Starting phenix.real_space_refine
on Tue May 13 16:44:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kbd_62222/05_2025/9kbd_62222.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kbd_62222/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kbd_62222/05_2025/9kbd_62222.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kbd_62222/05_2025/9kbd_62222.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kbd_62222/05_2025/9kbd_62222.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kbd_62222/05_2025/9kbd_62222.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.46, per 1000 atoms: 0.70
  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: 2.35
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 1.12
  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: 3.29

  Time building geometry restraints manager: 2.80 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:             3.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.260
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.180
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.032   0.002   TRP A 581 
 HIS   0.007   0.001   HIS A 343 
 PHE   0.019   0.001   PHE A 566 
 TYR   0.026   0.002   TYR A 244 
 ARG   0.010   0.000   ARG A 274 

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

*********************** 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  : 1.183 
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  130 LYS cc_start: 0.8150 (mmtp) cc_final: 0.7888 (mmtm)
REVERT: C   73 GLN cc_start: 0.7756 (tt0) cc_final: 0.7491 (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: 0.7875 (ptpp)
REVERT: C  325 GLN cc_start: 0.6942 (tm-30) cc_final: 0.6544 (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: 0.7371 (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: 0.2659
  time to fit residues: 92.9747
Evaluate side-chains
  147 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    3.9990
   chunk 98 optimal weight:    0.6980
   chunk 54 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 66 optimal weight:    0.5980
   chunk 52 optimal weight:    9.9990
   chunk 101 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 118 optimal weight:   20.0000
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
B   7 GLN
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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.202610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.170670 restraints weight = 14727.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.170959 restraints weight = 35298.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.172130 restraints weight = 29812.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.065  10946  Z= 0.289
  Angle     :  0.692   8.346  14787  Z= 0.367
  Chirality :  0.045   0.163   1629
  Planarity :  0.005   0.054   1898
  Dihedral  :  4.333  26.188   1439
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 11.70 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.23), residues: 1308
  helix:  0.34 (0.19), residues: 727
  sheet: -2.77 (0.48), residues: 76
  loop : -1.04 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 159 
 HIS   0.007   0.001   HIS A 343 
 PHE   0.026   0.002   PHE A 402 
 TYR   0.022   0.002   TYR C 363 
 ARG   0.006   0.001   ARG A 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04482 (  547)
  hydrogen bonds       : angle       5.17229 ( 1632)
  covalent geometry    : bond        0.00679 (10946)
  covalent geometry    : angle       0.69209 (14787)

*********************** 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
  168 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 1.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  136 ARG cc_start: 0.8818 (mtm-85) cc_final: 0.8218 (mtm110)
REVERT: A  157 TYR cc_start: 0.8427 (m-80) cc_final: 0.7880 (m-80)
REVERT: A  468 LYS cc_start: 0.7938 (mtpp) cc_final: 0.7596 (ttmm)
REVERT: A  508 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7505 (m-80)
  outliers start: 20
  outliers final: 12
  residues processed: 160
  average time/residue: 0.2256
  time to fit residues: 51.7551
Evaluate side-chains
  139 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 SER
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain C residue   12 THR
Chi-restraints excluded: chain C residue  307 THR
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 122 optimal weight:    7.9990
   chunk 45 optimal weight:    8.9990
   chunk 67 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9980
   chunk 48 optimal weight:   10.0000
   chunk 79 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   chunk 74 optimal weight:    0.0980
   chunk 81 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 152 GLN
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.208786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.179633 restraints weight = 14807.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.178907 restraints weight = 32432.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.180159 restraints weight = 27048.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.4109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7015
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10946  Z= 0.129
  Angle     :  0.538   6.700  14787  Z= 0.285
  Chirality :  0.040   0.161   1629
  Planarity :  0.004   0.058   1898
  Dihedral  :  4.187  25.458   1439
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 14.56 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.23), residues: 1308
  helix:  0.85 (0.19), residues: 727
  sheet: -2.33 (0.49), residues: 85
  loop : -0.90 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  21 
 HIS   0.008   0.001   HIS A 143 
 PHE   0.023   0.002   PHE C 184 
 TYR   0.022   0.001   TYR A 260 
 ARG   0.010   0.001   ARG C 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03732 (  547)
  hydrogen bonds       : angle       4.64820 ( 1632)
  covalent geometry    : bond        0.00288 (10946)
  covalent geometry    : angle       0.53849 (14787)

