Starting phenix.real_space_refine
on Tue Aug  4 22:11:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x06_37970/08_2026/8x06_37970.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x06_37970/08_2026/8x06_37970.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x06_37970/08_2026/8x06_37970.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x06_37970/08_2026/8x06_37970.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x06_37970/08_2026/8x06_37970.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x06_37970/08_2026/8x06_37970.map"
  }
  resolution = 3.24
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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      59      5.16       5
     C    4514      2.51       5
     N    1197      2.21       5
     O    1283      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7053
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 536, 4320
          Classifications: {'peptide': 536}
          Link IDs: {'PTRANS': 26, 'TRANS': 509}
          Chain breaks: 10
    Chain: "C"
      Number of atoms: 359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 359
          Classifications: {'peptide': 46}
          Link IDs: {'PTRANS': 1, 'TRANS': 44}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 261
          Classifications: {'peptide': 33}
          Link IDs: {'PTRANS': 1, 'TRANS': 31}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 2113
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 10, 'TRANS': 243}
          Chain breaks: 10
  Time building chain proxies: 1.61, per 1000 atoms: 0.23
  Number of scatterers: 7053
  At special positions: 0
  Unit cell: (77.88, 92.4, 110.88, 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      59     16.00
     O    1283      8.00
     N    1197      7.00
     C    4514      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=20, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   8 " - pdb=" SG  CYS A  26 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 126 " - pdb=" SG  CYS A 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 169 " - pdb=" SG  CYS A 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 192 " - pdb=" SG  CYS A 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 196 " - pdb=" SG  CYS A 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 208 " - pdb=" SG  CYS A 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 212 " - pdb=" SG  CYS A 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 228 " - pdb=" SG  CYS A 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 241 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 259 " - pdb=" SG  CYS A 284 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 266 " - pdb=" SG  CYS A 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 288 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 312 " - pdb=" SG  CYS A 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 435 " - pdb=" SG  CYS A 468 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   6 " - pdb=" SG  CYS C  48 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  18 " - pdb=" SG  CYS C  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  47 " - pdb=" SG  CYS C  52 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   6 " - pdb=" SG  CYS D  48 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  18 " - pdb=" SG  CYS D  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 625 " - pdb=" SG  CYS B 658 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.58
  Conformation dependent library (CDL) restraints added in 475.6 milliseconds
  

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1634

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 14 sheets defined
      16.6% alpha, 12.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 24
      removed outlier: 3.546A  pdb=" N   LEU A  20 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   HIS A  21 " --> pdb=" O   THR A  18 " (cutoff:3.500A)
      removed outlier: 5.306A  pdb=" N   GLU A  22 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 46
    Processing helix  chain 'A' and resid 127 through 131
      removed outlier: 3.544A  pdb=" N   THR A 130 " --> pdb=" O   TYR A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 268
      removed outlier: 3.663A  pdb=" N   CYS A 266 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ASN A 268 " --> pdb=" O   HIS A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 329
      removed outlier: 3.597A  pdb=" N   ALA A 327 " --> pdb=" O   SER A 323 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   GLU A 329 " --> pdb=" O   THR A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 358
    Processing helix  chain 'A' and resid 394 through 396
      No H-bonds generated for 'chain 'A' and resid 394 through 396'
    Processing helix  chain 'A' and resid 435 through 447
      removed outlier: 3.780A  pdb=" N   ILE A 439 " --> pdb=" O   CYS A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 452
      removed outlier: 3.535A  pdb=" N   GLN A 452 " --> pdb=" O   LYS A 449 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 18
