Starting phenix.real_space_refine
on Wed Sep 17 19:24:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kbd_62222/09_2025/9kbd_62222.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kbd_62222/09_2025/9kbd_62222.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kbd_62222/09_2025/9kbd_62222.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kbd_62222/09_2025/9kbd_62222.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kbd_62222/09_2025/9kbd_62222.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kbd_62222/09_2025/9kbd_62222.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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      56      5.16       5
     C    6824      2.51       5
     N    1813      2.21       5
     O    2035      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10728
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 1281
          Classifications: {'peptide': 160}
          Link IDs: {'PTRANS': 9, 'TRANS': 150}
    Chain: "C"
      Number of atoms: 3277
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 405, 3277
          Classifications: {'peptide': 405}
          Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 383}
    Chain: "R"
      Number of atoms: 144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 144
          Classifications: {'peptide': 16}
          Link IDs: {'TRANS': 15}
    Chain: "A"
      Number of atoms: 6026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 737, 6026
          Classifications: {'peptide': 737}
          Link IDs: {'PTRANS': 13, 'TRANS': 723}
          Chain breaks: 1
  Time building chain proxies: 2.44, per 1000 atoms: 0.23
  Number of scatterers: 10728
  At special positions: 0
  Unit cell: (82, 127.1, 179.58, 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      56     16.00
     O    2035      8.00
     N    1813      7.00
     C    6824      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: 0.90
  Conformation dependent library (CDL) restraints added in 345.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2528

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 14 sheets defined
      58.0% alpha, 9.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'B' and resid 18 through 22
    Processing helix  chain 'B' and resid 24 through 34
      removed outlier: 3.600A  pdb=" N   LEU B  34 " --> pdb=" O   MET B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 65
    Processing helix  chain 'B' and resid 81 through 85
      removed outlier: 3.607A  pdb=" N   ASP B  84 " --> pdb=" O   ARG B  81 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ILE B  85 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 81 through 85'
    Processing helix  chain 'B' and resid 86 through 93
    Processing helix  chain 'B' and resid 96 through 110
    Processing helix  chain 'B' and resid 112 through 126
      removed outlier: 3.536A  pdb=" N   MET B 126 " --> pdb=" O   THR B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 140
    Processing helix  chain 'B' and resid 146 through 158
      removed outlier: 4.306A  pdb=" N   GLU B 156 " --> pdb=" O   GLN B 152 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLN B 158 " --> pdb=" O   ARG B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'C' and resid 17 through 27
      removed outlier: 3.603A  pdb=" N   PHE C  27 " --> pdb=" O   LEU C  23 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 36
    Processing helix  chain 'C' and resid 37 through 39
      No H-bonds generated for 'chain 'C' and resid 37 through 39'
    Processing helix  chain 'C' and resid 40 through 48
    Processing helix  chain 'C' and resid 50 through 54
    Processing helix  chain 'C' and resid 64 through 72
    Processing helix  chain 'C' and resid 74 through 87
      removed outlier: 3.579A  pdb=" N   ASP C  85 " --> pdb=" O   ASP C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 111
      removed outlier: 4.541A  pdb=" N   ALA C  94 " --> pdb=" O   ILE C  90 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   ALA C  95 " --> pdb=" O   ASP C  91 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   GLU C 108 " --> pdb=" O   LYS C 104 " (cutoff:3.500A)
      Proline residue:  C 109  - end of helix
    Processing helix  chain 'C' and resid 111 through 118
      removed outlier: 3.670A  pdb=" N   VAL C 115 " --> pdb=" O   CYS C 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 135
      removed outlier: 3.568A  pdb=" N   LEU C 127 " --> pdb=" O   ARG C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 147
      removed outlier: 3.617A  pdb=" N   SER C 145 " --> pdb=" O   ASP C 141 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   TYR C 146 " --> pdb=" O   TYR C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 183
    Processing helix  chain 'C' and resid 244 through 259
      removed outlier: 3.544A  pdb=" N   GLY C 259 " --> pdb=" O   ASN C 255 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 297
    Processing helix  chain 'C' and resid 409 through 414
      removed outlier: 3.705A  pdb=" N   LEU C 413 " --> pdb=" O   SER C 409 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLU C 414 " --> pdb=" O   ILE C 410 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 409 through 414'
    Processing helix  chain 'A' and resid 20 through 33
    Processing helix  chain 'A' and resid 38 through 54
      removed outlier: 3.529A  pdb=" N   TYR A  52 " --> pdb=" O   HIS A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 105
      removed outlier: 3.640A  pdb=" N   LYS A 105 " --> pdb=" O   THR A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 137
      removed outlier: 3.629A  pdb=" N   GLY A 135 " --> pdb=" O   LYS A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 144
      removed outlier: 3.667A  pdb=" N   TRP A 144 " --> pdb=" O   LEU A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 151
      removed outlier: 3.708A  pdb=" N   GLU A 151 " --> pdb=" O   ARG A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 171