*********************** 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
  160 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 1.141 
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: 0.7896 (p-90) cc_final: 0.7435 (p-90)
REVERT: A  346 ASN cc_start: 0.8340 (t0) cc_final: 0.8108 (t0)
REVERT: A  468 LYS cc_start: 0.8086 (mtpp) cc_final: 0.7716 (ttmm)
  outliers start: 14
  outliers final: 6
  residues processed: 154
  average time/residue: 0.2134
  time to fit residues: 47.4918
Evaluate side-chains
  138 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 132
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  451 VAL
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 38 optimal weight:    0.9980
   chunk 47 optimal weight:    9.9990
   chunk 35 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 49 optimal weight:   20.0000
   chunk 103 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 52 optimal weight:    9.9990
   chunk 112 optimal weight:   10.0000
   chunk 50 optimal weight:    7.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
C 152 GLN
A  30 GLN
A 361 ASN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.206567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.176938 restraints weight = 14566.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.177225 restraints weight = 30953.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.178305 restraints weight = 24736.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.4098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7017
moved from start:          0.2974

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= 0.163
  Angle     :  0.550   7.065  14787  Z= 0.288
  Chirality :  0.040   0.146   1629
  Planarity :  0.004   0.053   1898
  Dihedral  :  4.086  25.513   1439
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 17.00 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.23), residues: 1308
  helix:  0.97 (0.19), residues: 729
  sheet: -2.41 (0.49), residues: 88
  loop : -0.86 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  21 
 HIS   0.007   0.001   HIS A 143 
 PHE   0.019   0.002   PHE C 184 
 TYR   0.017   0.002   TYR A 260 
 ARG   0.004   0.000   ARG C 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03605 (  547)
  hydrogen bonds       : angle       4.52712 ( 1632)
  covalent geometry    : bond        0.00380 (10946)
  covalent geometry    : angle       0.54989 (14787)

*********************** 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
  160 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  159 TRP cc_start: 0.7782 (p-90) cc_final: 0.7401 (p-90)
REVERT: A  237 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8415 (mt)
REVERT: A  261 MET cc_start: 0.7619 (mtm) cc_final: 0.6785 (mtm)
REVERT: A  346 ASN cc_start: 0.8377 (t0) cc_final: 0.8125 (t0)
REVERT: A  468 LYS cc_start: 0.7908 (mtpp) cc_final: 0.7574 (ttmm)
  outliers start: 22
  outliers final: 15
  residues processed: 151
  average time/residue: 0.2199
  time to fit residues: 48.3111
Evaluate side-chains
  145 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 1.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  204 LEU
Chi-restraints excluded: chain C residue  238 MET
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain C residue  375 TYR
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  237 LEU
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  508 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 42 optimal weight:   10.0000
   chunk 68 optimal weight:    0.1980
   chunk 52 optimal weight:    9.9990
   chunk 113 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   chunk 79 optimal weight:    0.0980
   chunk 99 optimal weight:    1.9990
   chunk 60 optimal weight:    0.3980
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
C 152 GLN
** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 400 HIS
A 361 ASN
A 518 ASN
** 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 = 0.4301 r_free = 0.4301 target = 0.198110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.170166 restraints weight = 15102.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.167567 restraints weight = 34132.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.164513 restraints weight = 24097.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  10946  Z= 0.128
  Angle     :  0.546  14.145  14787  Z= 0.283
  Chirality :  0.039   0.146   1629
  Planarity :  0.003   0.049   1898
  Dihedral  :  4.081  30.238   1439
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 18.10 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.24), residues: 1308
  helix:  1.10 (0.19), residues: 733
  sheet: -2.32 (0.54), residues: 81
  loop : -0.83 (0.29), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP C 248 
 HIS   0.007   0.001   HIS A 143 
 PHE   0.023   0.001   PHE C 306 
 TYR   0.015   0.001   TYR A 278 
 ARG   0.003   0.000   ARG C 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03452 (  547)
  hydrogen bonds       : angle       4.38207 ( 1632)
  covalent geometry    : bond        0.00289 (10946)
  covalent geometry    : angle       0.54598 (14787)