      removed outlier: 3.717A  pdb=" N   VAL C  11 " --> pdb=" O   GLY C   7 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU C  14 " --> pdb=" O   LEU C  10 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 48
    Processing helix  chain 'C' and resid 53 through 58
    Processing helix  chain 'C' and resid 59 through 61
      No H-bonds generated for 'chain 'C' and resid 59 through 61'
    Processing helix  chain 'D' and resid 9 through 15
    Processing helix  chain 'D' and resid 53 through 57
      removed outlier: 3.819A  pdb=" N   ARG D  56 " --> pdb=" O   ASP D  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 542 through 546
      removed outlier: 4.052A  pdb=" N   ALA B 546 " --> pdb=" O   ALA B 542 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 542 through 546'
    Processing helix  chain 'B' and resid 625 through 631
      removed outlier: 3.984A  pdb=" N   ILE B 629 " --> pdb=" O   CYS B 625 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 632 through 634
      No H-bonds generated for 'chain 'B' and resid 632 through 634'
    Processing helix  chain 'B' and resid 882 through 904
    Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8
      removed outlier: 3.668A  pdb=" N   ILE A  29 " --> pdb=" O   MET A  56 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ILE A  57 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ILE A  82 " --> pdb=" O   ASN A 111 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 38
      removed outlier: 3.919A  pdb=" N   PHE A  64 " --> pdb=" O   ILE A  35 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   VAL A  66 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   LEU A  61 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   PHE A  96 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   LEU A  63 " --> pdb=" O   PHE A  96 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   LEU A  93 " --> pdb=" O   ARG A 118 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   GLU A 120 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   ILE A  95 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   TYR A 144 " --> pdb=" O   VAL A 117 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ILE A 119 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 233
    Processing sheet with id=AA4, first strand: chain 'A' and resid 245 through 246
    Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 293
    Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313
      removed outlier: 3.796A  pdb=" N   ASN A 337 " --> pdb=" O   CYS A 312 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   ILE A 336 " --> pdb=" O   SER A 365 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   ILE A 364 " --> pdb=" O   ARG A 389 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 320 through 321
    Processing sheet with id=AA8, first strand: chain 'A' and resid 368 through 370
      removed outlier: 4.280A  pdb=" N   TYR A 398 " --> pdb=" O   LYS A 425 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   PHE A 427 " --> pdb=" O   TYR A 398 " (cutoff:3.500A)
      removed outlier: 5.871A  pdb=" N   PHE A 400 " --> pdb=" O   PHE A 427 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 484 through 487
      removed outlier: 3.905A  pdb=" N   ILE A 485 " --> pdb=" O   MET A 553 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   MET A 553 " --> pdb=" O   ILE A 485 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   LEU A 487 " --> pdb=" O   TRP A 551 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 531 through 534
      removed outlier: 3.640A  pdb=" N   PHE A 506 " --> pdb=" O   PHE A 565 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   PHE A 565 " --> pdb=" O   PHE A 506 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 525 through 526
      removed outlier: 3.510A  pdb=" N   ILE B 526 " --> pdb=" O   GLU B 553 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ILE B 554 " --> pdb=" O   LEU B 577 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 558 through 560
    Processing sheet with id=AB4, first strand: chain 'B' and resid 665 through 670
      removed outlier: 3.550A  pdb=" N   ARG B 678 " --> pdb=" O   SER B 666 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   ILE B 668 " --> pdb=" O   LEU B 676 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   LEU B 676 " --> pdb=" O   ILE B 668 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 722 through 724
      removed outlier: 4.145A  pdb=" N   GLY B 692 " --> pdb=" O   LEU B 759 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LEU B 759 " --> pdb=" O   GLY B 692 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   PHE B 755 " --> pdb=" O   PHE B 696 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS B 698 " --> pdb=" O   ALA B 753 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ALA B 753 " --> pdb=" O   LYS B 698 " (cutoff:3.500A)

    103 hydrogen bonds defined for protein.
    258 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.01

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2264
        1.35 -     1.46: 1718
        1.46 -     1.58: 3148
        1.58 -     1.70: 0
        1.70 -     1.82: 73
  Bond restraints: 7203
  Sorted by residual:
  bond pdb=" CA  LYS B 631 "
