OD1 ASP A 309 "
            pdb=" OG1 THR A 312 "
     model   vdw
     2.108 3.040
  nonbonded pdb=" OE1 GLU A 336 "
            pdb="MG    MG A 802 "
     model   vdw
     2.119 2.170
  nonbonded pdb=" OE2 GLU A 336 "
            pdb="MG    MG A 802 "
     model   vdw
     2.137 2.170
  nonbonded pdb=" OH  TYR B 314 "
            pdb=" OD2 ASP B 393 "
     model   vdw
     2.183 3.040
  ... (remaining 70904 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:             3.820
  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:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.620
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8794  Z= 0.169
  Angle     :  0.557   7.752  11908  Z= 0.298
  Chirality :  0.045   0.328   1354
  Planarity :  0.004   0.036   1548
  Dihedral  : 14.005  88.541   3272
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  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: -0.16 (0.25), residues: 1111
  helix:  0.97 (0.27), residues: 388
  sheet:  0.72 (0.37), residues: 199
  loop : -1.29 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 243 
 TYR   0.026   0.002   TYR A 473 
 PHE   0.012   0.001   PHE B 380 
 TRP   0.006   0.001   TRP B 531 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 8794)
  covalent geometry    : angle       0.55670 (11908)
  hydrogen bonds       : bond        0.15475 (  387)
  hydrogen bonds       : angle       6.56725 ( 1080)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 MET cc_start: 0.6040 (ttt) cc_final: 0.5049 (mpm)
REVERT: F   84 MET cc_start: 0.7464 (mtp) cc_final: 0.7015 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.7070
  time to fit residues: 71.6596
Evaluate side-chains
  77 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0070
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:   50.0000
   chunk 62 optimal weight:   40.0000
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    1.2004

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

Flipped N/Q/H residues before XYZ refinement:
A 286 ASN
F 241 GLN
F 276 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.162463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.089442 restraints weight = 13917.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 2.90
r_work: 0.2915 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2782 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8767
moved from start:          0.0920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8794  Z= 0.152
  Angle     :  0.581   7.689  11908  Z= 0.297
  Chirality :  0.045   0.267   1354
  Planarity :  0.004   0.033   1548
  Dihedral  :  6.957  89.628   1241
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  7.20 %
    Favored  : 92.16 %
  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:  0.04 (0.25), residues: 1111
  helix:  1.21 (0.27), residues: 394
  sheet:  0.67 (0.37), residues: 195
  loop : -1.18 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 243 
 TYR   0.023   0.001   TYR A 473 
 PHE   0.021   0.001   PHE A 152 
 TRP   0.007   0.001   TRP A 284 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8794)
  covalent geometry    : angle       0.58082 (11908)
  hydrogen bonds       : bond        0.04701 (  387)
  hydrogen bonds       : angle       5.26729 ( 1080)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.8915 (tpp) cc_final: 0.8681 (mmt)
REVERT: A  229 MET cc_start: 0.7100 (ttt) cc_final: 0.5576 (mpm)
REVERT: A  350 MET cc_start: 0.8764 (tmm) cc_final: 0.8526 (tmm)
REVERT: A  448 MET cc_start: 0.8393 (tmt) cc_final: 0.7383 (tmt)
REVERT: A  666 MET cc_start: 0.6938 (mmm) cc_final: 0.6699 (mmm)
REVERT: A  695 MET cc_start: 0.9206 (tmm) cc_final: 0.8996 (tmm)
REVERT: B  304 THR cc_start: 0.9464 (p) cc_final: 0.9248 (t)
REVERT: F   84 MET cc_start: 0.7664 (mtp) cc_final: 0.7284 (mtm)
REVERT: F  289 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.5061 (ptp-170)
  outliers start: 6
  outliers final: 1
  residues processed: 83
  average time/residue: 0.6448
  time to fit residues: 56.5541
Evaluate side-chains
  82 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain F residue  289 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 37 optimal weight:    0.4980
   chunk 55 optimal weight:    2.9990
   chunk 102 optimal weight:    0.5980
   chunk 107 optimal weight:    0.5980
   chunk 59 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 GLN
B 321 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.163128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.090675 restraints weight = 13871.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 2.81
r_work: 0.2938 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2805 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8751
moved from start:          0.1219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8794  Z= 0.125
  Angle     :  0.540   7.430  11908  Z= 0.276
  Chirality :  0.044   0.215   1354
  Planarity :  0.004   0.031   1548
  Dihedral  :  6.730  87.046   1241
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  9.02 %
    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:  0.10 (0.25), residues: 1111
  helix:  1.30 (0.27), residues: 395
  sheet:  0.54 (0.37), residues: 199
  loop : -1.12 (0.26), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 243 
 TYR   0.019   0.001   TYR A 473 
 PHE   0.010   0.001   PHE B 384 
 TRP   0.014   0.001   TRP A 284 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8794)
  covalent geometry    : angle       0.53954 (11908)
  hydrogen bonds       : bond        0.04068 (  387)
  hydrogen bonds       : angle       4.92456 ( 1080)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.9007 (tpp) cc_final: 0.8693 (mmt)
REVERT: A  217 MET cc_start: 0.8743 (mpm) cc_final: 0.8515 (mpm)
REVERT: A  229 MET cc_start: 0.6989 (ttt) cc_final: 0.5455 (mpm)
REVERT: A  350 MET cc_start: 0.8804 (tmm) cc_final: 0.8534 (tmm)
REVERT: A  448 MET cc_start: 0.8410 (tmt) cc_final: 0.7451 (tmt)
REVERT: A  666 MET cc_start: 0.7217 (mmm) cc_final: 0.6988 (mmm)
REVERT: A  695 MET cc_start: 0.9208 (tmm) cc_final: 0.8965 (tmm)
REVERT: F   84 MET cc_start: 0.7665 (mtp) cc_final: 0.7320 (mtm)
REVERT: F  289 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.4933 (ptp-170)
  outliers start: 5
  outliers final: 1
  residues processed: 87
  average time/residue: 0.5959
  time to fit residues: 54.7474
Evaluate side-chains
  82 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  499 ILE
Chi-restraints excluded: chain F residue  289 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 104 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 17 optimal weight:   20.0000
   chunk 6 optimal weight:    9.9990
   chunk 52 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 82 optimal weight:    0.0050
   chunk 21 optimal weight:   10.0000
   overall best weight:    2.3800