    Processing helix  chain 'A' and resid 175 through 192
      removed outlier: 3.676A  pdb=" N   VAL A 179 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 211
      removed outlier: 3.947A  pdb=" N   ILE A 201 " --> pdb=" O   ASN A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 232
    Processing helix  chain 'A' and resid 232 through 252
      removed outlier: 3.932A  pdb=" N   GLU A 241 " --> pdb=" O   LEU A 237 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   ARG A 242 " --> pdb=" O   ALA A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 274
      removed outlier: 3.775A  pdb=" N   LYS A 262 " --> pdb=" O   THR A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 296
      removed outlier: 4.720A  pdb=" N   GLU A 286 " --> pdb=" O   SER A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 314
      removed outlier: 3.575A  pdb=" N   PHE A 303 " --> pdb=" O   HIS A 299 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   THR A 305 " --> pdb=" O   GLU A 301 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLN A 308 " --> pdb=" O   HIS A 304 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   ASN A 309 " --> pdb=" O   THR A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 327
    Processing helix  chain 'A' and resid 333 through 356
      removed outlier: 3.619A  pdb=" N   LYS A 338 " --> pdb=" O   GLY A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 362
      removed outlier: 4.287A  pdb=" N   ASN A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 383
      removed outlier: 3.688A  pdb=" N   LEU A 380 " --> pdb=" O   LYS A 376 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   VAL A 381 " --> pdb=" O   TYR A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 404
      removed outlier: 4.045A  pdb=" N   ASN A 404 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 412
    Processing helix  chain 'A' and resid 416 through 431
      removed outlier: 3.546A  pdb=" N   LEU A 430 " --> pdb=" O   CYS A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 454
    Processing helix  chain 'A' and resid 458 through 475
      removed outlier: 3.873A  pdb=" N   PHE A 462 " --> pdb=" O   ASP A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 496
    Processing helix  chain 'A' and resid 501 through 528
    Processing helix  chain 'A' and resid 556 through 574
    Processing helix  chain 'A' and resid 605 through 617
    Processing helix  chain 'A' and resid 622 through 630
    Processing helix  chain 'A' and resid 632 through 646
    Processing helix  chain 'A' and resid 688 through 723
      removed outlier: 4.076A  pdb=" N   GLN A 692 " --> pdb=" O   MET A 688 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   LYS A 693 " --> pdb=" O   LYS A 689 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   GLN A 694 " --> pdb=" O   THR A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 739
    Processing helix  chain 'A' and resid 745 through 758
    Processing sheet with id=AA1, first strand: chain 'B' and resid 14 through 17
      removed outlier: 8.954A  pdb=" N   VAL B  45 " --> pdb=" O   SER B   3 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   LYS B   5 " --> pdb=" O   VAL B  45 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 162 through 163
    Processing sheet with id=AA3, first strand: chain 'C' and resid 173 through 174
    Processing sheet with id=AA4, first strand: chain 'C' and resid 193 through 195
    Processing sheet with id=AA5, first strand: chain 'C' and resid 221 through 222
      removed outlier: 7.128A  pdb=" N   VAL C 221 " --> pdb=" O   ILE C 241 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 263 through 264
    Processing sheet with id=AA7, first strand: chain 'C' and resid 284 through 285
      removed outlier: 3.518A  pdb=" N   GLU C 313 " --> pdb=" O   THR C 285 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   TYR C 363 " --> pdb=" O   ILE C 310 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 291 through 292
    Processing sheet with id=AA9, first strand: chain 'C' and resid 340 through 341
      removed outlier: 3.766A  pdb=" N   GLU C 377 " --> pdb=" O   ARG C 332 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   TYR C 379 " --> pdb=" O   ARG C 329 " (cutoff:3.500A)
      removed outlier: 5.097A  pdb=" N   ARG C 329 " --> pdb=" O   TYR C 379 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   THR C 381 " --> pdb=" O   ASP C 327 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   CYS C 324 " --> pdb=" O   ILE C 355 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 340 through 341
      removed outlier: 3.766A  pdb=" N   GLU C 377 " --> pdb=" O   ARG C 332 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   GLY C 378 " --> pdb=" O   ILE C 396 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 534 through 541
      removed outlier: 3.819A  pdb=" N   ALA R  31 " --> pdb=" O   GLN A 538 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 534 through 541
      removed outlier: 3.819A  pdb=" N   ALA R  31 " --> pdb=" O   GLN A 538 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLU R  23 " --> pdb=" O   VAL A 591 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   GLU A 589 " --> pdb=" O   LYS R  25 " (cutoff:3.500A)
      removed outlier: 4.934A  pdb=" N   TRP R  27 " --> pdb=" O   LYS A 587 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   LYS A 587 " --> pdb=" O   TRP R  27 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU A 601 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 620 through 621
    Processing sheet with id=AB5, first strand: chain 'A' and resid 725 through 726
      removed outlier: 4.208A  pdb=" N   LEU A 725 " --> pdb=" O   TYR A 772 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   TYR A 772 " --> pdb=" O   LEU A 725 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5

    559 hydrogen bonds defined for protein.
