Starting phenix.real_space_refine
on Thu Jul  2 21:28:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qog_18537/07_2026/8qog_18537.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qog_18537/07_2026/8qog_18537.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qog_18537/07_2026/8qog_18537.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qog_18537/07_2026/8qog_18537.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qog_18537/07_2026/8qog_18537.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qog_18537/07_2026/8qog_18537.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.044
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      56      5.16       5
     C    6712      2.51       5
     N    1731      2.21       5
     O    1944      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10444
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1448
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 177, 1448
          Classifications: {'peptide': 177}
          Link IDs: {'PTRANS': 7, 'TRANS': 169}
    Chain: "B"
      Number of atoms: 3903
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 500, 3903
          Classifications: {'peptide': 500}
          Link IDs: {'PTRANS': 24, 'TRANS': 475}
    Chain: "C"
      Number of atoms: 4395
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 555, 4395
          Classifications: {'peptide': 555}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 525}
    Chain: "D"
      Number of atoms: 552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 552
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 2, 'TRANS': 62}
    Chain: "A"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 50
          Unusual residues: {'WAR': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 96
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 96
          Unusual residues: {'PLP': 1, 'Q7G': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'PLP:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 1.78, per 1000 atoms: 0.17
  Number of scatterers: 10444
  At special positions: 0
  Unit cell: (90.552, 95.172, 123.816, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      56     16.00
     P       1     15.00
     O    1944      8.00
     N    1731      7.00
     C    6712      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.87
  Conformation dependent library (CDL) restraints added in 265.4 milliseconds
  