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

Flipped N/Q/H residues before XYZ refinement:
A 273 GLN
A 286 ASN
B 446 HIS
F 115 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.160829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.087111 restraints weight = 13953.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 2.85
r_work: 0.2868 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2735 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8808
moved from start:          0.1307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.076   8794  Z= 0.232
  Angle     :  0.594   8.037  11908  Z= 0.306
  Chirality :  0.047   0.188   1354
  Planarity :  0.004   0.035   1548
  Dihedral  :  6.690  86.165   1241
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 10.85 %
    Favored  : 88.08 %
  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: -0.01 (0.25), residues: 1111
  helix:  1.20 (0.27), residues: 393
  sheet:  0.46 (0.37), residues: 201
  loop : -1.17 (0.26), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 243 
 TYR   0.023   0.001   TYR A 473 
 PHE   0.026   0.002   PHE A 152 
 TRP   0.018   0.002   TRP A 284 
 HIS   0.005   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 ( 8794)
  covalent geometry    : angle       0.59383 (11908)
  hydrogen bonds       : bond        0.05149 (  387)
  hydrogen bonds       : angle       4.95271 ( 1080)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  217 MET cc_start: 0.8714 (mpm) cc_final: 0.8488 (mpm)
REVERT: A  229 MET cc_start: 0.7189 (ttt) cc_final: 0.5583 (mpm)
REVERT: A  350 MET cc_start: 0.8795 (tmm) cc_final: 0.8520 (tmm)
REVERT: A  549 MET cc_start: 0.9458 (OUTLIER) cc_final: 0.9194 (mtp)
REVERT: A  695 MET cc_start: 0.9187 (tmm) cc_final: 0.8862 (tmm)
REVERT: B  463 MET cc_start: 0.4813 (mmm) cc_final: 0.4399 (mpm)
REVERT: F   84 MET cc_start: 0.7705 (mtp) cc_final: 0.7338 (mtm)
REVERT: F  289 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.5172 (ptp-170)
  outliers start: 10
  outliers final: 3
  residues processed: 87
  average time/residue: 0.6288
  time to fit residues: 57.8740
Evaluate side-chains
  85 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  499 ILE
Chi-restraints excluded: chain A residue  549 MET
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain F residue  289 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 107 optimal weight:    0.7980
   chunk 98 optimal weight:   20.0000
   chunk 16 optimal weight:    9.9990
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0370
   chunk 59 optimal weight:    4.9990
   chunk 62 optimal weight:    8.9990
   chunk 35 optimal weight:    6.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.9462