    1632 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: 1.95

  Time building geometry restraints manager: 1.19 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: 3501
        1.34 -     1.46: 1890
        1.46 -     1.58: 5472
        1.58 -     1.69: 0
        1.69 -     1.81: 83
  Bond restraints: 10946
  Sorted by residual:
  bond pdb=" N   TRP B 159 "
       pdb=" CA  TRP B 159 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.027 1.35e-02 5.49e+03 4.13e+00
  bond pdb=" CB  VAL A 183 "
       pdb=" CG1 VAL A 183 "
    ideal  model  delta    sigma   weight residual
    1.521  1.466  0.055 3.30e-02 9.18e+02 2.78e+00
  bond pdb=" N   GLU B 161 "
       pdb=" CA  GLU B 161 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.90e-02 2.77e+03 2.27e+00
  bond pdb=" CB  LYS A 647 "
       pdb=" CG  LYS A 647 "
    ideal  model  delta    sigma   weight residual
    1.520  1.557 -0.037 3.00e-02 1.11e+03 1.53e+00
  bond pdb=" N   CYS B 160 "
       pdb=" CA  CYS B 160 "
    ideal  model  delta    sigma   weight residual
    1.460  1.486 -0.026 2.20e-02 2.07e+03 1.45e+00
  ... (remaining 10941 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 14502
        1.81 -     3.62: 236
        3.62 -     5.43: 33
        5.43 -     7.24: 13
        7.24 -     9.05: 3
  Bond angle restraints: 14787
  Sorted by residual:
  angle pdb=" CA  LYS A 647 "
        pdb=" CB  LYS A 647 "
        pdb=" CG  LYS A 647 "
      ideal   model   delta    sigma   weight residual
     114.10  121.92   -7.82 2.00e+00 2.50e-01 1.53e+01
  angle pdb=" CB  ARG A 274 "
        pdb=" CG  ARG A 274 "
        pdb=" CD  ARG A 274 "
      ideal   model   delta    sigma   weight residual
     111.30  119.44   -8.14 2.30e+00 1.89e-01 1.25e+01
  angle pdb=" C   VAL C 348 "
        pdb=" N   VAL C 349 "
        pdb=" CA  VAL C 349 "
      ideal   model   delta    sigma   weight residual
     121.97  128.27   -6.30 1.80e+00 3.09e-01 1.22e+01
  angle pdb=" C   ALA A 412 "
        pdb=" N   GLN A 413 "
        pdb=" CA  GLN A 413 "
      ideal   model   delta    sigma   weight residual
     121.54  127.69   -6.15 1.91e+00 2.74e-01 1.04e+01
  angle pdb=" C   ARG A 722 "
        pdb=" N   LYS A 723 "
        pdb=" CA  LYS A 723 "
      ideal   model   delta    sigma   weight residual
     121.54  127.41   -5.87 1.91e+00 2.74e-01 9.44e+00
  ... (remaining 14782 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 5873
       17.84 -    35.67: 650
       35.67 -    53.51: 98
       53.51 -    71.34: 26
       71.34 -    89.18: 16
  Dihedral angle restraints: 6663
    sinusoidal: 2762
      harmonic: 3901
  Sorted by residual:
  dihedral pdb=" CA  THR A 249 "
           pdb=" C   THR A 249 "
           pdb=" N   GLU A 250 "
           pdb=" CA  GLU A 250 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.33   26.67     0      5.00e+00 4.00e-02 2.85e+01
  dihedral pdb=" CA  ARG A 274 "
           pdb=" C   ARG A 274 "
           pdb=" N   VAL A 275 "
           pdb=" CA  VAL A 275 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.96   22.04     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  GLU A 271 "
           pdb=" C   GLU A 271 "
           pdb=" N   GLN A 272 "
           pdb=" CA  GLN A 272 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.37   19.63     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 6660 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1373
       0.056 -    0.111: 228
       0.111 -    0.167: 24
       0.167 -    0.223: 3
       0.223 -    0.278: 1
  Chirality restraints: 1629
  Sorted by residual:
  chirality pdb=" CB  VAL C 349 "
            pdb=" CA  VAL C 349 "
            pdb=" CG1 VAL C 349 "
            pdb=" CG2 VAL C 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" CB  VAL C 286 "
            pdb=" CA  VAL C 286 "
            pdb=" CG1 VAL C 286 "
            pdb=" CG2 VAL C 286 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  TYR A 244 "
            pdb=" N   TYR A 244 "
            pdb=" C   TYR A 244 "
            pdb=" CB  TYR A 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 1626 not shown)

  Planarity restraints: 1898
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 581 "   -0.012 2.00e-02 2.50e+03   1.24e-02 3.86e+00
        pdb=" CG  TRP A 581 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 581 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 581 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 581 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 581 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 581 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 581 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 581 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 581 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 664 "    0.029 5.00e-02 4.00e+02   4.44e-02 3.16e+00
        pdb=" N   PRO A 665 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 665 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 665 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 746 "   -0.028 5.00e-02 4.00e+02   4.15e-02 2.75e+00
        pdb=" N   PRO A 747 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 747 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 747 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1895 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1982
        2.77 -     3.30: 10536
        3.30 -     3.83: 18492
        3.83 -     4.37: 20851
        4.37 -     4.90: 35536
  Nonbonded interactions: 87397
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 514 "
