Starting phenix.real_space_refine
on Wed Feb  4 07:17:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zv5_60508/02_2026/8zv5_60508.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zv5_60508/02_2026/8zv5_60508.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zv5_60508/02_2026/8zv5_60508.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zv5_60508/02_2026/8zv5_60508.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zv5_60508/02_2026/8zv5_60508.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zv5_60508/02_2026/8zv5_60508.cif"
  }
  resolution = 3.1
  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=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      51      5.16       5
     C    5714      2.51       5
     N    1590      2.21       5
     O    1718      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: 9073
  Number of models: 1
  Model: ""
    Number of chains: 3
    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: 1910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 247, 1910
          Classifications: {'peptide': 247}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 231}
    Chain: "F"
      Number of atoms: 1973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1973
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
  Time building chain proxies: 1.68, per 1000 atoms: 0.19
  Number of scatterers: 9073
  At special positions: 0
  Unit cell: (95.76, 97.44, 134.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      51     16.00
     O    1718      8.00
     N    1590      7.00
     C    5714      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: 0.71
  Conformation dependent library (CDL) restraints added in 353.6 milliseconds
  

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2176

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 14 sheets defined
      40.4% alpha, 18.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 72 through 86
    Processing helix  chain 'A' and resid 95 through 99
      removed outlier: 4.100A  pdb=" N   SER A  99 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 106
      removed outlier: 3.529A  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
      removed outlier: 3.769A  pdb=" N   ILE A 127 " --> pdb=" O   ASN A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 159
    Processing helix  chain 'A' and resid 167 through 176
    Processing helix  chain 'A' and resid 176 through 187
    Processing helix  chain 'A' and resid 201 through 213
    Processing helix  chain 'A' and resid 234 through 253
    Processing helix  chain 'A' and resid 309 through 327
    Processing helix  chain 'A' and resid 358 through 366
      removed outlier: 4.378A  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 507
      removed outlier: 3.537A  pdb=" N   ASP A 506 " --> pdb=" O   LYS A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 541
    Processing helix  chain 'A' and resid 641 through 647
    Processing helix  chain 'A' and resid 648 through 650
      No H-bonds generated for 'chain 'A' and resid 648 through 650'
    Processing helix  chain 'B' and resid 299 through 303
    Processing helix  chain 'B' and resid 315 through 324
      removed outlier: 3.852A  pdb=" N   ILE B 319 " --> pdb=" O   ASN B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 327
      No H-bonds generated for 'chain 'B' and resid 325 through 327'
    Processing helix  chain 'B' and resid 360 through 365
      removed outlier: 3.749A  pdb=" N   SER B 363 " --> pdb=" O   LYS B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 384
      removed outlier: 3.541A  pdb=" N   PHE B 377 " --> pdb=" O   LYS B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 406
      removed outlier: 3.614A  pdb=" N   GLU B 404 " --> pdb=" O   GLY B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 421
    Processing helix  chain 'B' and resid 437 through 442
    Processing helix  chain 'B' and resid 444 through 448
    Processing helix  chain 'B' and resid 464 through 473
    Processing helix  chain 'B' and resid 478 through 491
      removed outlier: 3.723A  pdb=" N   ALA B 482 " --> pdb=" O   ASN B 478 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ALA B 484 " --> pdb=" O   GLU B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 493 through 499
    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 48
      removed outlier: 3.552A  pdb=" N   LEU F  48 " --> pdb=" O   ARG F  44 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 51 through 61
    Processing helix  chain 'F' and resid 65 through 74
    Processing helix  chain 'F' and resid 97 through 101
    Processing helix  chain 'F' and resid 128 through 132
    Processing helix  chain 'F' and resid 134 through 152
    Processing helix  chain 'F' and resid 169 through 186
      removed outlier: 4.098A  pdb=" N   LEU F 173 " --> pdb=" O   GLY F 169 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 205 through 210
      removed outlier: 3.644A  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 65 through 68