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2440

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 7 sheets defined
      49.6% alpha, 8.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 62
    Processing helix  chain 'A' and resid 72 through 76
      removed outlier: 3.706A  pdb=" N   VAL A  75 " --> pdb=" O   ALA A  72 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ASP A  76 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 72 through 76'
    Processing helix  chain 'A' and resid 82 through 98
      removed outlier: 3.926A  pdb=" N   PHE A  98 " --> pdb=" O   PHE A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 123
      removed outlier: 3.573A  pdb=" N   TRP A 106 " --> pdb=" O   PRO A 102 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   LEU A 123 " --> pdb=" O   ILE A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 145
    Processing helix  chain 'A' and resid 146 through 148
      No H-bonds generated for 'chain 'A' and resid 146 through 148'
    Processing helix  chain 'A' and resid 152 through 170
      Proline residue:  A 162  - end of helix
    Processing helix  chain 'A' and resid 171 through 173
      No H-bonds generated for 'chain 'A' and resid 171 through 173'
    Processing helix  chain 'A' and resid 176 through 192
    Processing helix  chain 'B' and resid 55 through 72
    Processing helix  chain 'B' and resid 89 through 91
      No H-bonds generated for 'chain 'B' and resid 89 through 91'
    Processing helix  chain 'B' and resid 92 through 100
      removed outlier: 3.838A  pdb=" N   LEU B  96 " --> pdb=" O   GLU B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 120
      removed outlier: 3.870A  pdb=" N   ALA B 119 " --> pdb=" O   SER B 115 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LYS B 120 " --> pdb=" O   TRP B 116 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 115 through 120'
    Processing helix  chain 'B' and resid 161 through 176
    Processing helix  chain 'B' and resid 191 through 203
    Processing helix  chain 'B' and resid 213 through 216
    Processing helix  chain 'B' and resid 217 through 222
    Processing helix  chain 'B' and resid 223 through 226
      removed outlier: 3.582A  pdb=" N   THR B 226 " --> pdb=" O   PRO B 223 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 223 through 226'
    Processing helix  chain 'B' and resid 239 through 250
      removed outlier: 4.023A  pdb=" N   ARG B 250 " --> pdb=" O   LEU B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 279
      removed outlier: 3.511A  pdb=" N   LEU B 264 " --> pdb=" O   ASP B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 314
    Processing helix  chain 'B' and resid 334 through 339
      removed outlier: 3.786A  pdb=" N   HIS B 338 " --> pdb=" O   GLY B 334 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE B 339 " --> pdb=" O   LEU B 335 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 334 through 339'
    Processing helix  chain 'B' and resid 342 through 347
      removed outlier: 3.649A  pdb=" N   ILE B 347 " --> pdb=" O   ARG B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 379
      removed outlier: 4.120A  pdb=" N   ILE B 377 " --> pdb=" O   LEU B 373 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER B 379 " --> pdb=" O   GLN B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 384
    Processing helix  chain 'B' and resid 389 through 406
      removed outlier: 4.010A  pdb=" N   VAL B 393 " --> pdb=" O   PRO B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 426
      removed outlier: 4.065A  pdb=" N   GLN B 411 " --> pdb=" O   ASN B 407 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   SER B 426 " --> pdb=" O   ASP B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 458
    Processing helix  chain 'B' and resid 461 through 476
    Processing helix  chain 'B' and resid 482 through 504
      removed outlier: 3.575A  pdb=" N   GLU B 486 " --> pdb=" O   ILE B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 534 through 553
    Processing helix  chain 'C' and resid 19 through 28
    Processing helix  chain 'C' and resid 57 through 86
      removed outlier: 4.078A  pdb=" N   SER C  61 " --> pdb=" O   PRO C  57 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 107
      No H-bonds generated for 'chain 'C' and resid 105 through 107'
    Processing helix  chain 'C' and resid 108 through 114
    Processing helix  chain 'C' and resid 118 through 122
    Processing helix  chain 'C' and resid 173 through 186
    Processing helix  chain 'C' and resid 200 through 215
      removed outlier: 3.553A  pdb=" N   ILE C 204 " --> pdb=" O   THR C 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 231
      removed outlier: 3.650A  pdb=" N   ASN C 229 " --> pdb=" O   GLY C 225 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 236
      removed outlier: 3.559A  pdb=" N   PHE C 236 " --> pdb=" O   PHE C 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 261