            pdb=" O   VAL A 539 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OH  TYR B 109 "
            pdb=" OG1 THR A  47 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   LYS A 459 "
            pdb=" OH  TYR A 500 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OH  TYR A 260 "
            pdb=" O   LEU A 295 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OG1 THR A 552 "
            pdb=" O   GLN A 630 "
     model   vdw
     2.289 3.040
  ... (remaining 87392 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.500
  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:             0.020
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.150
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:1.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10946  Z= 0.151
  Angle     :  0.601   9.054  14787  Z= 0.318
  Chirality :  0.042   0.278   1629
  Planarity :  0.004   0.044   1898
  Dihedral  : 15.304  89.177   4135
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.17 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole: -1.05 (0.22), residues: 1308
  helix:  0.03 (0.18), residues: 714
  sheet: -2.96 (0.47), residues: 76
  loop : -1.24 (0.26), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 274 
 TYR   0.026   0.002   TYR A 244 
 PHE   0.019   0.001   PHE A 566 
 TRP   0.032   0.002   TRP A 581 
 HIS   0.007   0.001   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (10946)
  covalent geometry    : angle       0.60062 (14787)
  hydrogen bonds       : bond        0.17836 (  547)
  hydrogen bonds       : angle       6.85546 ( 1632)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 255
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  130 LYS cc_start: 0.8150 (mmtp) cc_final: 0.7889 (mmtm)
REVERT: C   73 GLN cc_start: 0.7756 (tt0) cc_final: 0.7490 (mt0)
REVERT: C   80 ILE cc_start: 0.8371 (mt) cc_final: 0.8142 (mt)
REVERT: C  137 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7871 (ptpp)
REVERT: C  325 GLN cc_start: 0.6942 (tm-30) cc_final: 0.6543 (tm-30)
REVERT: A  346 ASN cc_start: 0.8209 (t0) cc_final: 0.7981 (t0)
REVERT: A  450 MET cc_start: 0.7819 (tpp) cc_final: 0.7372 (mmp)
REVERT: A  468 LYS cc_start: 0.8521 (mtpp) cc_final: 0.8190 (ttmm)
  outliers start: 2
  outliers final: 0
  residues processed: 256
  average time/residue: 0.1229
  time to fit residues: 42.9320
Evaluate side-chains
  148 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    0.0770
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:   10.0000
   chunk 129 optimal weight:   20.0000
   overall best weight:    0.8140

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

Flipped N/Q/H residues before XYZ refinement:
B  90 GLN
C  56 HIS
C  72 ASN
C 168 HIS
A 361 ASN
A 509 GLN
** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.200017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.170659 restraints weight = 15026.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.171000 restraints weight = 34986.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.169489 restraints weight = 21742.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.167671 restraints weight = 21076.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.168274 restraints weight = 16588.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7082
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10946  Z= 0.164
  Angle     :  0.587   7.276  14787  Z= 0.312
  Chirality :  0.041   0.163   1629
  Planarity :  0.004   0.052   1898
  Dihedral  :  4.156  25.721   1439
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 10.86 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole: -0.40 (0.23), residues: 1308
  helix:  0.55 (0.19), residues: 728
  sheet: -2.67 (0.48), residues: 76
  loop : -0.96 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 154 
 TYR   0.021   0.002   TYR C 363 
 PHE   0.026   0.002   PHE C 306 
 TRP   0.020   0.002   TRP B 159 
 HIS   0.006   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (10946)
  covalent geometry    : angle       0.58696 (14787)
  hydrogen bonds       : bond        0.04157 (  547)
  hydrogen bonds       : angle       4.97773 ( 1632)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 154
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  136 ARG cc_start: 0.8768 (mtm-85) cc_final: 0.8197 (mtm110)
REVERT: B  159 TRP cc_start: 0.7809 (p-90) cc_final: 0.7470 (p-90)
REVERT: A  346 ASN cc_start: 0.8336 (t0) cc_final: 0.8039 (t0)
REVERT: A  468 LYS cc_start: 0.7929 (mtpp) cc_final: 0.7595 (ttmm)
REVERT: A  508 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7452 (m-80)
  outliers start: 15
  outliers final: 8
  residues processed: 163
  average time/residue: 0.1072
  time to fit residues: 25.0215
Evaluate side-chains
  137 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 SER
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue  405 THR
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  341 GLU
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  511 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 120 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 79 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 56 optimal weight:    8.9990
   chunk 124 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 60 optimal weight:    0.1980
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B   7 GLN
B 152 GLN
C 168 HIS
A  35 GLN
A 361 ASN
** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 694 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.207759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.179216 restraints weight = 14956.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.179237 restraints weight = 33018.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.178862 restraints weight = 22509.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.177796 restraints weight = 17449.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.178343 restraints weight = 14936.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.4082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7032
moved from start:          0.2603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10946  Z= 0.146
  Angle     :  0.543   6.311  14787  Z= 0.287
  Chirality :  0.040   0.163   1629
  Planarity :  0.004   0.057   1898
  Dihedral  :  4.074  26.057   1439
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 13.64 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole: -0.03 (0.23), residues: 1308
  helix:  0.90 (0.19), residues: 726
  sheet: -2.51 (0.50), residues: 76
  loop : -0.88 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 170 
 TYR   0.025   0.002   TYR A 260 
 PHE   0.022   0.002   PHE C 184 
 TRP   0.012   0.001   TRP A  21 
 HIS   0.006   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (10946)
  covalent geometry    : angle       0.54318 (14787)
  hydrogen bonds       : bond        0.03725 (  547)
  hydrogen bonds       : angle       4.60411 ( 1632)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  159 TRP cc_start: 0.7768 (p-90) cc_final: 0.7380 (p-90)
REVERT: A  346 ASN cc_start: 0.8339 (t0) cc_final: 0.8046 (t0)
REVERT: A  468 LYS cc_start: 0.7933 (mtpp) cc_final: 0.7666 (ttmm)
REVERT: A  508 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7492 (m-80)
  outliers start: 20
  outliers final: 13
  residues processed: 156
  average time/residue: 0.1016
  time to fit residues: 22.8806
Evaluate side-chains
  146 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  341 GLU
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  511 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 121 optimal weight:    8.9990
   chunk 99 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
C 152 GLN
C 168 HIS
A 361 ASN
A 518 ASN
** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.202339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.172749 restraints weight = 14955.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.174407 restraints weight = 38401.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.173469 restraints weight = 20138.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.173505 restraints weight = 15409.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.173832 restraints weight = 13463.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.4031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  10946  Z= 0.243
  Angle     :  0.616   6.843  14787  Z= 0.324
  Chirality :  0.043   0.153   1629
  Planarity :  0.004   0.058   1898
  Dihedral  :  4.209  26.439   1439
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.91 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole: -0.14 (0.23), residues: 1308
  helix:  0.80 (0.19), residues: 724
  sheet: -2.62 (0.48), residues: 81
  loop : -0.86 (0.29), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  55 
 TYR   0.019   0.002   TYR A 278 
 PHE   0.026   0.002   PHE A 402 
 TRP   0.013   0.002   TRP A  21 
 HIS   0.008   0.002   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 (10946)
  covalent geometry    : angle       0.61554 (14787)
  hydrogen bonds       : bond        0.03918 (  547)
  hydrogen bonds       : angle       4.63685 ( 1632)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  159 TRP cc_start: 0.7819 (p-90) cc_final: 0.7408 (p-90)
REVERT: C   80 ILE cc_start: 0.7837 (mt) cc_final: 0.7621 (mt)
REVERT: A  157 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.7785 (m-80)
REVERT: A  468 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7672 (ttmm)
  outliers start: 27
  outliers final: 15
  residues processed: 153
  average time/residue: 0.0904
  time to fit residues: 20.6445
Evaluate side-chains
  142 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain C residue  405 THR
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  341 GLU
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  507 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   chunk 119 optimal weight:    0.1980
   chunk 128 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 98 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 27 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9980
   chunk 103 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
C 152 GLN
C 168 HIS
A 361 ASN
A 641 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.195860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.167492 restraints weight = 15091.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.165629 restraints weight = 34406.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.161452 restraints weight = 20768.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.160502 restraints weight = 25601.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.161232 restraints weight = 19748.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10946  Z= 0.158
  Angle     :  0.551   8.186  14787  Z= 0.288
  Chirality :  0.040   0.156   1629
  Planarity :  0.003   0.054   1898
  Dihedral  :  4.114  25.539   1439
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 17.76 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole:  0.07 (0.24), residues: 1308
  helix:  0.97 (0.19), residues: 727
  sheet: -2.22 (0.49), residues: 90
  loop : -0.81 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 170 