      removed outlier: 6.337A  pdb=" N   ILE A  66 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139
    Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 219
    Processing sheet with id=AA4, first strand: chain 'A' and resid 282 through 284
      removed outlier: 6.456A  pdb=" N   THR A 334 " --> pdb=" O   MET A 350 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   MET A 350 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLU A 336 " --> pdb=" O   LEU A 348 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 282 through 284
      removed outlier: 4.733A  pdb=" N   HIS A 269 " --> pdb=" O   CYS A 290 " (cutoff:3.500A)
      removed outlier: 5.062A  pdb=" N   SER A 291 " --> pdb=" O   VAL A 300 " (cutoff:3.500A)
      removed outlier: 7.990A  pdb=" N   VAL A 300 " --> pdb=" O   SER A 291 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   GLN A 293 " --> pdb=" O   LYS A 298 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   LYS A 298 " --> pdb=" O   GLN A 293 " (cutoff:3.500A)
      removed outlier: 14.444A  pdb=" N   GLN A 297 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 11.258A  pdb=" N   TYR A 401 " --> pdb=" O   GLN A 297 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   VAL A 299 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 403 through 404
    Processing sheet with id=AA7, first strand: chain 'A' and resid 415 through 416
      removed outlier: 4.276A  pdb=" N   GLY A 415 " --> pdb=" O   ILE A 441 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 420 through 421
    Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 564
      removed outlier: 6.688A  pdb=" N   SER A 626 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   ARG A 619 " --> pdb=" O   ASN A 624 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ASN A 624 " --> pdb=" O   ARG A 619 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   THR A 632 " --> pdb=" O   PHE A 629 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASN A 637 " --> pdb=" O   LYS A 564 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 670 through 673
      removed outlier: 7.019A  pdb=" N   VAL A 689 " --> pdb=" O   VAL A 671 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   VAL A 673 " --> pdb=" O   ILE A 687 " (cutoff:3.500A)
      removed outlier: 8.776A  pdb=" N   ILE A 687 " --> pdb=" O   VAL A 673 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   CYS A 688 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   MET A 699 " --> pdb=" O   CYS A 688 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   ILE A 690 " --> pdb=" O   ASN A 697 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASN A 697 " --> pdb=" O   ILE A 690 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 709 through 710
      removed outlier: 3.667A  pdb=" N   SER A 709 " --> pdb=" O   GLU A 726 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 329 through 332
      removed outlier: 4.692A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   LYS B 426 " --> pdb=" O   THR B 451 " (cutoff:3.500A)
      removed outlier: 8.132A  pdb=" N   TYR B 453 " --> pdb=" O   LYS B 426 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   THR B 428 " --> pdb=" O   TYR B 453 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ASP B 504 " --> pdb=" O   ASN B 452 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 80 through 82
      removed outlier: 4.667A  pdb=" N   THR F 109 " --> pdb=" O   SER F  82 " (cutoff:3.500A)
      removed outlier: 8.554A  pdb=" N   ILE F 156 " --> pdb=" O   LEU F 118 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   TYR F 120 " --> pdb=" O   ILE F 156 " (cutoff:3.500A)
      removed outlier: 8.082A  pdb=" N   LEU F 158 " --> pdb=" O   TYR F 120 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   PHE F 122 " --> pdb=" O   LEU F 158 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   VAL F 155 " --> pdb=" O   ILE F 193 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   LEU F 195 " --> pdb=" O   VAL F 155 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLY F 157 " --> pdb=" O   LEU F 195 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   ARG F 259 " --> pdb=" O   THR F 214 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 199 through 201
      removed outlier: 6.392A  pdb=" N   CYS F 200 " --> pdb=" O   PHE F 224 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5

    405 hydrogen bonds defined for protein.
    1143 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: 1.30

  Time building geometry restraints manager: 0.89 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: 3057
        1.34 -     1.46: 1707
        1.46 -     1.58: 4391
        1.58 -     1.69: 1
        1.69 -     1.81: 82
  Bond restraints: 9238
  Sorted by residual:
  bond pdb=" CB  PRO A 193 "
       pdb=" CG  PRO A 193 "
    ideal  model  delta    sigma   weight residual
    1.492  1.612 -0.120 5.00e-02 4.00e+02 5.71e+00
  bond pdb=" CG  PRO A 193 "
       pdb=" CD  PRO A 193 "