*********************** 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
  162 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 1.240 
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: 0.7767 (p-90) cc_final: 0.6718 (p-90)
REVERT: C   80 ILE cc_start: 0.7510 (mt) cc_final: 0.7302 (mt)
REVERT: A  244 TYR cc_start: 0.8475 (m-10) cc_final: 0.7893 (m-10)
REVERT: A  468 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7598 (ttmm)
  outliers start: 23
  outliers final: 13
  residues processed: 152
  average time/residue: 0.2080
  time to fit residues: 46.8076
Evaluate side-chains
  139 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
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  141 ILE
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  247 ASP
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain C residue  375 TYR
Chi-restraints excluded: chain C residue  405 THR
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  451 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 52 optimal weight:    7.9990
   chunk 115 optimal weight:   20.0000
   chunk 111 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 90 optimal weight:    0.8980
   chunk 31 optimal weight:   10.0000
   chunk 122 optimal weight:    9.9990
   chunk 128 optimal weight:    6.9990
   overall best weight:    1.3782

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.193382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.164659 restraints weight = 14833.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.164664 restraints weight = 37114.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.162714 restraints weight = 21441.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  10946  Z= 0.219
  Angle     :  0.615   8.035  14787  Z= 0.322
  Chirality :  0.042   0.146   1629
  Planarity :  0.004   0.048   1898
  Dihedral  :  4.156  25.752   1439
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.19 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.23), residues: 1308
  helix:  0.97 (0.19), residues: 726
  sheet: -2.07 (0.56), residues: 78
  loop : -0.84 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 248 
 HIS   0.007   0.001   HIS A 143 
 PHE   0.024   0.002   PHE A 402 
 TYR   0.016   0.002   TYR A 278 
 ARG   0.004   0.000   ARG C 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03677 (  547)
  hydrogen bonds       : angle       4.52990 ( 1632)
  covalent geometry    : bond        0.00517 (10946)
  covalent geometry    : angle       0.61527 (14787)

*********************** 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
  162 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 1.159 
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: A  157 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.7989 (m-80)
REVERT: A  237 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8281 (mp)
REVERT: A  468 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7639 (ttmm)
  outliers start: 27
  outliers final: 19
  residues processed: 154
  average time/residue: 0.2040
  time to fit residues: 46.5799
Evaluate side-chains
  143 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  105 LEU
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  204 LEU
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain C residue  375 TYR
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  275 VAL
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  508 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 123 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 75 optimal weight:    3.9990
   chunk 35 optimal weight:    0.3980
   chunk 6 optimal weight:    3.9990
   chunk 121 optimal weight:   20.0000
   chunk 36 optimal weight:    0.4980
   chunk 88 optimal weight:    1.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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**
** R  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 361 ASN
** A 641 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 = 0.4254 r_free = 0.4254 target = 0.193458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.165410 restraints weight = 14975.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.163729 restraints weight = 35582.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.160280 restraints weight = 21182.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
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      :  0.005   0.049  10946  Z= 0.213
  Angle     :  0.614   9.155  14787  Z= 0.319
  Chirality :  0.042   0.145   1629
  Planarity :  0.004   0.051   1898
  Dihedral  :  4.196  25.491   1439
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 19.95 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.23), residues: 1308
  helix:  0.93 (0.19), residues: 731
  sheet: -2.45 (0.52), residues: 81
  loop : -0.87 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 248 
 HIS   0.009   0.001   HIS C 300 
 PHE   0.021   0.002   PHE A 402 
 TYR   0.021   0.002   TYR A 260 
 ARG   0.003   0.000   ARG C 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03677 (  547)
  hydrogen bonds       : angle       4.49772 ( 1632)
  covalent geometry    : bond        0.00505 (10946)
  covalent geometry    : angle       0.61419 (14787)