 TYR   0.017   0.002   TYR A 278 
 PHE   0.015   0.002   PHE C 184 
 TRP   0.014   0.001   TRP A  21 
 HIS   0.006   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (10946)
  covalent geometry    : angle       0.55144 (14787)
  hydrogen bonds       : bond        0.03546 (  547)
  hydrogen bonds       : angle       4.42008 ( 1632)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 138
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  159 TRP cc_start: 0.7822 (p-90) cc_final: 0.7004 (p-90)
REVERT: C   80 ILE cc_start: 0.7799 (mt) cc_final: 0.7220 (mt)
REVERT: A  157 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.7894 (m-80)
REVERT: A  237 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8362 (mt)
REVERT: A  261 MET cc_start: 0.7453 (mtm) cc_final: 0.7088 (mtm)
REVERT: A  468 LYS cc_start: 0.8160 (mtpp) cc_final: 0.7726 (ttmm)
  outliers start: 25
  outliers final: 16
  residues processed: 155
  average time/residue: 0.0963
  time to fit residues: 21.9834
Evaluate side-chains
  145 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   94 LYS
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain A residue  587 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 101 optimal weight:    9.9990
   chunk 108 optimal weight:    3.9990
   chunk 118 optimal weight:   30.0000
   chunk 14 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 201 HIS
A 361 ASN
** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.190765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.158693 restraints weight = 15130.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.160649 restraints weight = 42437.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.161042 restraints weight = 25737.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.160368 restraints weight = 20075.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.161202 restraints weight = 14109.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.3527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062  10946  Z= 0.295
  Angle     :  0.671   8.919  14787  Z= 0.348
  Chirality :  0.044   0.155   1629
  Planarity :  0.004   0.052   1898
  Dihedral  :  4.280  26.098   1439
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 18.10 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole: -0.22 (0.23), residues: 1308
  helix:  0.69 (0.19), residues: 728
  sheet: -2.19 (0.47), residues: 98
  loop : -0.86 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 412 
 TYR   0.019   0.002   TYR A 260 
 PHE   0.028   0.002   PHE A 402 
 TRP   0.010   0.002   TRP A 167 
 HIS   0.008   0.002   HIS C 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00698 (10946)
  covalent geometry    : angle       0.67115 (14787)
  hydrogen bonds       : bond        0.03969 (  547)
  hydrogen bonds       : angle       4.67555 ( 1632)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 129
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   27 TRP cc_start: 0.7675 (t60) cc_final: 0.6802 (t60)
REVERT: A  157 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.7839 (m-80)
REVERT: A  237 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8366 (mp)
REVERT: A  468 LYS cc_start: 0.8125 (mtpp) cc_final: 0.7685 (ttmm)
  outliers start: 35
  outliers final: 28
  residues processed: 153
  average time/residue: 0.0975
  time to fit residues: 21.5008
Evaluate side-chains
  147 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 117
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue   94 LYS
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain C residue   89 TYR
Chi-restraints excluded: chain C residue   91 ASP
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  163 MET
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  220 GLU
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain C residue  405 THR
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  285 ASP
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  402 PHE
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  587 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 128 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0570
   chunk 23 optimal weight:    0.5980
   chunk 103 optimal weight:    0.9980
   chunk 85 optimal weight:    0.5980
   chunk 26 optimal weight:    5.9990
   chunk 119 optimal weight:    6.9990
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 374 HIS
A 641 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.196653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.168271 restraints weight = 15031.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.165096 restraints weight = 33615.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.160484 restraints weight = 21517.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.160014 restraints weight = 24309.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.160624 restraints weight = 19975.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10946  Z= 0.123
  Angle     :  0.558   9.617  14787  Z= 0.287
  Chirality :  0.039   0.179   1629
  Planarity :  0.003   0.051   1898
  Dihedral  :  4.082  24.727   1439
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.70 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole:  0.11 (0.24), residues: 1308
  helix:  1.05 (0.19), residues: 731
  sheet: -1.98 (0.49), residues: 98
  loop : -0.92 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 401 
 TYR   0.017   0.001   TYR A 278 
 PHE   0.028   0.002   PHE C 269 
 TRP   0.016   0.002   TRP C 248 
 HIS   0.006   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10946)