    ideal  model  delta    sigma   weight residual
    1.503  1.448  0.055 3.40e-02 8.65e+02 2.60e+00
  bond pdb=" CB  LYS F 232 "
       pdb=" CG  LYS F 232 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.12e+00
  bond pdb=" CG1 ILE F 196 "
       pdb=" CD1 ILE F 196 "
    ideal  model  delta    sigma   weight residual
    1.513  1.472  0.041 3.90e-02 6.57e+02 1.09e+00
  bond pdb=" CG  MET A 128 "
       pdb=" SD  MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.803  1.778  0.025 2.50e-02 1.60e+03 1.01e+00
  ... (remaining 9233 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 12385
        2.49 -     4.99: 98
        4.99 -     7.48: 9
        7.48 -     9.98: 3
        9.98 -    12.47: 1
  Bond angle restraints: 12496
  Sorted by residual:
  angle pdb=" CA  PRO A 193 "
        pdb=" N   PRO A 193 "
        pdb=" CD  PRO A 193 "
      ideal   model   delta    sigma   weight residual
     112.00  103.48    8.52 1.40e+00 5.10e-01 3.70e+01
  angle pdb=" C   ILE A 127 "
        pdb=" N   MET A 128 "
        pdb=" CA  MET A 128 "
      ideal   model   delta    sigma   weight residual
     121.14  113.01    8.13 1.75e+00 3.27e-01 2.16e+01
  angle pdb=" CB  MET A 466 "
        pdb=" CG  MET A 466 "
        pdb=" SD  MET A 466 "
      ideal   model   delta    sigma   weight residual
     112.70  125.17  -12.47 3.00e+00 1.11e-01 1.73e+01
  angle pdb=" N   PRO A 193 "
        pdb=" CD  PRO A 193 "
        pdb=" CG  PRO A 193 "
      ideal   model   delta    sigma   weight residual
     103.20   97.30    5.90 1.50e+00 4.44e-01 1.55e+01
  angle pdb=" CB  LYS F 232 "
        pdb=" CG  LYS F 232 "
        pdb=" CD  LYS F 232 "
      ideal   model   delta    sigma   weight residual
     111.30  119.55   -8.25 2.30e+00 1.89e-01 1.29e+01
  ... (remaining 12491 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.59: 4961
       13.59 -    27.17: 451
       27.17 -    40.76: 145
       40.76 -    54.35: 21
       54.35 -    67.93: 22
  Dihedral angle restraints: 5600
    sinusoidal: 2216
      harmonic: 3384
  Sorted by residual:
  dihedral pdb=" CA  GLU A 726 "
           pdb=" C   GLU A 726 "
           pdb=" N   LEU A 727 "
           pdb=" CA  LEU A 727 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.68  -28.32     0      5.00e+00 4.00e-02 3.21e+01
  dihedral pdb=" CA  VAL A 661 "
           pdb=" C   VAL A 661 "
           pdb=" N   LEU A 662 "
           pdb=" CA  LEU A 662 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.85   24.15     0      5.00e+00 4.00e-02 2.33e+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  -89.11   59.11     1      2.00e+01 2.50e-03 1.17e+01
  ... (remaining 5597 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 942
       0.040 -    0.079: 330
       0.079 -    0.119: 125
       0.119 -    0.158: 17
       0.158 -    0.198: 2
  Chirality restraints: 1416
  Sorted by residual:
  chirality pdb=" CG  LEU A 727 "
            pdb=" CB  LEU A 727 "
            pdb=" CD1 LEU A 727 "
            pdb=" CD2 LEU A 727 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 9.79e-01
  chirality pdb=" CA  ILE A 192 "
            pdb=" N   ILE A 192 "
            pdb=" C   ILE A 192 "
            pdb=" CB  ILE A 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.41e-01
  chirality pdb=" CA  VAL B 355 "
            pdb=" N   VAL B 355 "
            pdb=" C   VAL B 355 "
            pdb=" CB  VAL B 355 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.98e-01
  ... (remaining 1413 not shown)

  Planarity restraints: 1633
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 192 "   -0.071 5.00e-02 4.00e+02   1.02e-01 1.66e+01
        pdb=" N   PRO A 193 "    0.176 5.00e-02 4.00e+02
        pdb=" CA  PRO A 193 "   -0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO A 193 "   -0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 473 "    0.015 2.00e-02 2.50e+03   1.21e-02 2.93e+00
        pdb=" CG  TYR A 473 "   -0.030 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
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 513 "   -0.008 2.00e-02 2.50e+03   1.68e-02 2.83e+00
        pdb=" C   ALA B 513 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ALA B 513 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ARG B 514 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1630 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2001
        2.79 -     3.31: 8924
        3.31 -     3.84: 15231
        3.84 -     4.37: 17767
        4.37 -     4.90: 30336
  Nonbonded interactions: 74259
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 420 "
            pdb=" OH  TYR A 473 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" NH2 ARG F 117 "
            pdb=" O   LEU F 278 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" NH1 ARG A 230 "
            pdb=" O   GLY A 241 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" NH2 ARG A 268 "
            pdb=" O   GLY A 497 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" O   GLY A 226 "