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

Flipped N/Q/H residues before XYZ refinement:
A 273 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.162525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.089553 restraints weight = 13888.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 2.88
r_work: 0.2915 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2782 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8768
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8794  Z= 0.126
  Angle     :  0.534   9.139  11908  Z= 0.274
  Chirality :  0.044   0.168   1354
  Planarity :  0.004   0.030   1548
  Dihedral  :  6.050  84.234   1241
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 12.14 %
    Favored  : 86.90 %
  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:  0.11 (0.25), residues: 1111
  helix:  1.33 (0.27), residues: 394
  sheet:  0.46 (0.38), residues: 200
  loop : -1.08 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 243 
 TYR   0.016   0.001   TYR A 473 
 PHE   0.028   0.001   PHE A 307 
 TRP   0.020   0.002   TRP A 284 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8794)
  covalent geometry    : angle       0.53353 (11908)
  hydrogen bonds       : bond        0.03947 (  387)
  hydrogen bonds       : angle       4.72109 ( 1080)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.8984 (tpp) cc_final: 0.8760 (mmt)
REVERT: A  217 MET cc_start: 0.8677 (mpm) cc_final: 0.8463 (mpm)
REVERT: A  229 MET cc_start: 0.7174 (ttt) cc_final: 0.5593 (mpm)
REVERT: A  350 MET cc_start: 0.8814 (tmm) cc_final: 0.8499 (tmm)
REVERT: A  695 MET cc_start: 0.9159 (tmm) cc_final: 0.8873 (tmm)
REVERT: B  433 LYS cc_start: 0.7387 (tppt) cc_final: 0.7093 (tptt)
REVERT: F   84 MET cc_start: 0.7660 (mtp) cc_final: 0.7325 (mtm)
REVERT: F  289 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.4841 (ptp-170)
  outliers start: 9
  outliers final: 1
  residues processed: 82
  average time/residue: 0.6941
  time to fit residues: 60.1367
Evaluate side-chains
  78 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  499 ILE
Chi-restraints excluded: chain F residue  289 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 5 optimal weight:    9.9990
   chunk 99 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 67 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0770
   chunk 94 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 65 optimal weight:   20.0000
   chunk 103 optimal weight:    1.9990
   overall best weight:    1.2142

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

Flipped N/Q/H residues before XYZ refinement:
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.162342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.089330 restraints weight = 13886.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 2.87
r_work: 0.2909 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8776
moved from start:          0.1536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8794  Z= 0.145
  Angle     :  0.564  11.079  11908  Z= 0.286
  Chirality :  0.045   0.167   1354
  Planarity :  0.004   0.031   1548
  Dihedral  :  5.688  84.553   1241
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 12.67 %
    Favored  : 86.36 %
  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:  0.12 (0.26), residues: 1111
  helix:  1.27 (0.27), residues: 394
  sheet:  0.48 (0.38), residues: 200
  loop : -1.03 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 289 
 TYR   0.015   0.001   TYR A 473 
 PHE   0.028   0.001   PHE A 307 
 TRP   0.023   0.002   TRP A 284 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 8794)
  covalent geometry    : angle       0.56431 (11908)
  hydrogen bonds       : bond        0.04114 (  387)
  hydrogen bonds       : angle       4.71716 ( 1080)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.8969 (tpp) cc_final: 0.8713 (mmt)
REVERT: A  229 MET cc_start: 0.7190 (ttt) cc_final: 0.5565 (mpm)
REVERT: A  350 MET cc_start: 0.8834 (tmm) cc_final: 0.8482 (tmm)
REVERT: A  448 MET cc_start: 0.8466 (tmt) cc_final: 0.7406 (tmt)
REVERT: A  695 MET cc_start: 0.9156 (tmm) cc_final: 0.8813 (tmm)
REVERT: B  463 MET cc_start: 0.4500 (mmm) cc_final: 0.4037 (mpm)
REVERT: F   84 MET cc_start: 0.7641 (mtp) cc_final: 0.7280 (mtm)
REVERT: F  289 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.4955 (ptp-170)
  outliers start: 9
  outliers final: 3
  residues processed: 84
  average time/residue: 0.6711
  time to fit residues: 59.6626
Evaluate side-chains
  83 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  499 ILE
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  289 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 73 optimal weight:    0.0020
   chunk 25 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 26 optimal weight:   20.0000
   chunk 63 optimal weight:    0.0870
   chunk 87 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 40 optimal weight:    8.9990
   chunk 97 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.5166