       pdb=" C   LYS B 631 "
    ideal  model  delta    sigma   weight residual
    1.523  1.570 -0.047 1.41e-02 5.03e+03 1.11e+01
  bond pdb=" C   PRO A 243 "
       pdb=" N   PRO A 244 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.027 1.28e-02 6.10e+03 4.33e+00
  bond pdb=" CB  PRO A 307 "
       pdb=" CG  PRO A 307 "
    ideal  model  delta    sigma   weight residual
    1.492  1.542 -0.050 5.00e-02 4.00e+02 9.88e-01
  bond pdb=" CB  TRP B 604 "
       pdb=" CG  TRP B 604 "
    ideal  model  delta    sigma   weight residual
    1.498  1.524 -0.026 3.10e-02 1.04e+03 7.14e-01
  bond pdb=" CA  TYR D  60 "
       pdb=" CB  TYR D  60 "
    ideal  model  delta    sigma   weight residual
    1.524  1.535 -0.011 1.31e-02 5.83e+03 6.91e-01
  ... (remaining 7198 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 9575
        2.07 -     4.14: 128
        4.14 -     6.21: 10
        6.21 -     8.28: 2
        8.28 -    10.35: 3
  Bond angle restraints: 9718
  Sorted by residual:
  angle pdb=" CB  MET A 294 "
        pdb=" CG  MET A 294 "
        pdb=" SD  MET A 294 "
      ideal   model   delta    sigma   weight residual
     112.70  122.46   -9.76 3.00e+00 1.11e-01 1.06e+01
  angle pdb=" CA  LEU B 550 "
        pdb=" CB  LEU B 550 "
        pdb=" CG  LEU B 550 "
      ideal   model   delta    sigma   weight residual
     116.30  126.65  -10.35 3.50e+00 8.16e-02 8.75e+00
  angle pdb=" CA  LYS B 631 "
        pdb=" C   LYS B 631 "
        pdb=" O   LYS B 631 "
      ideal   model   delta    sigma   weight residual
     119.28  122.83   -3.55 1.21e+00 6.83e-01 8.60e+00
  angle pdb=" N   GLY D  19 "
        pdb=" CA  GLY D  19 "
        pdb=" C   GLY D  19 "
      ideal   model   delta    sigma   weight residual
     111.35  114.80   -3.45 1.20e+00 6.94e-01 8.27e+00
  angle pdb=" CB  ARG C  55 "
        pdb=" CG  ARG C  55 "
        pdb=" CD  ARG C  55 "
      ideal   model   delta    sigma   weight residual
     111.30  117.54   -6.24 2.30e+00 1.89e-01 7.36e+00
  ... (remaining 9713 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.10: 3560
       17.10 -    34.20: 533
       34.20 -    51.31: 188
       51.31 -    68.41: 42
       68.41 -    85.51: 19
  Dihedral angle restraints: 4342
    sinusoidal: 1827
      harmonic: 2515
  Sorted by residual:
  dihedral pdb=" CB  CYS A 169 "
           pdb=" SG  CYS A 169 "
           pdb=" SG  CYS A 188 "
           pdb=" CB  CYS A 188 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -171.51   85.51     1      1.00e+01 1.00e-02 8.85e+01
  dihedral pdb=" CB  CYS A 259 "
           pdb=" SG  CYS A 259 "
           pdb=" SG  CYS A 284 "
           pdb=" CB  CYS A 284 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -164.02   78.02     1      1.00e+01 1.00e-02 7.61e+01
  dihedral pdb=" CB  CYS A 266 "
           pdb=" SG  CYS A 266 "
           pdb=" SG  CYS A 274 "
           pdb=" CB  CYS A 274 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.29  -72.29     1      1.00e+01 1.00e-02 6.68e+01
  ... (remaining 4339 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 635
       0.026 -    0.051: 249
       0.051 -    0.077: 93
       0.077 -    0.102: 44
       0.102 -    0.128: 40
  Chirality restraints: 1061
  Sorted by residual:
  chirality pdb=" CA  ILE A 585 "
            pdb=" N   ILE A 585 "
            pdb=" C   ILE A 585 "
            pdb=" CB  ILE A 585 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.08e-01
  chirality pdb=" CA  ILE A  95 "
            pdb=" N   ILE A  95 "
            pdb=" C   ILE A  95 "
            pdb=" CB  ILE A  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.91e-01
  chirality pdb=" CA  ILE A 370 "
            pdb=" N   ILE A 370 "
            pdb=" C   ILE A 370 "
            pdb=" CB  ILE A 370 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.62e-01
  ... (remaining 1058 not shown)

  Planarity restraints: 1233
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 306 "   -0.042 5.00e-02 4.00e+02   6.30e-02 6.34e+00
        pdb=" N   PRO A 307 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 307 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 307 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 243 "    0.035 5.00e-02 4.00e+02   5.23e-02 4.38e+00
        pdb=" N   PRO A 244 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 244 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 244 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 316 "    0.007 2.00e-02 2.50e+03   1.38e-02 1.89e+00
        pdb=" C   GLU A 316 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   GLU A 316 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLY A 317 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1230 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1567
        2.79 -     3.32: 5823
        3.32 -     3.84: 10999
        3.84 -     4.37: 12266
        4.37 -     4.90: 21398
  Nonbonded interactions: 52053
  Sorted by model distance:
  nonbonded pdb=" O   ILE A  29 "
            pdb=" OG1 THR A  58 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OG1 THR A  41 "
            pdb=" O   TYR A  67 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   TYR B 697 "