            pdb=" ND2 ASN A 296 "
     model   vdw
     2.317 3.120
  ... (remaining 74254 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:             3.610
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.300
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
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      :  0.005   0.120   9238  Z= 0.189
  Angle     :  0.603  12.470  12496  Z= 0.328
  Chirality :  0.045   0.198   1416
  Planarity :  0.005   0.102   1633
  Dihedral  : 12.459  67.932   3424
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.24), residues: 1175
  helix:  0.28 (0.25), residues: 429
  sheet:  0.48 (0.37), residues: 193
  loop : -0.96 (0.26), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 529 
 TYR   0.030   0.002   TYR A 473 
 PHE   0.019   0.002   PHE F 122 
 TRP   0.026   0.002   TRP A 394 
 HIS   0.007   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 9238)
  covalent geometry    : angle       0.60251 (12496)
  hydrogen bonds       : bond        0.14856 (  403)
  hydrogen bonds       : angle       6.58703 ( 1143)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  105 MET cc_start: 0.7658 (mmp) cc_final: 0.7387 (ptm)
REVERT: A  128 MET cc_start: 0.9183 (pmm) cc_final: 0.8909 (pmm)
REVERT: A  233 TRP cc_start: 0.7867 (m100) cc_final: 0.6874 (m100)
REVERT: A  373 MET cc_start: 0.7346 (tpt) cc_final: 0.7064 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0985
  time to fit residues: 13.8992
Evaluate side-chains
  83 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    0.2980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 140 HIS
A 169 HIS
A 344 ASN
A 355 GLN
B 446 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.171061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.101950 restraints weight = 16053.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 3.58
r_work: 0.3006 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.0903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9238  Z= 0.124
  Angle     :  0.542   6.971  12496  Z= 0.286
  Chirality :  0.044   0.164   1416
  Planarity :  0.004   0.048   1633
  Dihedral  :  4.223  26.135   1275
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  5.21 %
    Favored  : 94.28 %
  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: -0.14 (0.24), residues: 1175
  helix:  0.60 (0.25), residues: 434
  sheet:  0.45 (0.37), residues: 199
  loop : -0.82 (0.27), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 529 
 TYR   0.021   0.001   TYR A 473 
 PHE   0.014   0.001   PHE A 152 
 TRP   0.014   0.001   TRP A 394 
 HIS   0.004   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9238)
  covalent geometry    : angle       0.54223 (12496)
  hydrogen bonds       : bond        0.04327 (  403)
  hydrogen bonds       : angle       5.24309 ( 1143)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.7926 (mmp) cc_final: 0.7427 (ptm)
REVERT: A  124 MET cc_start: 0.9078 (tpp) cc_final: 0.8866 (tpt)
REVERT: A  174 MET cc_start: 0.8302 (ppp) cc_final: 0.8093 (ppp)
REVERT: A  233 TRP cc_start: 0.7958 (m100) cc_final: 0.7406 (m100)
REVERT: A  316 MET cc_start: 0.9002 (mmm) cc_final: 0.8728 (mmm)
REVERT: A  373 MET cc_start: 0.7697 (tpt) cc_final: 0.7485 (tpt)
REVERT: A  394 TRP cc_start: 0.8064 (t-100) cc_final: 0.7623 (t-100)
REVERT: F   61 ARG cc_start: 0.8453 (mtm-85) cc_final: 0.8250 (mtm-85)
  outliers start: 5
  outliers final: 4
  residues processed: 98
  average time/residue: 0.0896
  time to fit residues: 12.4727
Evaluate side-chains
  90 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain B residue  446 HIS
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  212 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 60 optimal weight:   20.0000
   chunk 91 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 2 optimal weight:    7.9990
   chunk 34 optimal weight:    9.9990
   chunk 80 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 14 optimal weight:    8.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 273 GLN
F 236 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.169227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.094864 restraints weight = 16007.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.91
r_work: 0.3023 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.1100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9238  Z= 0.208
  Angle     :  0.562   8.786  12496  Z= 0.295
  Chirality :  0.046   0.156   1416
  Planarity :  0.004   0.040   1633
  Dihedral  :  4.281  28.641   1275
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  6.84 %
    Favored  : 92.03 %
  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 (0.24), residues: 1175
  helix:  0.57 (0.24), residues: 439
  sheet:  0.55 (0.36), residues: 195
  loop : -0.88 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 529 
 TYR   0.020   0.001   TYR A 473 
 PHE   0.019   0.002   PHE F 122 
 TRP   0.009   0.001   TRP A 394 
 HIS   0.011   0.001   HIS B 446 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 9238)