  covalent geometry    : angle       0.55774 (14787)
  hydrogen bonds       : bond        0.03441 (  547)
  hydrogen bonds       : angle       4.33177 ( 1632)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   27 TRP cc_start: 0.7829 (t60) cc_final: 0.6902 (t60)
REVERT: A  157 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.7860 (m-80)
REVERT: A  244 TYR cc_start: 0.8546 (m-10) cc_final: 0.7959 (m-10)
REVERT: A  468 LYS cc_start: 0.8104 (mtpp) cc_final: 0.7604 (ttmm)
  outliers start: 27
  outliers final: 16
  residues processed: 151
  average time/residue: 0.0881
  time to fit residues: 19.9324
Evaluate side-chains
  140 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   94 LYS
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain C residue  405 THR
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  285 ASP
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  402 PHE
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  587 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 122 optimal weight:    7.9990
   chunk 125 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   chunk 40 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 97 optimal weight:    0.4980
   chunk 107 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** C 152 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 = 0.4271 r_free = 0.4271 target = 0.195273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.167150 restraints weight = 15057.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.165174 restraints weight = 34814.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.161969 restraints weight = 22334.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.161085 restraints weight = 22526.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.161073 restraints weight = 20420.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10946  Z= 0.151
  Angle     :  0.589  10.414  14787  Z= 0.300
  Chirality :  0.041   0.181   1629
  Planarity :  0.004   0.053   1898
  Dihedral  :  4.054  25.281   1439
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 20.79 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole:  0.13 (0.24), residues: 1308
  helix:  1.06 (0.19), residues: 734
  sheet: -2.04 (0.50), residues: 95
  loop : -0.91 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 154 
 TYR   0.015   0.002   TYR A 260 
 PHE   0.018   0.002   PHE C 269 
 TRP   0.017   0.002   TRP C 248 
 HIS   0.006   0.001   HIS C 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (10946)
  covalent geometry    : angle       0.58893 (14787)
  hydrogen bonds       : bond        0.03438 (  547)
  hydrogen bonds       : angle       4.30908 ( 1632)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   34 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8546 (mt)
REVERT: R   27 TRP cc_start: 0.7699 (t60) cc_final: 0.7057 (t60)
REVERT: A  157 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.7797 (m-80)
REVERT: A  244 TYR cc_start: 0.8539 (m-10) cc_final: 0.8019 (m-10)
REVERT: A  261 MET cc_start: 0.7530 (mpp) cc_final: 0.6740 (mpp)
REVERT: A  468 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7555 (ttmm)
  outliers start: 22
  outliers final: 19
  residues processed: 139
  average time/residue: 0.0917
  time to fit residues: 19.1968
Evaluate side-chains
  138 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   94 LYS
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   89 TYR
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain C residue  405 THR
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  285 ASP
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  402 PHE
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  587 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 120 optimal weight:    0.9990
   chunk 127 optimal weight:    0.2980
   chunk 82 optimal weight:    0.9980
   chunk 111 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 67 optimal weight:    0.4980
   chunk 128 optimal weight:    4.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** C 152 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 = 0.4279 r_free = 0.4279 target = 0.196179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.165899 restraints weight = 14832.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.166802 restraints weight = 37404.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.166865 restraints weight = 24930.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.166763 restraints weight = 16935.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.167066 restraints weight = 15015.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
moved from start:          0.3743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10946  Z= 0.136
  Angle     :  0.583  11.797  14787  Z= 0.298
  Chirality :  0.040   0.184   1629
  Planarity :  0.004   0.051   1898
  Dihedral  :  4.016  25.043   1439
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 20.79 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole:  0.19 (0.24), residues: 1308
  helix:  1.11 (0.19), residues: 733
  sheet: -1.98 (0.50), residues: 98
  loop : -0.88 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.000   ARG C 398 
 TYR   0.016   0.001   TYR A 260 
 PHE   0.026   0.002   PHE C 222 
 TRP   0.014   0.001   TRP C 248 
 HIS   0.006   0.001   HIS C 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (10946)
  covalent geometry    : angle       0.58294 (14787)
  hydrogen bonds       : bond        0.03374 (  547)
  hydrogen bonds       : angle       4.26390 ( 1632)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   34 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8541 (mt)