            pdb=" OG1 THR B 720 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" O   LYS B 747 "
            pdb=" OG1 THR B 750 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   ILE A 336 "
            pdb=" OG  SER A 365 "
     model   vdw
     2.306 3.040
  ... (remaining 52048 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             11.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.030
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
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      :  0.002   0.050   7223  Z= 0.123
  Angle     :  0.579  10.354   9758  Z= 0.323
  Chirality :  0.040   0.128   1061
  Planarity :  0.003   0.063   1233
  Dihedral  : 18.499  82.436   2648
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 34.39 %
    Favored  : 65.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.30), residues: 816
  helix:  0.05 (0.55), residues: 118
  sheet:  0.45 (0.68), residues: 77
  loop : -0.96 (0.25), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  55 
 TYR   0.012   0.001   TYR A 477 
 PHE   0.012   0.000   PHE B 696 
 TRP   0.020   0.001   TRP B 604 
 HIS   0.002   0.000   HIS A 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00220 /  0.12 ( 7203)
  covalent geometry    : angle       0.58035 /  0.32 ( 9718)
  SS BOND              : bond        0.00083 /  0.06 (   20)
  SS BOND              : angle       0.24514 /  0.16 (   40)
  hydrogen bonds       : bond        0.20241 / 13.97 (  103)
  hydrogen bonds       : angle       6.48183 /  4.62 (  258)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A  487 LEU cc_start: 0.7393 (tp) cc_final: 0.6991 (pp)
  outliers start: 2
  outliers final: 0
  residues processed: 66
  average time/residue: 0.0897
  time to fit residues: 8.2969
Evaluate side-chains
  65 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.8586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 405 ASN ** 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 = 0.3827 r_free = 0.3827 target = 0.096596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.071326 restraints weight = 20544.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 3.86
r_work: 0.3132 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   7223  Z= 0.250
  Angle     :  0.643   9.047   9758  Z= 0.331
  Chirality :  0.045   0.159   1061
  Planarity :  0.005   0.048   1233
  Dihedral  :  4.031  16.087    931
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 27.26 %
    Favored  : 67.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.29), residues: 816
  helix: -0.48 (0.49), residues: 128
  sheet: -0.84 (0.50), residues: 121
  loop : -1.14 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  42 
 TYR   0.020   0.002   TYR B 591 
 PHE   0.030   0.002   PHE B 696 
 TRP   0.013   0.001   TRP B 604 
 HIS   0.004   0.001   HIS A  21 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00566 /  0.25 ( 7203)
  covalent geometry    : angle       0.64085 /  0.33 ( 9718)
  SS BOND              : bond        0.00440 /  0.27 (   20)
  SS BOND              : angle       0.97726 /  0.57 (   40)
  hydrogen bonds       : bond        0.04634 /  3.19 (  103)
  hydrogen bonds       : angle       5.05371 /  3.63 (  258)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 73
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 TRP cc_start: 0.9204 (OUTLIER) cc_final: 0.8482 (m-90)
REVERT: C   55 ARG cc_start: 0.8884 (ttp80) cc_final: 0.8452 (tpt90)
REVERT: B  621 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7602 (p0)
  outliers start: 43
  outliers final: 25
  residues processed: 107
  average time/residue: 0.0823
  time to fit residues: 12.1423
Evaluate side-chains
  95 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 68
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain D residue   21 ARG
Chi-restraints excluded: chain B residue  523 CYS
Chi-restraints excluded: chain B residue  621 ASN
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  676 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  722 VAL
Chi-restraints excluded: chain B residue  775 ILE
Chi-restraints excluded: chain B residue  905 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 410 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.096173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.070890 restraints weight = 20027.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 3.83
r_work: 0.3119 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7223  Z= 0.151
  Angle     :  0.516   9.415   9758  Z= 0.257
  Chirality :  0.041   0.131   1061
  Planarity :  0.004   0.064   1233
  Dihedral  :  3.735  14.750    931
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 28.79 %
    Favored  : 67.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.42 (0.29), residues: 816
  helix: -0.14 (0.50), residues: 128
  sheet: -0.47 (0.59), residues: 90
  loop : -1.28 (0.25), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  55 
 TYR   0.012   0.001   TYR B 697 
 PHE   0.024   0.001   PHE B 696 
 TRP   0.010   0.001   TRP B 604 
 HIS   0.003   0.001   HIS B 619 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.15 ( 7203)