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

Flipped N/Q/H residues before XYZ refinement:
A 273 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.163960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.091646 restraints weight = 13937.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 2.93
r_work: 0.2957 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8794  Z= 0.103
  Angle     :  0.533  10.910  11908  Z= 0.269
  Chirality :  0.044   0.142   1354
  Planarity :  0.003   0.032   1548
  Dihedral  :  5.295  85.032   1241
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 13.21 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.26), residues: 1111
  helix:  1.41 (0.27), residues: 394
  sheet:  0.53 (0.38), residues: 200
  loop : -0.97 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 289 
 TYR   0.012   0.001   TYR A 473 
 PHE   0.028   0.001   PHE A 307 
 TRP   0.030   0.002   TRP A 284 
 HIS   0.007   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 8794)
  covalent geometry    : angle       0.53317 (11908)
  hydrogen bonds       : bond        0.03368 (  387)
  hydrogen bonds       : angle       4.56938 ( 1080)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.8909 (tpp) cc_final: 0.8564 (mmt)
REVERT: A  128 MET cc_start: 0.9239 (mmm) cc_final: 0.8876 (mmm)
REVERT: A  229 MET cc_start: 0.7203 (ttt) cc_final: 0.5584 (mpm)
REVERT: A  350 MET cc_start: 0.8895 (tmm) cc_final: 0.8486 (tmm)
REVERT: A  448 MET cc_start: 0.8434 (tmt) cc_final: 0.7404 (tmt)
REVERT: A  695 MET cc_start: 0.9160 (tmm) cc_final: 0.8775 (tmm)
REVERT: B  463 MET cc_start: 0.4646 (mmm) cc_final: 0.4195 (mpm)
REVERT: F   84 MET cc_start: 0.7635 (mtp) cc_final: 0.7316 (mtm)
REVERT: F  289 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.4672 (ptp-170)
  outliers start: 7
  outliers final: 1
  residues processed: 87
  average time/residue: 0.6433
  time to fit residues: 59.3310
Evaluate side-chains
  79 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain F residue  289 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 44 optimal weight:    8.9990
   chunk 109 optimal weight:    1.9990
   chunk 12 optimal weight:   20.0000
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0670
   chunk 2 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 49 optimal weight:    0.7980
   chunk 28 optimal weight:   10.0000
   overall best weight:    1.1522