  covalent geometry    : angle       0.56243 (12496)
  hydrogen bonds       : bond        0.04596 (  403)
  hydrogen bonds       : angle       5.05011 ( 1143)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A  105 MET cc_start: 0.8009 (mmp) cc_final: 0.7419 (ptm)
REVERT: A  128 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8932 (ppp)
REVERT: A  174 MET cc_start: 0.8357 (ppp) cc_final: 0.7901 (ppp)
REVERT: A  233 TRP cc_start: 0.7969 (m100) cc_final: 0.7349 (m100)
REVERT: A  316 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8849 (mmm)
REVERT: A  350 MET cc_start: 0.6736 (ptt) cc_final: 0.6463 (tmm)
  outliers start: 11
  outliers final: 6
  residues processed: 94
  average time/residue: 0.0958
  time to fit residues: 12.6117
Evaluate side-chains
  87 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 MET
Chi-restraints excluded: chain A residue  316 MET
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain B residue  463 MET
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  212 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 7 optimal weight:   20.0000
   chunk 96 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:   20.0000
   chunk 91 optimal weight:    7.9990
   chunk 31 optimal weight:    6.9990
   chunk 90 optimal weight:    0.0040
   chunk 2 optimal weight:    6.9990
   chunk 75 optimal weight:    0.5980
   overall best weight:    0.8994

-------------------------------------------------------------------------------
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 = 0.4345 r_free = 0.4345 target = 0.170774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.098729 restraints weight = 16289.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 3.08
r_work: 0.3034 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   9238  Z= 0.121
  Angle     :  0.525  10.578  12496  Z= 0.274
  Chirality :  0.044   0.154   1416
  Planarity :  0.004   0.040   1633
  Dihedral  :  4.121  24.513   1275
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  8.27 %
    Favored  : 90.30 %
  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:  0.02 (0.24), residues: 1175
  helix:  0.78 (0.25), residues: 434
  sheet:  0.55 (0.36), residues: 200
  loop : -0.79 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 529 
 TYR   0.017   0.001   TYR A 473 
 PHE   0.013   0.001   PHE B 384 
 TRP   0.009   0.001   TRP A 394 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 9238)
  covalent geometry    : angle       0.52513 (12496)
  hydrogen bonds       : bond        0.03748 (  403)
  hydrogen bonds       : angle       4.84974 ( 1143)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.7989 (mmp) cc_final: 0.7437 (ptm)
REVERT: A  128 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.9033 (ppp)
REVERT: A  174 MET cc_start: 0.8371 (ppp) cc_final: 0.7926 (ppp)
REVERT: A  233 TRP cc_start: 0.7986 (m100) cc_final: 0.7427 (m100)
REVERT: A  350 MET cc_start: 0.6815 (ptt) cc_final: 0.6553 (tmm)
REVERT: F   61 ARG cc_start: 0.8457 (mtm-85) cc_final: 0.7776 (mtm-85)
  outliers start: 14
  outliers final: 8
  residues processed: 97
  average time/residue: 0.0884
  time to fit residues: 12.1421
Evaluate side-chains
  91 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 MET
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  670 VAL
Chi-restraints excluded: chain B residue  463 MET
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  212 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 34 optimal weight:    9.9990
   chunk 67 optimal weight:    4.9990
   chunk 104 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 98 optimal weight:    0.9980
   chunk 27 optimal weight:    8.9990
   chunk 42 optimal weight:    0.3980
   chunk 91 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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 = 0.4335 r_free = 0.4335 target = 0.169689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.094871 restraints weight = 16216.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 3.18
r_work: 0.3035 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9238  Z= 0.169
  Angle     :  0.560  10.975  12496  Z= 0.288
  Chirality :  0.045   0.150   1416
  Planarity :  0.004   0.041   1633
  Dihedral  :  4.191  28.068   1275
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  8.99 %
    Favored  : 89.79 %
  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: -0.00 (0.24), residues: 1175
  helix:  0.74 (0.25), residues: 440
  sheet:  0.59 (0.36), residues: 200
  loop : -0.82 (0.27), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 529 
 TYR   0.016   0.001   TYR A 473 
 PHE   0.017   0.001   PHE F 122 
 TRP   0.008   0.001   TRP A 284 
 HIS   0.007   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 9238)
  covalent geometry    : angle       0.56041 (12496)
  hydrogen bonds       : bond        0.04104 (  403)
  hydrogen bonds       : angle       4.79412 ( 1143)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.7955 (mmp) cc_final: 0.7431 (ptm)