  covalent geometry    : angle       0.51554 /  0.26 ( 9718)
  SS BOND              : bond        0.00704 /  0.71 (   20)
  SS BOND              : angle       0.65544 /  0.39 (   40)
  hydrogen bonds       : bond        0.03161 /  2.22 (  103)
  hydrogen bonds       : angle       4.93119 /  3.53 (  258)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 75
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 TRP cc_start: 0.9139 (OUTLIER) cc_final: 0.7910 (m-90)
  outliers start: 29
  outliers final: 16
  residues processed: 97
  average time/residue: 0.0758
  time to fit residues: 10.2909
Evaluate side-chains
  81 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain B residue  518 GLN
Chi-restraints excluded: chain B residue  593 LEU
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  657 SER
Chi-restraints excluded: chain B residue  676 LEU
Chi-restraints excluded: chain B residue  705 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 20 optimal weight:    0.2980
   chunk 57 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 33 optimal weight:    0.4980
   chunk 2 optimal weight:    0.0570
   chunk 46 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.5698

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.096169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.070932 restraints weight = 20252.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 3.82
r_work: 0.3125 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.3773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7223  Z= 0.100
  Angle     :  0.481   6.346   9758  Z= 0.239
  Chirality :  0.041   0.172   1061
  Planarity :  0.003   0.048   1233
  Dihedral  :  3.529  14.406    931
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 29.30 %
    Favored  : 67.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.29), residues: 816
  helix: -0.01 (0.51), residues: 128
  sheet: -0.54 (0.58), residues: 90
  loop : -1.28 (0.25), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  55 
 TYR   0.010   0.001   TYR B 591 
 PHE   0.019   0.001   PHE B 696 
 TRP   0.008   0.001   TRP B 604 
 HIS   0.002   0.000   HIS B 619 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.10 ( 7203)
  covalent geometry    : angle       0.48125 /  0.24 ( 9718)
  SS BOND              : bond        0.00160 /  0.11 (   20)
  SS BOND              : angle       0.46963 /  0.27 (   40)
  hydrogen bonds       : bond        0.02477 /  1.70 (  103)
  hydrogen bonds       : angle       4.80372 /  3.46 (  258)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 TRP cc_start: 0.9116 (OUTLIER) cc_final: 0.7979 (m-90)
  outliers start: 22
  outliers final: 15
  residues processed: 83
  average time/residue: 0.0770
  time to fit residues: 9.1037
Evaluate side-chains
  81 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  518 GLN
Chi-restraints excluded: chain B residue  593 LEU
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  676 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 43 optimal weight:    0.0060
   chunk 75 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 49 optimal weight:    7.9990
   chunk 22 optimal weight:    0.3980
   chunk 2 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 56.6628 > 50:)
   chunk 83 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 52 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.8598

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.095078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.069796 restraints weight = 20190.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 3.85
r_work: 0.3097 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.4115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7223  Z= 0.130
  Angle     :  0.492   6.311   9758  Z= 0.248
  Chirality :  0.041   0.149   1061
  Planarity :  0.003   0.047   1233
  Dihedral  :  3.711  15.485    931
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 28.28 %
    Favored  : 67.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.29), residues: 816
  helix:  0.01 (0.50), residues: 128
  sheet: -0.61 (0.58), residues: 90
  loop : -1.30 (0.25), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 454 
 TYR   0.009   0.001   TYR B 697 
 PHE   0.020   0.001   PHE B 696 
 TRP   0.005   0.001   TRP B 604 
 HIS   0.003   0.000   HIS B 630 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.13 ( 7203)
  covalent geometry    : angle       0.49125 /  0.25 ( 9718)
  SS BOND              : bond        0.00215 /  0.14 (   20)
  SS BOND              : angle       0.57612 /  0.32 (   40)
  hydrogen bonds       : bond        0.02707 /  1.85 (  103)
  hydrogen bonds       : angle       4.76855 /  3.43 (  258)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 64
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: A  412 TRP cc_start: 0.9154 (OUTLIER) cc_final: 0.7978 (m-90)
REVERT: C   55 ARG cc_start: 0.9159 (tmt-80) cc_final: 0.8942 (tpt90)
  outliers start: 30
  outliers final: 25
  residues processed: 89
  average time/residue: 0.0750
  time to fit residues: 9.5912
Evaluate side-chains
  85 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 59
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain D residue   60 TYR