      removed outlier: 3.535A  pdb=" N   ARG C 254 " --> pdb=" O   HIS C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 271 through 286
      removed outlier: 3.713A  pdb=" N   VAL C 284 " --> pdb=" O   ARG C 280 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 313 through 325
      removed outlier: 3.572A  pdb=" N   LEU C 317 " --> pdb=" O   ASN C 313 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 345 through 351
    Processing helix  chain 'C' and resid 378 through 389
      removed outlier: 3.812A  pdb=" N   LEU C 387 " --> pdb=" O   ASP C 383 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 390 through 395
    Processing helix  chain 'C' and resid 399 through 415
    Processing helix  chain 'C' and resid 421 through 444
      removed outlier: 3.593A  pdb=" N   GLY C 444 " --> pdb=" O   LEU C 440 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 464 through 476
      removed outlier: 4.014A  pdb=" N   ALA C 468 " --> pdb=" O   SER C 464 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   PHE C 469 " --> pdb=" O   LYS C 465 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   SER C 470 " --> pdb=" O   MET C 466 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 504 through 523
    Processing helix  chain 'C' and resid 541 through 553
      Proline residue:  C 550  - end of helix
    Processing helix  chain 'D' and resid 29 through 42
    Processing helix  chain 'D' and resid 50 through 68
      removed outlier: 3.773A  pdb=" N   PHE D  54 " --> pdb=" O   LEU D  50 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 52
    Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 124
      removed outlier: 6.273A  pdb=" N   ILE B 133 " --> pdb=" O   ASN B 146 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ASN B 146 " --> pdb=" O   ILE B 133 " (cutoff:3.500A)
      removed outlier: 8.268A  pdb=" N   LEU B 506 " --> pdb=" O   ASN B 146 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   PHE B 148 " --> pdb=" O   LEU B 506 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 211
      removed outlier: 3.623A  pdb=" N   THR B 350 " --> pdb=" O   LEU B 366 " (cutoff:3.500A)
      removed outlier: 7.850A  pdb=" N   PHE B 318 " --> pdb=" O   LYS B 286 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   ILE B 288 " --> pdb=" O   PHE B 318 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   ASP B 320 " --> pdb=" O   ILE B 288 " (cutoff:3.500A)
      removed outlier: 7.583A  pdb=" N   THR B 290 " --> pdb=" O   ASP B 320 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   VAL B 231 " --> pdb=" O   PHE B 287 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   VAL B 289 " --> pdb=" O   VAL B 231 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   VAL B 233 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 9.146A  pdb=" N   GLU B 291 " --> pdb=" O   VAL B 233 " (cutoff:3.500A)
      removed outlier: 9.173A  pdb=" N   ASP B 235 " --> pdb=" O   GLU B 291 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   PHE B 256 " --> pdb=" O   ALA B 234 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 434 through 436
      removed outlier: 3.685A  pdb=" N   THR B 508 " --> pdb=" O   LYS B 526 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 126 through 127
      removed outlier: 3.923A  pdb=" N   ARG C 135 " --> pdb=" O   THR C 127 " (cutoff:3.500A)
      removed outlier: 5.851A  pdb=" N   ALA C 153 " --> pdb=" O   ASP C 138 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   ILE C 140 " --> pdb=" O   SER C 151 " (cutoff:3.500A)
      removed outlier: 8.006A  pdb=" N   SER C 151 " --> pdb=" O   ILE C 140 " (cutoff:3.500A)
      removed outlier: 7.525A  pdb=" N   HIS C 142 " --> pdb=" O   THR C 149 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   THR C 149 " --> pdb=" O   HIS C 142 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 218 through 222
      removed outlier: 4.482A  pdb=" N   THR C 363 " --> pdb=" O   GLU C 332 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ILE C 297 " --> pdb=" O   TYR C 327 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   PHE C 329 " --> pdb=" O   ILE C 297 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   ILE C 299 " --> pdb=" O   PHE C 329 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   ASP C 331 " --> pdb=" O   ILE C 299 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ALA C 301 " --> pdb=" O   ASP C 331 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ASP C 246 " --> pdb=" O   CYS C 300 " (cutoff:3.500A)
      removed outlier: 8.147A  pdb=" N   GLU C 302 " --> pdb=" O   ASP C 246 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   VAL C 243 " --> pdb=" O   ARG C 265 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   PHE C 267 " --> pdb=" O   VAL C 243 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   SER C 245 " --> pdb=" O   PHE C 267 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 455 through 459
      removed outlier: 4.166A  pdb=" N   VAL C 481 " --> pdb=" O   ARG C 496 " (cutoff:3.500A)