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

Flipped N/Q/H residues before XYZ refinement:
F 236 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.162929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.089859 restraints weight = 13754.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 2.89
r_work: 0.2924 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2790 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8767
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8794  Z= 0.141
  Angle     :  0.587  18.198  11908  Z= 0.288
  Chirality :  0.044   0.148   1354
  Planarity :  0.004   0.032   1548
  Dihedral  :  5.268  86.086   1241
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 13.64 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.26), residues: 1111
  helix:  1.43 (0.27), residues: 394
  sheet:  0.53 (0.38), residues: 200
  loop : -0.97 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 289 
 TYR   0.013   0.001   TYR A 214 
 PHE   0.029   0.001   PHE A 307 
 TRP   0.034   0.002   TRP A 284 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8794)
  covalent geometry    : angle       0.58695 (11908)
  hydrogen bonds       : bond        0.03938 (  387)
  hydrogen bonds       : angle       4.55776 ( 1080)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.8911 (tpp) cc_final: 0.8583 (mmt)
REVERT: A  128 MET cc_start: 0.9323 (mmm) cc_final: 0.9016 (mmm)
REVERT: A  174 MET cc_start: 0.8939 (mmm) cc_final: 0.8502 (tmt)
REVERT: A  229 MET cc_start: 0.7192 (ttt) cc_final: 0.5580 (mpm)
REVERT: A  350 MET cc_start: 0.8857 (tmm) cc_final: 0.8404 (tmm)
REVERT: A  448 MET cc_start: 0.8439 (tmt) cc_final: 0.7439 (tmt)
REVERT: A  695 MET cc_start: 0.9139 (tmm) cc_final: 0.8765 (tmm)
REVERT: B  328 GLU cc_start: 0.9026 (tt0) cc_final: 0.8783 (tt0)
REVERT: B  463 MET cc_start: 0.4950 (mmm) cc_final: 0.4512 (mpm)
REVERT: F   84 MET cc_start: 0.7631 (mtp) cc_final: 0.7345 (mtm)
REVERT: F  289 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.4947 (ptp-170)
  outliers start: 4
  outliers final: 3
  residues processed: 82
  average time/residue: 0.6906
  time to fit residues: 59.7881
Evaluate side-chains
  82 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  499 ILE
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  289 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0570
   chunk 36 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 14 optimal weight:   20.0000
   chunk 109 optimal weight:    0.9990
   chunk 24 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 86 optimal weight:    0.7980
   chunk 105 optimal weight:    0.8980
   overall best weight:    0.7300