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  518 GLN
Chi-restraints excluded: chain B residue  593 LEU
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  676 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  722 VAL
Chi-restraints excluded: chain B residue  905 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    1.0384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.093731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.068437 restraints weight = 20437.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 3.78
r_work: 0.3074 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.4465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7223  Z= 0.150
  Angle     :  0.519   5.967   9758  Z= 0.263
  Chirality :  0.041   0.148   1061
  Planarity :  0.004   0.047   1233
  Dihedral  :  3.901  17.518    931
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 27.26 %
    Favored  : 67.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.29), residues: 816
  helix:  0.05 (0.50), residues: 128
  sheet: -0.57 (0.59), residues: 90
  loop : -1.35 (0.25), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  21 
 TYR   0.012   0.001   TYR D  24 
 PHE   0.020   0.002   PHE B 696 
 TRP   0.006   0.001   TRP B 604 
 HIS   0.002   0.000   HIS B 630 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.15 ( 7203)
  covalent geometry    : angle       0.51832 /  0.26 ( 9718)
  SS BOND              : bond        0.00327 /  0.32 (   20)
  SS BOND              : angle       0.62417 /  0.34 (   40)
  hydrogen bonds       : bond        0.02763 /  1.88 (  103)
  hydrogen bonds       : angle       4.76691 /  3.42 (  258)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 66
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 TRP cc_start: 0.9174 (OUTLIER) cc_final: 0.7989 (m-90)
REVERT: C   55 ARG cc_start: 0.9161 (tmt-80) cc_final: 0.8897 (tpt90)
REVERT: C   56 ARG cc_start: 0.8964 (tpm170) cc_final: 0.8698 (tpm170)
REVERT: B  545 GLU cc_start: 0.8654 (tp30) cc_final: 0.8240 (mm-30)
  outliers start: 38
  outliers final: 29
  residues processed: 98
  average time/residue: 0.0811
  time to fit residues: 11.1014
Evaluate side-chains
  94 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 64
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain D residue   21 ARG
Chi-restraints excluded: chain D residue   60 TYR
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  518 GLN
Chi-restraints excluded: chain B residue  523 CYS
Chi-restraints excluded: chain B residue  593 LEU
Chi-restraints excluded: chain B residue  619 HIS
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  663 LEU
Chi-restraints excluded: chain B residue  676 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  722 VAL
Chi-restraints excluded: chain B residue  905 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0470
   chunk 58 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.1882

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.092889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.067497 restraints weight = 20419.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 3.80
r_work: 0.3055 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.4769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7223  Z= 0.166
  Angle     :  0.527   5.991   9758  Z= 0.269
  Chirality :  0.042   0.149   1061
  Planarity :  0.003   0.046   1233
  Dihedral  :  4.036  16.923    931
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 27.52 %
    Favored  : 67.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.29), residues: 816
  helix: -0.04 (0.49), residues: 129
  sheet: -0.67 (0.57), residues: 95
  loop : -1.39 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 454 
 TYR   0.011   0.001   TYR B 697 
 PHE   0.020   0.002   PHE B 696 
 TRP   0.013   0.001   TRP B 604 
 HIS   0.002   0.000   HIS B 619 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.17 ( 7203)
  covalent geometry    : angle       0.52653 /  0.27 ( 9718)
  SS BOND              : bond        0.00344 /  0.14 (   20)
  SS BOND              : angle       0.67606 /  0.36 (   40)
  hydrogen bonds       : bond        0.02975 /  2.01 (  103)
  hydrogen bonds       : angle       4.85253 /  3.47 (  258)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 64
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  412 TRP cc_start: 0.9184 (OUTLIER) cc_final: 0.8073 (m-90)
REVERT: A  559 TRP cc_start: 0.5929 (p90) cc_final: 0.5674 (p90)
REVERT: C   24 TYR cc_start: 0.8822 (t80) cc_final: 0.8612 (t80)
REVERT: C   55 ARG cc_start: 0.9156 (tmt-80) cc_final: 0.8882 (tpt90)
  outliers start: 42
  outliers final: 32
  residues processed: 98
  average time/residue: 0.0792
  time to fit residues: 10.8493
Evaluate side-chains
  96 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 63
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  535 ASP
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain D residue   60 TYR
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  518 GLN
Chi-restraints excluded: chain B residue  523 CYS
Chi-restraints excluded: chain B residue  593 LEU