    461 hydrogen bonds defined for protein.
    1338 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: 1.16

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 3172
        1.34 -     1.46: 1976
        1.46 -     1.58: 5448
        1.58 -     1.70: 2
        1.70 -     1.82: 87
  Bond restraints: 10685
  Sorted by residual:
  bond pdb=" N   PRO B  75 "
       pdb=" CD  PRO B  75 "
    ideal  model  delta    sigma   weight residual
    1.473  1.824 -0.351 1.40e-02 5.10e+03 6.28e+02
  bond pdb=" C15 WAR A 301 "
       pdb=" O49 WAR A 301 "
    ideal  model  delta    sigma   weight residual
    1.448  1.363  0.085 2.00e-02 2.50e+03 1.81e+01
  bond pdb=" O4P PLP C 601 "
       pdb=" P   PLP C 601 "
    ideal  model  delta    sigma   weight residual
    1.687  1.608  0.079 2.00e-02 2.50e+03 1.55e+01
  bond pdb=" CA  LEU D  50 "
       pdb=" C   LEU D  50 "
    ideal  model  delta    sigma   weight residual
    1.524  1.570 -0.046 1.25e-02 6.40e+03 1.34e+01
  bond pdb=" N   TYR D  49 "
       pdb=" CA  TYR D  49 "
    ideal  model  delta    sigma   weight residual
    1.457  1.501 -0.044 1.29e-02 6.01e+03 1.16e+01
  ... (remaining 10680 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.88: 14370
        2.88 -     5.76: 111
        5.76 -     8.64: 9
        8.64 -    11.52: 4
       11.52 -    14.40: 2
  Bond angle restraints: 14496
  Sorted by residual:
  angle pdb=" N   MET D  51 "
        pdb=" CA  MET D  51 "
        pdb=" C   MET D  51 "
      ideal   model   delta    sigma   weight residual
     113.28   98.88   14.40 1.22e+00 6.72e-01 1.39e+02
  angle pdb=" C   SER D  53 "
        pdb=" N   PHE D  54 "
        pdb=" CA  PHE D  54 "
      ideal   model   delta    sigma   weight residual
     120.28  109.26   11.02 1.34e+00 5.57e-01 6.76e+01
  angle pdb=" CA  PRO B  90 "
        pdb=" N   PRO B  90 "
        pdb=" CD  PRO B  90 "
      ideal   model   delta    sigma   weight residual
     112.00  102.06    9.94 1.40e+00 5.10e-01 5.04e+01
  angle pdb=" CA  PRO B  75 "
        pdb=" N   PRO B  75 "
        pdb=" CD  PRO B  75 "
      ideal   model   delta    sigma   weight residual
     112.00  102.08    9.92 1.40e+00 5.10e-01 5.02e+01
  angle pdb=" N   PRO B  75 "
        pdb=" CA  PRO B  75 "
        pdb=" CB  PRO B  75 "
      ideal   model   delta    sigma   weight residual
     103.25  109.02   -5.77 1.05e+00 9.07e-01 3.02e+01
  ... (remaining 14491 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.56: 6191
       25.56 -    51.11: 342
       51.11 -    76.67: 29
       76.67 -   102.23: 20
      102.23 -   127.78: 9
  Dihedral angle restraints: 6591
    sinusoidal: 2800
      harmonic: 3791
  Sorted by residual:
  dihedral pdb=" C   TYR D  49 "
           pdb=" N   TYR D  49 "
           pdb=" CA  TYR D  49 "
           pdb=" CB  TYR D  49 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.80   16.20     0      2.50e+00 1.60e-01 4.20e+01
  dihedral pdb=" N   TYR D  49 "
           pdb=" C   TYR D  49 "
           pdb=" CA  TYR D  49 "
           pdb=" CB  TYR D  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.20  -12.40     0      2.50e+00 1.60e-01 2.46e+01
  dihedral pdb=" C   PHE D  54 "
           pdb=" N   PHE D  54 "
           pdb=" CA  PHE D  54 "
           pdb=" CB  PHE D  54 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.02   11.42     0      2.50e+00 1.60e-01 2.09e+01
  ... (remaining 6588 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.103: 1591
       0.103 -    0.205: 53
       0.205 -    0.308: 5
       0.308 -    0.411: 1
       0.411 -    0.514: 2
  Chirality restraints: 1652
  Sorted by residual:
  chirality pdb=" CA  TYR D  49 "
            pdb=" N   TYR D  49 "
            pdb=" C   TYR D  49 "
            pdb=" CB  TYR D  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.59e+00
  chirality pdb=" C15 WAR A 301 "
            pdb=" C14 WAR A 301 "
            pdb=" C16 WAR A 301 "
            pdb=" O49 WAR A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.69    2.21    0.48 2.00e-01 2.50e+01 5.84e+00
  chirality pdb=" CA  PHE D  54 "
            pdb=" N   PHE D  54 "
            pdb=" C   PHE D  54 "
            pdb=" CB  PHE D  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 2.99e+00
  ... (remaining 1649 not shown)