-------------------------------------------------------------------------------
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 = 0.4217 r_free = 0.4217 target = 0.163527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.090976 restraints weight = 13789.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 2.90
r_work: 0.2944 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2814 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8794  Z= 0.113
  Angle     :  0.554  11.825  11908  Z= 0.276
  Chirality :  0.044   0.149   1354
  Planarity :  0.003   0.036   1548
  Dihedral  :  5.154  86.528   1241
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 13.64 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.26), residues: 1111
  helix:  1.46 (0.27), residues: 394
  sheet:  0.55 (0.37), residues: 200
  loop : -0.95 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 135 
 TYR   0.012   0.001   TYR A 473 
 PHE   0.028   0.001   PHE A 307 
 TRP   0.039   0.002   TRP A 284 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8794)
  covalent geometry    : angle       0.55394 (11908)
  hydrogen bonds       : bond        0.03544 (  387)
  hydrogen bonds       : angle       4.48393 ( 1080)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.8882 (tpp) cc_final: 0.8575 (mmt)
REVERT: A  128 MET cc_start: 0.9304 (mmm) cc_final: 0.9039 (mmm)
REVERT: A  174 MET cc_start: 0.8905 (mmm) cc_final: 0.8536 (tmt)
REVERT: A  229 MET cc_start: 0.7189 (ttt) cc_final: 0.5583 (mpm)
REVERT: A  350 MET cc_start: 0.8887 (tmm) cc_final: 0.8497 (tmm)
REVERT: A  448 MET cc_start: 0.8432 (tmt) cc_final: 0.7432 (tmt)
REVERT: A  549 MET cc_start: 0.9388 (OUTLIER) cc_final: 0.8981 (mtm)
REVERT: A  695 MET cc_start: 0.9106 (tmm) cc_final: 0.8702 (tmm)
REVERT: B  328 GLU cc_start: 0.8990 (tt0) cc_final: 0.8734 (tt0)
REVERT: B  433 LYS cc_start: 0.7286 (tppt) cc_final: 0.7061 (tptt)
REVERT: B  463 MET cc_start: 0.5255 (mmm) cc_final: 0.4829 (mpm)
REVERT: F   84 MET cc_start: 0.7595 (mtp) cc_final: 0.7303 (mtm)
REVERT: F  236 ASN cc_start: 0.9484 (t0) cc_final: 0.9170 (t0)
REVERT: F  289 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.4798 (ptp-170)
  outliers start: 4
  outliers final: 2
  residues processed: 84
  average time/residue: 0.7089
  time to fit residues: 62.9869
Evaluate side-chains
  82 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  499 ILE
Chi-restraints excluded: chain A residue  549 MET
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain F residue  289 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 44 optimal weight:    8.9990
   chunk 68 optimal weight:    3.9990
   chunk 17 optimal weight:   20.0000
   chunk 48 optimal weight:    2.9990
   chunk 24 optimal weight:    9.9990
   chunk 45 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 95 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 16 optimal weight:    9.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.162675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.089432 restraints weight = 13841.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 2.92
r_work: 0.2913 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2781 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8774
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      :  0.004   0.048   8794  Z= 0.150
  Angle     :  0.583  11.944  11908  Z= 0.292
  Chirality :  0.044   0.157   1354
  Planarity :  0.004   0.039   1548
  Dihedral  :  5.207  86.958   1241
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 13.96 %
    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:  0.23 (0.26), residues: 1111
  helix:  1.38 (0.27), residues: 394
  sheet:  0.51 (0.37), residues: 200
  loop : -0.96 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 289 
 TYR   0.014   0.001   TYR A 473 
 PHE   0.030   0.001   PHE A 307 
 TRP   0.072   0.003   TRP A 284 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 8794)
  covalent geometry    : angle       0.58274 (11908)
  hydrogen bonds       : bond        0.04135 (  387)
  hydrogen bonds       : angle       4.53052 ( 1080)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.8969 (tpp) cc_final: 0.8561 (mmt)
REVERT: A  128 MET cc_start: 0.9320 (mmm) cc_final: 0.9043 (mmm)
REVERT: A  174 MET cc_start: 0.8853 (mmm) cc_final: 0.8571 (tmt)
REVERT: A  448 MET cc_start: 0.8454 (tmt) cc_final: 0.7471 (tmt)
REVERT: A  549 MET cc_start: 0.9438 (OUTLIER) cc_final: 0.9046 (mtm)
REVERT: A  695 MET cc_start: 0.9099 (tmm) cc_final: 0.8680 (tmm)
REVERT: B  328 GLU cc_start: 0.8943 (tt0) cc_final: 0.8681 (tt0)
REVERT: B  433 LYS cc_start: 0.7350 (tppt) cc_final: 0.7140 (tptt)
REVERT: B  463 MET cc_start: 0.5327 (mmm) cc_final: 0.4904 (mpm)
REVERT: F   84 MET cc_start: 0.7642 (mtp) cc_final: 0.7354 (mtm)
REVERT: F  236 ASN cc_start: 0.9487 (t0) cc_final: 0.9260 (t0)
REVERT: F  289 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.4947 (ptp-170)
  outliers start: 5
  outliers final: 3
  residues processed: 80
  average time/residue: 0.7523
  time to fit residues: 63.4679
Evaluate side-chains
  82 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  499 ILE
Chi-restraints excluded: chain A residue  549 MET
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain F residue  289 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 14 optimal weight:   40.0000
   chunk 21 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 64 optimal weight:   10.0000
   chunk 68 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 88 optimal weight:    9.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 344 ASN
** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.161266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.087642 restraints weight = 13844.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 2.84
r_work: 0.2878 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8803
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072   8794  Z= 0.220
  Angle     :  0.636  12.126  11908  Z= 0.320
  Chirality :  0.046   0.157   1354
  Planarity :  0.004   0.041   1548
  Dihedral  :  5.354  87.152   1241
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 13.43 %
    Favored  : 85.61 %
  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:  0.12 (0.26), residues: 1111
  helix:  1.27 (0.27), residues: 393
  sheet:  0.45 (0.37), residues: 200
  loop : -1.00 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 230 
 TYR   0.017   0.001   TYR A 473 
 PHE   0.030   0.002   PHE A 307 
 TRP   0.057   0.003   TRP A 284 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 ( 8794)
  covalent geometry    : angle       0.63588 (11908)
  hydrogen bonds       : bond        0.04853 (  387)
  hydrogen bonds       : angle       4.65845 ( 1080)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4529.70 seconds
wall clock time: 77 minutes 40.37 seconds (4660.37 seconds total)