REVERT: R   27 TRP cc_start: 0.7477 (t60) cc_final: 0.7222 (t60)
REVERT: A  157 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.7796 (m-80)
REVERT: A  244 TYR cc_start: 0.8524 (m-10) cc_final: 0.8029 (m-10)
REVERT: A  261 MET cc_start: 0.7465 (mpp) cc_final: 0.6647 (mpp)
REVERT: A  468 LYS cc_start: 0.7922 (mtpp) cc_final: 0.7519 (ttmm)
  outliers start: 23
  outliers final: 19
  residues processed: 138
  average time/residue: 0.0969
  time to fit residues: 19.9171
Evaluate side-chains
  138 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   94 LYS
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain C residue  405 THR
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  285 ASP
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  402 PHE
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  507 MET
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  587 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 10 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 95 optimal weight:    0.5980
   chunk 68 optimal weight:    0.2980
   chunk 58 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0370
   chunk 28 optimal weight:    2.9990
   chunk 70 optimal weight:    0.2980
   chunk 99 optimal weight:    0.5980
   chunk 121 optimal weight:   20.0000
   overall best weight:    0.3658

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

Flipped N/Q/H residues before XYZ refinement:
** C 152 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 = 0.4305 r_free = 0.4305 target = 0.198644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.167034 restraints weight = 14696.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.165225 restraints weight = 32687.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.166448 restraints weight = 31927.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.166293 restraints weight = 19259.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.166905 restraints weight = 19222.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7048
moved from start:          0.3864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10946  Z= 0.116
  Angle     :  0.574  11.120  14787  Z= 0.293
  Chirality :  0.039   0.183   1629
  Planarity :  0.004   0.055   1898
  Dihedral  :  3.993  24.849   1439
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 21.13 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole:  0.35 (0.24), residues: 1308
  helix:  1.26 (0.20), residues: 733
  sheet: -1.93 (0.51), residues: 95
  loop : -0.84 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG C 398 
 TYR   0.017   0.001   TYR C  89 
 PHE   0.018   0.002   PHE C 222 
 TRP   0.014   0.001   TRP C 248 
 HIS   0.007   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10946)
  covalent geometry    : angle       0.57384 (14787)
  hydrogen bonds       : bond        0.03247 (  547)
  hydrogen bonds       : angle       4.18008 ( 1632)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.7728 (m-80)
REVERT: A  244 TYR cc_start: 0.8478 (m-10) cc_final: 0.7951 (m-10)
REVERT: A  261 MET cc_start: 0.7421 (mpp) cc_final: 0.6598 (mpp)
REVERT: A  468 LYS cc_start: 0.7802 (mtpp) cc_final: 0.7514 (ttmm)
  outliers start: 18
  outliers final: 15
  residues processed: 141
  average time/residue: 0.0875
  time to fit residues: 18.1908
Evaluate side-chains
  133 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   94 LYS
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  405 THR
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  285 ASP
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  587 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 112 optimal weight:   40.0000
   chunk 102 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 120 optimal weight:   20.0000
   chunk 60 optimal weight:    0.5980
   chunk 121 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 49 optimal weight:    7.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 615 ASN
** A 696 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 = 0.4250 r_free = 0.4250 target = 0.193574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.162019 restraints weight = 14802.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.163413 restraints weight = 37466.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.164121 restraints weight = 27136.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.165192 restraints weight = 16998.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.165381 restraints weight = 14786.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.4002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  10946  Z= 0.229
  Angle     :  0.645  10.400  14787  Z= 0.334
  Chirality :  0.043   0.176   1629
  Planarity :  0.004   0.053   1898
  Dihedral  :  4.148  26.296   1439
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 21.13 %
    Favored  : 76.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole:  0.12 (0.24), residues: 1308
  helix:  1.00 (0.20), residues: 729
  sheet: -2.00 (0.55), residues: 83
  loop : -0.86 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C 398 
 TYR   0.017   0.002   TYR A 278 
 PHE   0.026   0.002   PHE A 402 
 TRP   0.036   0.002   TRP R  27 
 HIS   0.006   0.001   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 (10946)
  covalent geometry    : angle       0.64494 (14787)
  hydrogen bonds       : bond        0.03587 (  547)
  hydrogen bonds       : angle       4.38943 ( 1632)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1685.60 seconds
wall clock time: 30 minutes 8.52 seconds (1808.52 seconds total)