Chi-restraints excluded: chain B residue  619 HIS
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  663 LEU
Chi-restraints excluded: chain B residue  676 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  722 VAL
Chi-restraints excluded: chain B residue  775 ILE
Chi-restraints excluded: chain B residue  905 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 56 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 31 optimal weight:    0.4980
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.2184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.092051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.066583 restraints weight = 20381.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 3.79
r_work: 0.3031 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.5016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7223  Z= 0.170
  Angle     :  0.553   9.324   9758  Z= 0.278
  Chirality :  0.042   0.145   1061
  Planarity :  0.004   0.046   1233
  Dihedral  :  4.129  18.462    931
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 28.03 %
    Favored  : 67.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.29), residues: 816
  helix: -0.03 (0.50), residues: 129
  sheet: -0.73 (0.57), residues: 95
  loop : -1.49 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  21 
 TYR   0.012   0.001   TYR B 697 
 PHE   0.020   0.002   PHE B 696 
 TRP   0.013   0.001   TRP B 604 
 HIS   0.001   0.000   HIS B 630 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00400 /  0.17 ( 7203)
  covalent geometry    : angle       0.55271 /  0.28 ( 9718)
  SS BOND              : bond        0.00229 /  0.13 (   20)
  SS BOND              : angle       0.68747 /  0.37 (   40)
  hydrogen bonds       : bond        0.03019 /  2.04 (  103)
  hydrogen bonds       : angle       4.88606 /  3.49 (  258)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 63
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A   37 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8749 (mm)
REVERT: A  294 MET cc_start: 0.7981 (tpp) cc_final: 0.7740 (tpp)
REVERT: A  412 TRP cc_start: 0.9195 (OUTLIER) cc_final: 0.8134 (m-90)
REVERT: A  454 ARG cc_start: 0.7838 (tpt170) cc_final: 0.7564 (tpt90)
REVERT: A  559 TRP cc_start: 0.5914 (p90) cc_final: 0.5677 (p90)
REVERT: A  562 TYR cc_start: 0.8489 (m-10) cc_final: 0.8289 (m-10)
REVERT: C   55 ARG cc_start: 0.9151 (tmt-80) cc_final: 0.8854 (tpt90)
REVERT: B  599 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8671 (ttp80)
  outliers start: 39
  outliers final: 27
  residues processed: 94
  average time/residue: 0.0781
  time to fit residues: 10.2903
Evaluate side-chains
  88 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 58
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  535 ASP
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  518 GLN
Chi-restraints excluded: chain B residue  523 CYS
Chi-restraints excluded: chain B residue  593 LEU
Chi-restraints excluded: chain B residue  599 ARG
Chi-restraints excluded: chain B residue  619 HIS
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  676 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  722 VAL
Chi-restraints excluded: chain B residue  775 ILE
Chi-restraints excluded: chain B residue  905 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0170
   chunk 70 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    1.2026

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.091811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.066390 restraints weight = 20425.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 3.79
r_work: 0.3025 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.5201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7223  Z= 0.168
  Angle     :  0.569  11.787   9758  Z= 0.283
  Chirality :  0.042   0.146   1061
  Planarity :  0.004   0.046   1233
  Dihedral  :  4.239  17.652    931
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 28.54 %
    Favored  : 66.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.69 (0.29), residues: 816
  helix: -0.03 (0.50), residues: 129
  sheet: -0.70 (0.59), residues: 90
  loop : -1.55 (0.25), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  55 
 TYR   0.015   0.001   TYR C  24 
 PHE   0.020   0.002   PHE B 696 
 TRP   0.007   0.001   TRP A 493 
 HIS   0.002   0.000   HIS A 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00397 /  0.17 ( 7203)
  covalent geometry    : angle       0.56831 /  0.28 ( 9718)
  SS BOND              : bond        0.00244 /  0.15 (   20)
  SS BOND              : angle       0.70651 /  0.38 (   40)
  hydrogen bonds       : bond        0.03074 /  2.07 (  103)
  hydrogen bonds       : angle       4.90212 /  3.49 (  258)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 62
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8756 (mm)
REVERT: A  127 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7660 (t80)
REVERT: A  294 MET cc_start: 0.7990 (tpp) cc_final: 0.7669 (tpp)
REVERT: A  412 TRP cc_start: 0.9186 (OUTLIER) cc_final: 0.8018 (m-90)
REVERT: A  559 TRP cc_start: 0.5948 (p90) cc_final: 0.5663 (p90)
REVERT: B  599 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8673 (ttp80)