REVERT: A  174 MET cc_start: 0.8349 (ppp) cc_final: 0.7981 (ppp)
REVERT: A  229 MET cc_start: 0.4794 (mtt) cc_final: 0.3940 (mpp)
REVERT: A  233 TRP cc_start: 0.8052 (m100) cc_final: 0.7453 (m100)
REVERT: A  316 MET cc_start: 0.9209 (mmm) cc_final: 0.8951 (mmm)
REVERT: F   61 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.7766 (mtm-85)
  outliers start: 12
  outliers final: 8
  residues processed: 93
  average time/residue: 0.0995
  time to fit residues: 13.1849
Evaluate side-chains
  92 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 MET
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  670 VAL
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  212 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 23 optimal weight:   20.0000
   chunk 0 optimal weight:   30.0000
   chunk 56 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 8 optimal weight:   20.0000
   chunk 13 optimal weight:    5.9990
   chunk 111 optimal weight:    0.0770
   chunk 107 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   chunk 90 optimal weight:    0.0040
   chunk 4 optimal weight:    0.0270
   overall best weight:    0.4008

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

Flipped N/Q/H residues before XYZ refinement:
B 446 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.171401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.097371 restraints weight = 16196.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 3.05
r_work: 0.3082 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9238  Z= 0.103
  Angle     :  0.554  13.927  12496  Z= 0.276
  Chirality :  0.044   0.154   1416
  Planarity :  0.003   0.040   1633
  Dihedral  :  4.010  23.031   1275
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 10.11 %
    Favored  : 88.97 %
  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: 1175
  helix:  0.89 (0.25), residues: 433
  sheet:  0.64 (0.37), residues: 200
  loop : -0.78 (0.27), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 529 
 TYR   0.012   0.001   TYR A 473 
 PHE   0.013   0.001   PHE A 263 
 TRP   0.009   0.001   TRP A 394 
 HIS   0.004   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 9238)
  covalent geometry    : angle       0.55381 (12496)
  hydrogen bonds       : bond        0.03425 (  403)
  hydrogen bonds       : angle       4.67462 ( 1143)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.7947 (mmp) cc_final: 0.7440 (ptm)
REVERT: A  146 LEU cc_start: 0.8739 (tp) cc_final: 0.8438 (pt)
REVERT: A  233 TRP cc_start: 0.8026 (m100) cc_final: 0.7499 (m100)
REVERT: A  316 MET cc_start: 0.9246 (mmm) cc_final: 0.8982 (mmm)
REVERT: F   61 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.7837 (mtm-85)
  outliers start: 9
  outliers final: 7
  residues processed: 97
  average time/residue: 0.0997
  time to fit residues: 13.6157
Evaluate side-chains
  93 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  670 VAL
Chi-restraints excluded: chain B residue  463 MET
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  212 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 106 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 26 optimal weight:   10.0000
   chunk 103 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 109 optimal weight:    0.8980
   chunk 46 optimal weight:    8.9990
   chunk 72 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4353 r_free = 0.4353 target = 0.171194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.096890 restraints weight = 16275.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 3.13
r_work: 0.3069 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9238  Z= 0.118
  Angle     :  0.557  11.839  12496  Z= 0.282
  Chirality :  0.044   0.198   1416
  Planarity :  0.003   0.040   1633
  Dihedral  :  4.010  23.785   1275
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 10.83 %
    Favored  : 88.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.25), residues: 1175
  helix:  0.94 (0.25), residues: 433
  sheet:  0.69 (0.37), residues: 199
  loop : -0.76 (0.27), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 529 
 TYR   0.017   0.001   TYR B 417 
 PHE   0.014   0.001   PHE B 384 
 TRP   0.008   0.001   TRP A 394 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9238)
  covalent geometry    : angle       0.55679 (12496)
  hydrogen bonds       : bond        0.03519 (  403)
  hydrogen bonds       : angle       4.63468 ( 1143)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.7970 (mmp) cc_final: 0.7437 (ptm)
REVERT: A  146 LEU cc_start: 0.8717 (tp) cc_final: 0.8476 (pt)
REVERT: A  174 MET cc_start: 0.8554 (ppp) cc_final: 0.8084 (ppp)
REVERT: A  229 MET cc_start: 0.4323 (mtt) cc_final: 0.3677 (mpp)
REVERT: A  233 TRP cc_start: 0.8111 (m100) cc_final: 0.7535 (m100)
REVERT: A  316 MET cc_start: 0.9281 (mmm) cc_final: 0.9007 (mmm)
REVERT: A  350 MET cc_start: 0.6895 (ptt) cc_final: 0.6549 (tmm)
REVERT: A  448 MET cc_start: 0.6589 (tpp) cc_final: 0.6058 (tpp)
REVERT: F   60 LYS cc_start: 0.9486 (tppp) cc_final: 0.9057 (tppp)