*********************** 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
  150 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 120
  time to evaluate  : 1.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  159 TRP cc_start: 0.7887 (p-90) cc_final: 0.7388 (p-90)
REVERT: A  157 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.7819 (m-80)
REVERT: A  237 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8332 (mp)
REVERT: A  244 TYR cc_start: 0.8606 (m-10) cc_final: 0.8080 (m-10)
REVERT: A  468 LYS cc_start: 0.8108 (mtpp) cc_final: 0.7668 (ttmm)
  outliers start: 30
  outliers final: 21
  residues processed: 140
  average time/residue: 0.2078
  time to fit residues: 44.2100
Evaluate side-chains
  138 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
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  105 LEU
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  163 MET
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  204 LEU
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain C residue  375 TYR
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  275 VAL
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  508 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 76 optimal weight:    0.4980
   chunk 99 optimal weight:    0.8980
   chunk 69 optimal weight:    0.3980
   chunk 86 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0060
   chunk 52 optimal weight:    3.9990
   chunk 79 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 127 optimal weight:    3.9990
   overall best weight:    0.4796

-------------------------------------------------------------------------------
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 ** 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 = 0.4291 r_free = 0.4291 target = 0.197363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.166807 restraints weight = 14666.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.166236 restraints weight = 35211.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.167001 restraints weight = 26686.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.3652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10946  Z= 0.123
  Angle     :  0.551  10.448  14787  Z= 0.285
  Chirality :  0.039   0.147   1629
  Planarity :  0.003   0.049   1898
  Dihedral  :  4.052  24.865   1439
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 21.04 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.24), residues: 1308
  helix:  1.14 (0.19), residues: 729
  sheet: -2.42 (0.52), residues: 81
  loop : -0.79 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 248 
 HIS   0.007   0.001   HIS A 143 
 PHE   0.015   0.001   PHE A 172 
 TYR   0.016   0.001   TYR A 260 
 ARG   0.004   0.000   ARG C 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03362 (  547)
  hydrogen bonds       : angle       4.31912 ( 1632)
  covalent geometry    : bond        0.00280 (10946)
  covalent geometry    : angle       0.55073 (14787)

*********************** 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
  149 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 1.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.7858 (m-80)
REVERT: A  244 TYR cc_start: 0.8542 (m-10) cc_final: 0.8036 (m-10)
REVERT: A  468 LYS cc_start: 0.7855 (mtpp) cc_final: 0.7486 (ttmm)
  outliers start: 23
  outliers final: 17
  residues processed: 140
  average time/residue: 0.2012
  time to fit residues: 42.1993
Evaluate side-chains
  136 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
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  141 ILE
Chi-restraints excluded: chain C residue   12 THR
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  204 LEU
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  375 TYR
Chi-restraints excluded: chain C residue  405 THR
Chi-restraints excluded: chain A residue   18 ASP
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  392 VAL
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  508 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 129 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 111 optimal weight:    0.9990
   chunk 107 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 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 = 0.4275 r_free = 0.4275 target = 0.195837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.166890 restraints weight = 14989.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.166972 restraints weight = 36194.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.165468 restraints weight = 20585.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
moved from start:          0.3795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10946  Z= 0.144
  Angle     :  0.594  13.912  14787  Z= 0.301
  Chirality :  0.041   0.146   1629
  Planarity :  0.004   0.051   1898
  Dihedral  :  4.037  25.209   1439
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 21.21 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.24), residues: 1308
  helix:  1.15 (0.20), residues: 732
  sheet: -2.49 (0.52), residues: 81
  loop : -0.81 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 248 
 HIS   0.007   0.001   HIS C 168 
 PHE   0.016   0.002   PHE A 521 
 TYR   0.019   0.002   TYR C 330 
 ARG   0.005   0.000   ARG B 154 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03380 (  547)
  hydrogen bonds       : angle       4.31200 ( 1632)
  covalent geometry    : bond        0.00337 (10946)
  covalent geometry    : angle       0.59380 (14787)