  outliers start: 37
  outliers final: 29
  residues processed: 93
  average time/residue: 0.0787
  time to fit residues: 10.3025
Evaluate side-chains
  93 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 60
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  535 ASP
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  518 GLN
Chi-restraints excluded: chain B residue  523 CYS
Chi-restraints excluded: chain B residue  593 LEU
Chi-restraints excluded: chain B residue  599 ARG
Chi-restraints excluded: chain B residue  619 HIS
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  663 LEU
Chi-restraints excluded: chain B residue  676 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  722 VAL
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  775 ILE
Chi-restraints excluded: chain B residue  905 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 6 optimal weight:    0.4980
   chunk 27 optimal weight:    0.6980
   chunk 75 optimal weight:    0.0030
   chunk 32 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0170
   overall best weight:    0.3628

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.093359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.067933 restraints weight = 20327.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 3.86
r_work: 0.3064 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.5114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7223  Z= 0.101
  Angle     :  0.570  12.789   9758  Z= 0.275
  Chirality :  0.042   0.146   1061
  Planarity :  0.003   0.047   1233
  Dihedral  :  3.979  16.531    931
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 29.30 %
    Favored  : 67.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.29), residues: 816
  helix:  0.06 (0.51), residues: 128
  sheet: -0.65 (0.59), residues: 90
  loop : -1.48 (0.25), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  21 
 TYR   0.013   0.001   TYR C  24 
 PHE   0.017   0.001   PHE B 696 
 TRP   0.009   0.001   TRP A 493 
 HIS   0.002   0.000   HIS A 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.10 ( 7203)
  covalent geometry    : angle       0.56810 /  0.27 ( 9718)
  SS BOND              : bond        0.00189 /  0.15 (   20)
  SS BOND              : angle       0.85790 /  0.47 (   40)
  hydrogen bonds       : bond        0.02715 /  1.81 (  103)
  hydrogen bonds       : angle       4.82797 /  3.47 (  258)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 63
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  412 TRP cc_start: 0.9104 (OUTLIER) cc_final: 0.8015 (m-90)
REVERT: A  559 TRP cc_start: 0.5865 (p90) cc_final: 0.5638 (p90)
REVERT: C   55 ARG cc_start: 0.9052 (tmt-80) cc_final: 0.8838 (tpt90)
REVERT: C   56 ARG cc_start: 0.8973 (tpm170) cc_final: 0.8616 (tpt170)
REVERT: D   21 ARG cc_start: 0.6922 (mtp180) cc_final: 0.6703 (ttp80)
REVERT: B  545 GLU cc_start: 0.8685 (mm-30) cc_final: 0.7980 (mm-30)
  outliers start: 29
  outliers final: 24
  residues processed: 85
  average time/residue: 0.0870
  time to fit residues: 10.1479
Evaluate side-chains
  87 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 62
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  518 GLN
Chi-restraints excluded: chain B residue  593 LEU
Chi-restraints excluded: chain B residue  619 HIS
Chi-restraints excluded: chain B residue  663 LEU
Chi-restraints excluded: chain B residue  676 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  722 VAL
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  905 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 25 optimal weight:    0.3980
   chunk 37 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 13 optimal weight:    0.3980
   chunk 47 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.6582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.093238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.067917 restraints weight = 20145.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 3.82
r_work: 0.3062 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.5148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7223  Z= 0.116
  Angle     :  0.559  12.565   9758  Z= 0.271
  Chirality :  0.041   0.146   1061
  Planarity :  0.004   0.047   1233
  Dihedral  :  3.990  16.583    931
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 29.17 %
    Favored  : 67.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.29), residues: 816
  helix:  0.02 (0.50), residues: 129
  sheet: -0.86 (0.55), residues: 100
  loop : -1.46 (0.25), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  55 
 TYR   0.012   0.001   TYR B 697 
 PHE   0.018   0.001   PHE B 696 
 TRP   0.009   0.001   TRP A 493 
 HIS   0.002   0.000   HIS A 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 7203)
  covalent geometry    : angle       0.55872 /  0.27 ( 9718)
  SS BOND              : bond        0.00181 /  0.09 (   20)
  SS BOND              : angle       0.66535 /  0.36 (   40)
  hydrogen bonds       : bond        0.02714 /  1.84 (  103)
  hydrogen bonds       : angle       4.74179 /  3.39 (  258)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2071.37 seconds
wall clock time: 36 minutes 14.41 seconds (2174.41 seconds total)