REVERT: F   61 ARG cc_start: 0.8352 (mtm-85) cc_final: 0.7949 (mtm-85)
  outliers start: 10
  outliers final: 9
  residues processed: 94
  average time/residue: 0.1031
  time to fit residues: 13.6174
Evaluate side-chains
  94 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  670 VAL
Chi-restraints excluded: chain B residue  446 HIS
Chi-restraints excluded: chain B residue  463 MET
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  212 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 25 optimal weight:    9.9990
   chunk 95 optimal weight:    0.8980
   chunk 17 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 8 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 104 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
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 = 0.4332 r_free = 0.4332 target = 0.169349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.094412 restraints weight = 16176.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.99
r_work: 0.3018 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9238  Z= 0.207
  Angle     :  0.601  13.387  12496  Z= 0.306
  Chirality :  0.046   0.181   1416
  Planarity :  0.004   0.041   1633
  Dihedral  :  4.219  31.064   1275
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 11.03 %
    Favored  : 87.84 %
  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:  0.08 (0.25), residues: 1175
  helix:  0.80 (0.25), residues: 439
  sheet:  0.67 (0.36), residues: 201
  loop : -0.78 (0.27), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 529 
 TYR   0.016   0.001   TYR B 435 
 PHE   0.022   0.002   PHE F 122 
 TRP   0.010   0.001   TRP A 394 
 HIS   0.009   0.001   HIS A  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 9238)
  covalent geometry    : angle       0.60121 (12496)
  hydrogen bonds       : bond        0.04297 (  403)
  hydrogen bonds       : angle       4.69281 ( 1143)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.8034 (mmp) cc_final: 0.7547 (ptm)
REVERT: A  146 LEU cc_start: 0.8758 (tp) cc_final: 0.8531 (pt)
REVERT: A  174 MET cc_start: 0.8485 (ppp) cc_final: 0.8106 (ptm)
REVERT: A  229 MET cc_start: 0.4693 (mtt) cc_final: 0.3848 (mpp)
REVERT: A  233 TRP cc_start: 0.8130 (m100) cc_final: 0.7562 (m100)
REVERT: A  316 MET cc_start: 0.9331 (mmm) cc_final: 0.9057 (mmm)
REVERT: A  350 MET cc_start: 0.7079 (ptt) cc_final: 0.6769 (tmm)
REVERT: F   60 LYS cc_start: 0.9481 (tppp) cc_final: 0.9055 (tppp)
REVERT: F   61 ARG cc_start: 0.8361 (mtm-85) cc_final: 0.7975 (mtm-85)
  outliers start: 11
  outliers final: 9
  residues processed: 90
  average time/residue: 0.1061
  time to fit residues: 13.4122
Evaluate side-chains
  90 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  670 VAL
Chi-restraints excluded: chain B residue  446 HIS
Chi-restraints excluded: chain B residue  463 MET
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  212 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 44 optimal weight:    0.0470
   chunk 50 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 116 optimal weight:    0.0270
   chunk 60 optimal weight:   20.0000
   chunk 6 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 95 optimal weight:    0.5980
   chunk 96 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.5336

-------------------------------------------------------------------------------
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 = 0.4351 r_free = 0.4351 target = 0.171038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.096635 restraints weight = 16058.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 3.15
r_work: 0.3062 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9238  Z= 0.109
  Angle     :  0.571  13.477  12496  Z= 0.288
  Chirality :  0.044   0.191   1416
  Planarity :  0.004   0.042   1633
  Dihedral  :  4.066  25.422   1275
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 11.03 %
    Favored  : 87.95 %
  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:  0.17 (0.25), residues: 1175
  helix:  0.93 (0.25), residues: 433
  sheet:  0.67 (0.36), residues: 201
  loop : -0.75 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 529 
 TYR   0.014   0.001   TYR B 417 
 PHE   0.013   0.001   PHE A 263 
 TRP   0.012   0.001   TRP A 394 
 HIS   0.007   0.001   HIS A  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 9238)
  covalent geometry    : angle       0.57130 (12496)
  hydrogen bonds       : bond        0.03528 (  403)
  hydrogen bonds       : angle       4.59946 ( 1143)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.8137 (mmp) cc_final: 0.7700 (ptm)
REVERT: A  124 MET cc_start: 0.9345 (mmm) cc_final: 0.9135 (tpp)
REVERT: A  174 MET cc_start: 0.8396 (ppp) cc_final: 0.7966 (ppp)
REVERT: A  229 MET cc_start: 0.4560 (mtt) cc_final: 0.3673 (mpp)
REVERT: A  233 TRP cc_start: 0.8124 (m100) cc_final: 0.7555 (m100)
REVERT: A  316 MET cc_start: 0.9315 (mmm) cc_final: 0.9030 (mmm)
REVERT: A  350 MET cc_start: 0.7038 (ptt) cc_final: 0.6764 (tmm)