  Planarity restraints: 1823
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  PLP C 601 "    0.015 2.00e-02 2.50e+03   9.97e-02 2.48e+02
        pdb=" C2A PLP C 601 "    0.049 2.00e-02 2.50e+03
        pdb=" C3  PLP C 601 "   -0.066 2.00e-02 2.50e+03
        pdb=" C4  PLP C 601 "   -0.096 2.00e-02 2.50e+03
        pdb=" C4A PLP C 601 "    0.237 2.00e-02 2.50e+03
        pdb=" C5  PLP C 601 "   -0.045 2.00e-02 2.50e+03
        pdb=" C5A PLP C 601 "   -0.080 2.00e-02 2.50e+03
        pdb=" C6  PLP C 601 "    0.035 2.00e-02 2.50e+03
        pdb=" N1  PLP C 601 "    0.065 2.00e-02 2.50e+03
        pdb=" O3  PLP C 601 "   -0.114 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C11 Q7G C 602 "    0.017 2.00e-02 2.50e+03   5.95e-02 4.42e+01
        pdb=" C13 Q7G C 602 "    0.006 2.00e-02 2.50e+03
        pdb=" C14 Q7G C 602 "    0.099 2.00e-02 2.50e+03
        pdb=" C15 Q7G C 602 "   -0.071 2.00e-02 2.50e+03
        pdb=" C16 Q7G C 602 "   -0.050 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  89 "   -0.091 5.00e-02 4.00e+02   1.30e-01 2.72e+01
        pdb=" N   PRO B  90 "    0.225 5.00e-02 4.00e+02
        pdb=" CA  PRO B  90 "   -0.066 5.00e-02 4.00e+02
        pdb=" CD  PRO B  90 "   -0.069 5.00e-02 4.00e+02
  ... (remaining 1820 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1803
        2.77 -     3.30: 9217
        3.30 -     3.84: 15766
        3.84 -     4.37: 17162
        4.37 -     4.90: 33208
  Nonbonded interactions: 77156
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B 213 "
            pdb=" OG  SER C 395 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   PHE D  67 "
            pdb=" C   SER D  68 "
     model   vdw
     2.291 3.270
  nonbonded pdb=" OD1 ASN D  21 "
            pdb=" N   GLY D  22 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" OD1 ASP A  60 "
            pdb=" NH1 ARG B 228 "
     model   vdw
     2.331 3.120
  nonbonded pdb=" OD1 ASP B 428 "
            pdb=" NH1 ARG B 431 "
     model   vdw
     2.386 3.120
  ... (remaining 77151 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.300
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.680
  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:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7162
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.351  10686  Z= 0.324
  Angle     :  0.635  14.396  14496  Z= 0.362
  Chirality :  0.048   0.514   1652
  Planarity :  0.006   0.130   1823
  Dihedral  : 16.348 127.781   4151
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  0.35 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    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:  0.98 (0.24), residues: 1289
  helix:  2.48 (0.23), residues: 543
  sheet:  1.33 (0.45), residues: 141
  loop : -1.34 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 292 
 TYR   0.025   0.001   TYR D  49 
 PHE   0.025   0.001   PHE D  62 
 TRP   0.006   0.001   TRP C 294 
 HIS   0.003   0.001   HIS B 498 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00518 /  0.32 (10685)
  covalent geometry    : angle       0.63523 /  0.36 (14496)
  hydrogen bonds       : bond        0.15829 / 10.05 (  461)
  hydrogen bonds       : angle       5.77170 /  4.30 ( 1338)
  Misc. bond           : bond        0.00073 /  0.05 (    1)