*********************** 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
  140 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   34 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8516 (mt)
REVERT: C  314 MET cc_start: 0.0641 (ppp) cc_final: -0.0009 (ppp)
REVERT: A  157 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.7818 (m-80)
REVERT: A  244 TYR cc_start: 0.8562 (m-10) cc_final: 0.8052 (m-10)
REVERT: A  468 LYS cc_start: 0.7887 (mtpp) cc_final: 0.7604 (ttmm)
  outliers start: 24
  outliers final: 19
  residues processed: 133
  average time/residue: 0.1961
  time to fit residues: 39.4326
Evaluate side-chains
  137 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
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  141 ILE
Chi-restraints excluded: chain C residue   12 THR
Chi-restraints excluded: chain C residue   34 ILE
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  204 LEU
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain C residue  375 TYR
Chi-restraints excluded: chain C residue  405 THR
Chi-restraints excluded: chain A residue   18 ASP
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  285 ASP
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  508 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 112 optimal weight:   10.0000
   chunk 95 optimal weight:    0.8980
   chunk 87 optimal weight:    0.5980
   chunk 33 optimal weight:    8.9990
   chunk 70 optimal weight:    0.5980
   chunk 106 optimal weight:   10.0000
   chunk 114 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9990
   chunk 30 optimal weight:    0.3980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 692 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 = 0.4292 r_free = 0.4292 target = 0.197445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.168861 restraints weight = 14772.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.169991 restraints weight = 33896.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.169445 restraints weight = 23901.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6993
moved from start:          0.3888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10946  Z= 0.140
  Angle     :  0.583  12.670  14787  Z= 0.297
  Chirality :  0.040   0.145   1629
  Planarity :  0.003   0.050   1898
  Dihedral  :  4.027  25.004   1439
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 21.80 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.24), residues: 1308
  helix:  1.16 (0.20), residues: 733
  sheet: -2.38 (0.53), residues: 78
  loop : -0.88 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 248 
 HIS   0.007   0.001   HIS C 168 
 PHE   0.014   0.001   PHE A 402 
 TYR   0.018   0.001   TYR C 361 
 ARG   0.005   0.000   ARG C 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03348 (  547)
  hydrogen bonds       : angle       4.28568 ( 1632)
  covalent geometry    : bond        0.00328 (10946)
  covalent geometry    : angle       0.58323 (14787)

********************** 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: 21
    poor density    : 125
  time to evaluate  : 1.337 
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: 0.7541 (t60) cc_final: 0.6459 (t60)
REVERT: A  157 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.7729 (m-80)
REVERT: A  244 TYR cc_start: 0.8569 (m-10) cc_final: 0.8001 (m-10)
REVERT: A  506 ARG cc_start: 0.6920 (ttp-110) cc_final: 0.6584 (ptm160)
  outliers start: 21
  outliers final: 18
  residues processed: 139
  average time/residue: 0.2164
  time to fit residues: 44.8544
Evaluate side-chains
  137 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
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  141 ILE
Chi-restraints excluded: chain C residue   12 THR
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  204 LEU
Chi-restraints excluded: chain C residue  307 THR
Chi-restraints excluded: chain C residue  368 THR
Chi-restraints excluded: chain C residue  375 TYR
Chi-restraints excluded: chain C residue  405 THR
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  285 ASP
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  508 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 119 optimal weight:    0.0970
   chunk 39 optimal weight:    0.3980
   chunk 25 optimal weight:    0.8980
   chunk 94 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0870
   chunk 126 optimal weight:   10.0000
   chunk 128 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 101 optimal weight:   10.0000
   overall best weight:    0.4356

-------------------------------------------------------------------------------
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 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 694 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.199211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.170406 restraints weight = 14764.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.170800 restraints weight = 33131.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.170617 restraints weight = 26347.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6967
moved from start:          0.3998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10946  Z= 0.119
  Angle     :  0.581  12.615  14787  Z= 0.296
  Chirality :  0.039   0.153   1629
  Planarity :  0.003   0.049   1898
  Dihedral  :  3.989  24.841   1439
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 21.89 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.24), residues: 1308
  helix:  1.22 (0.20), residues: 733
  sheet: -2.38 (0.54), residues: 78
  loop : -0.85 (0.29), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 159 
 HIS   0.007   0.001   HIS C 168 
 PHE   0.015   0.001   PHE A 521 
 TYR   0.017   0.001   TYR C 361 
 ARG   0.005   0.000   ARG B 154 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03234 (  547)
  hydrogen bonds       : angle       4.21710 ( 1632)
  covalent geometry    : bond        0.00270 (10946)
  covalent geometry    : angle       0.58090 (14787)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3128.30 seconds
wall clock time: 56 minutes 20.56 seconds (3380.56 seconds total)