REVERT: A  373 MET cc_start: 0.7470 (tpt) cc_final: 0.7122 (tpt)
REVERT: F   60 LYS cc_start: 0.9476 (tppp) cc_final: 0.9055 (tppp)
REVERT: F   61 ARG cc_start: 0.8337 (mtm-85) cc_final: 0.7996 (mtm-85)
  outliers start: 10
  outliers final: 9
  residues processed: 93
  average time/residue: 0.0964
  time to fit residues: 12.7865
Evaluate side-chains
  92 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  670 VAL
Chi-restraints excluded: chain B residue  446 HIS
Chi-restraints excluded: chain B residue  463 MET
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  212 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 76 optimal weight:    0.0000
   chunk 37 optimal weight:    7.9990
   chunk 113 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 4 optimal weight:    6.9990
   chunk 80 optimal weight:    0.6980
   chunk 105 optimal weight:    0.6980
   chunk 0 optimal weight:   40.0000
   chunk 110 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   overall best weight:    0.5584

-------------------------------------------------------------------------------
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 = 0.4360 r_free = 0.4360 target = 0.171803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.097886 restraints weight = 16093.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 3.14
r_work: 0.3091 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9238  Z= 0.105
  Angle     :  0.572  13.470  12496  Z= 0.285
  Chirality :  0.044   0.195   1416
  Planarity :  0.004   0.040   1633
  Dihedral  :  3.943  20.967   1275
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 11.34 %
    Favored  : 87.84 %
  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:  0.22 (0.25), residues: 1175
  helix:  0.99 (0.25), residues: 433
  sheet:  0.69 (0.36), residues: 202
  loop : -0.73 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 529 
 TYR   0.016   0.001   TYR B 417 
 PHE   0.011   0.001   PHE A 263 
 TRP   0.013   0.001   TRP A 394 
 HIS   0.005   0.001   HIS A  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 9238)
  covalent geometry    : angle       0.57226 (12496)
  hydrogen bonds       : bond        0.03281 (  403)
  hydrogen bonds       : angle       4.52419 ( 1143)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.8117 (mmp) cc_final: 0.7703 (ptm)
REVERT: A  124 MET cc_start: 0.9341 (mmm) cc_final: 0.9090 (tpp)
REVERT: A  174 MET cc_start: 0.8382 (ppp) cc_final: 0.7973 (ppp)
REVERT: A  229 MET cc_start: 0.4615 (mtt) cc_final: 0.3364 (mpp)
REVERT: A  233 TRP cc_start: 0.8150 (m100) cc_final: 0.7621 (m100)
REVERT: A  316 MET cc_start: 0.9311 (mmm) cc_final: 0.9028 (mmm)
REVERT: A  373 MET cc_start: 0.7448 (tpt) cc_final: 0.7077 (tpt)
REVERT: A  394 TRP cc_start: 0.8027 (t-100) cc_final: 0.7757 (t-100)
REVERT: F   60 LYS cc_start: 0.9464 (tppp) cc_final: 0.9054 (tppp)
REVERT: F   61 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.8019 (mtm-85)
  outliers start: 8
  outliers final: 8
  residues processed: 96
  average time/residue: 0.0946
  time to fit residues: 12.8600
Evaluate side-chains
  89 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  670 VAL
Chi-restraints excluded: chain B residue  463 MET
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  212 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 76 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 111 optimal weight:    0.9990
   chunk 92 optimal weight:    5.9990
   chunk 45 optimal weight:    8.9990
   chunk 87 optimal weight:    0.6980
   chunk 113 optimal weight:    0.4980
   chunk 22 optimal weight:   20.0000
   chunk 94 optimal weight:    0.0470
   overall best weight:    0.5880

-------------------------------------------------------------------------------
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 = 0.4359 r_free = 0.4359 target = 0.171761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.100290 restraints weight = 15867.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 3.08
r_work: 0.3058 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9238  Z= 0.105
  Angle     :  0.582  14.175  12496  Z= 0.286
  Chirality :  0.044   0.183   1416
  Planarity :  0.003   0.041   1633
  Dihedral  :  3.884  20.786   1275
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 11.44 %
    Favored  : 87.64 %
  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 (0.25), residues: 1175
  helix:  1.04 (0.25), residues: 435
  sheet:  0.76 (0.36), residues: 201
  loop : -0.68 (0.27), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 529 
 TYR   0.010   0.001   TYR B 435 
 PHE   0.011   0.001   PHE B 384 
 TRP   0.012   0.001   TRP A 394 
 HIS   0.005   0.001   HIS A  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 9238)
  covalent geometry    : angle       0.58169 (12496)
  hydrogen bonds       : bond        0.03230 (  403)
  hydrogen bonds       : angle       4.47995 ( 1143)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3805.96 seconds
wall clock time: 65 minutes 31.74 seconds (3931.74 seconds total)