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

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

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 187
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.7090 (tt0) cc_final: 0.5962 (tp40)
REVERT: C  135 ARG cc_start: 0.7504 (mtm180) cc_final: 0.7214 (mtm-85)
REVERT: C  521 LYS cc_start: 0.7281 (tttt) cc_final: 0.7055 (ttmm)
  outliers start: 4
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1021
  time to fit residues: 26.9728
Evaluate side-chains
  105 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    0.5980
   chunk 55 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 110 ASN
B 213 GLN
B 295 HIS
C  78 HIS
C 229 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.132540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.108469 restraints weight = 12659.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 1.97
r_work: 0.3117 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.099  10686  Z= 0.178
  Angle     :  0.650   9.708  14496  Z= 0.333
  Chirality :  0.046   0.210   1652
  Planarity :  0.005   0.073   1823
  Dihedral  :  9.201 120.924   1669
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  8.29 %
    Favored  : 90.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    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:  0.86 (0.24), residues: 1289
  helix:  2.35 (0.22), residues: 559
  sheet:  1.18 (0.44), residues: 147
  loop : -1.48 (0.24), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 437 
 TYR   0.022   0.002   TYR C 510 
 PHE   0.023   0.002   PHE B 215 
 TRP   0.013   0.001   TRP B 100 
 HIS   0.004   0.001   HIS B 295 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.18 (10685)
  covalent geometry    : angle       0.65034 /  0.33 (14496)
  hydrogen bonds       : bond        0.05519 /  3.72 (  461)
  hydrogen bonds       : angle       4.30987 /  3.17 ( 1338)
  Misc. bond           : bond        0.00179 /  0.12 (    1)

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

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

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.7758 (tt0) cc_final: 0.6465 (tp40)
REVERT: A   60 ASP cc_start: 0.8092 (m-30) cc_final: 0.7715 (m-30)
REVERT: A  182 SER cc_start: 0.8142 (t) cc_final: 0.7843 (m)
REVERT: C   97 ASP cc_start: 0.8265 (m-30) cc_final: 0.7983 (p0)
REVERT: C  135 ARG cc_start: 0.7915 (mtm180) cc_final: 0.7490 (mtp180)
REVERT: C  147 TYR cc_start: 0.8209 (p90) cc_final: 0.7835 (p90)
REVERT: C  212 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7384 (ttp-170)
REVERT: C  324 TYR cc_start: 0.7742 (m-10) cc_final: 0.7302 (m-80)
REVERT: C  547 ARG cc_start: 0.7010 (ttp80) cc_final: 0.6793 (ttp-110)
  outliers start: 13
  outliers final: 9
  residues processed: 127
  average time/residue: 0.0928
  time to fit residues: 17.0693
Evaluate side-chains
  103 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  297 SER
Chi-restraints excluded: chain C residue    8 THR
Chi-restraints excluded: chain C residue   33 SER
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  212 ARG
Chi-restraints excluded: chain C residue  335 SER
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   61 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 122 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 111 optimal weight:    0.4980
   chunk 37 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   overall best weight:    1.4384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  76 GLN
C  78 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.117196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.092382 restraints weight = 13048.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 2.02
r_work: 0.2907 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.5559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10686  Z= 0.182
  Angle     :  0.637   7.494  14496  Z= 0.333
  Chirality :  0.047   0.201   1652
  Planarity :  0.005   0.074   1823
  Dihedral  :  8.874 128.416   1669
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.04 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    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:  0.53 (0.24), residues: 1289
  helix:  1.99 (0.22), residues: 572
  sheet:  1.06 (0.43), residues: 137
  loop : -1.62 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 280 
 TYR   0.020   0.002   TYR B  70 
 PHE   0.018   0.002   PHE C 106 
 TRP   0.011   0.002   TRP A 104 
 HIS   0.004   0.001   HIS C 269 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00421 /  0.18 (10685)
  covalent geometry    : angle       0.63652 /  0.33 (14496)
  hydrogen bonds       : bond        0.07875 /  5.24 (  461)
  hydrogen bonds       : angle       4.27990 /  3.12 ( 1338)
  Misc. bond           : bond        0.00228 /  0.15 (    1)

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

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

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 ASP cc_start: 0.8204 (m-30) cc_final: 0.7803 (m-30)
REVERT: A   66 MET cc_start: 0.5599 (ptt) cc_final: 0.5346 (ptt)
REVERT: A  147 ASP cc_start: 0.8131 (t0) cc_final: 0.7812 (t0)
REVERT: A  209 ILE cc_start: 0.6747 (mt) cc_final: 0.6445 (tt)
REVERT: B   98 GLU cc_start: 0.7696 (tp30) cc_final: 0.7461 (tt0)
REVERT: B  125 MET cc_start: 0.8365 (mmm) cc_final: 0.8142 (mmt)
REVERT: B  497 ASP cc_start: 0.7632 (m-30) cc_final: 0.7317 (m-30)
REVERT: C  147 TYR cc_start: 0.8539 (p90) cc_final: 0.8128 (p90)
REVERT: C  182 SER cc_start: 0.7767 (t) cc_final: 0.7303 (m)
REVERT: C  212 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7443 (ttp-170)
REVERT: C  217 GLU cc_start: 0.7951 (tp30) cc_final: 0.7494 (tt0)
REVERT: C  292 ARG cc_start: 0.7435 (mtp85) cc_final: 0.7171 (mmm160)
REVERT: C  310 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8545 (p)
  outliers start: 21
  outliers final: 12
  residues processed: 117
  average time/residue: 0.0994
  time to fit residues: 16.2597
Evaluate side-chains
  102 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain C residue    8 THR
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  212 ARG
Chi-restraints excluded: chain C residue  308 GLU
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain C residue  357 VAL
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  560 VAL
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   61 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 116 optimal weight:    4.9990
   chunk 101 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    1.1986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 295 HIS
C  78 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.128788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.104813 restraints weight = 12718.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 1.88
r_work: 0.2968 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.5720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10686  Z= 0.146
  Angle     :  0.551   7.528  14496  Z= 0.289
  Chirality :  0.044   0.196   1652
  Planarity :  0.005   0.066   1823
  Dihedral  :  8.405 122.210   1669
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 12.48 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    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:  0.66 (0.24), residues: 1289
  helix:  2.23 (0.22), residues: 566
  sheet:  1.17 (0.43), residues: 135
  loop : -1.67 (0.23), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 547 
 TYR   0.018   0.002   TYR C 510 
 PHE   0.011   0.001   PHE B 256 
 TRP   0.013   0.001   TRP A 104 
 HIS   0.004   0.001   HIS C  78 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.15 (10685)
  covalent geometry    : angle       0.55092 /  0.29 (14496)
  hydrogen bonds       : bond        0.05989 /  4.01 (  461)
  hydrogen bonds       : angle       4.05989 /  2.96 ( 1338)
  Misc. bond           : bond        0.00025 /  0.02 (    1)

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

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

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
REVERT: A  147 ASP cc_start: 0.8238 (t0) cc_final: 0.7793 (t0)
REVERT: A  209 ILE cc_start: 0.6629 (mt) cc_final: 0.6354 (tt)
REVERT: B  463 GLU cc_start: 0.7496 (mp0) cc_final: 0.7269 (mp0)
REVERT: B  497 ASP cc_start: 0.7416 (m-30) cc_final: 0.7092 (m-30)
REVERT: C  147 TYR cc_start: 0.8496 (p90) cc_final: 0.8162 (p90)
REVERT: C  182 SER cc_start: 0.7754 (t) cc_final: 0.7297 (m)
REVERT: C  217 GLU cc_start: 0.7910 (tp30) cc_final: 0.7501 (tt0)
REVERT: C  268 LYS cc_start: 0.7781 (tttm) cc_final: 0.7133 (tppt)
REVERT: C  473 MET cc_start: 0.8393 (mmm) cc_final: 0.8109 (mmt)
REVERT: C  547 ARG cc_start: 0.7784 (ttp80) cc_final: 0.7568 (ttp80)
  outliers start: 16
  outliers final: 11
  residues processed: 109
  average time/residue: 0.1047
  time to fit residues: 16.2045
Evaluate side-chains
  99 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain C residue    8 THR
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  308 GLU
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  560 VAL
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   61 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9980
   chunk 125 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 116 optimal weight:    4.9990
   chunk 85 optimal weight:    6.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  78 HIS
C 196 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.114584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.090408 restraints weight = 13361.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 1.90
r_work: 0.2887 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.6027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10686  Z= 0.211
  Angle     :  0.631   8.649  14496  Z= 0.330
  Chirality :  0.047   0.217   1652
  Planarity :  0.005   0.066   1823
  Dihedral  :  8.654 118.906   1669
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 12.74 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    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:  0.49 (0.23), residues: 1289
  helix:  2.06 (0.22), residues: 564
  sheet:  0.91 (0.43), residues: 137
  loop : -1.68 (0.23), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 428 
 TYR   0.019   0.002   TYR B  66 
 PHE   0.017   0.002   PHE B 318 
 TRP   0.012   0.002   TRP A 104 
 HIS   0.004   0.001   HIS C  78 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00518 /  0.21 (10685)
  covalent geometry    : angle       0.63140 /  0.33 (14496)
  hydrogen bonds       : bond        0.07660 /  5.12 (  461)
  hydrogen bonds       : angle       4.16848 /  3.03 ( 1338)
  Misc. bond           : bond        0.00069 /  0.05 (    1)

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

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

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  147 ASP cc_start: 0.8251 (t0) cc_final: 0.7708 (t0)
REVERT: A  209 ILE cc_start: 0.6654 (mt) cc_final: 0.6239 (tt)
REVERT: B  112 ASP cc_start: 0.7962 (t0) cc_final: 0.7667 (m-30)
REVERT: B  497 ASP cc_start: 0.7513 (m-30) cc_final: 0.7252 (m-30)
REVERT: C  117 ARG cc_start: 0.7704 (mpt180) cc_final: 0.7272 (mmp80)
REVERT: C  147 TYR cc_start: 0.8568 (p90) cc_final: 0.8233 (p90)
REVERT: C  182 SER cc_start: 0.7727 (t) cc_final: 0.7281 (m)
REVERT: C  217 GLU cc_start: 0.8002 (tp30) cc_final: 0.7608 (tt0)
REVERT: C  268 LYS cc_start: 0.7893 (tttm) cc_final: 0.7265 (tppt)
REVERT: C  473 MET cc_start: 0.8376 (mmm) cc_final: 0.8051 (mmt)
REVERT: C  547 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7592 (ttp80)
  outliers start: 22
  outliers final: 16
  residues processed: 103
  average time/residue: 0.1008
  time to fit residues: 14.9711
Evaluate side-chains
  96 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain C residue    8 THR
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  187 SER
Chi-restraints excluded: chain C residue  308 GLU
Chi-restraints excluded: chain C residue  335 SER
Chi-restraints excluded: chain C residue  375 ILE
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  504 THR
Chi-restraints excluded: chain C residue  560 VAL
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   61 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 112 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 80 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 100 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    1.3986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  78 HIS
C 196 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.139396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.121252 restraints weight = 12551.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.24
r_work: 0.3340 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.6132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10686  Z= 0.157
  Angle     :  0.568   8.106  14496  Z= 0.298
  Chirality :  0.044   0.201   1652
  Planarity :  0.005   0.065   1823
  Dihedral  :  8.435 117.282   1669
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.79 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    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:  0.58 (0.24), residues: 1289
  helix:  2.18 (0.22), residues: 564
  sheet:  0.86 (0.43), residues: 137
  loop : -1.64 (0.23), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 456 
 TYR   0.018   0.002   TYR C 510 
 PHE   0.012   0.001   PHE B 256 
 TRP   0.011   0.001   TRP A 104 
 HIS   0.003   0.001   HIS C  78 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00378 /  0.16 (10685)
  covalent geometry    : angle       0.56787 /  0.30 (14496)
  hydrogen bonds       : bond        0.06376 /  4.26 (  461)
  hydrogen bonds       : angle       4.05172 /  2.96 ( 1338)
  Misc. bond           : bond        0.00048 /  0.03 (    1)

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

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

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  147 ASP cc_start: 0.8246 (t0) cc_final: 0.7732 (t0)
REVERT: A  209 ILE cc_start: 0.7458 (mt) cc_final: 0.7125 (tt)
REVERT: B   65 LEU cc_start: 0.8451 (tp) cc_final: 0.8199 (tp)
REVERT: C  147 TYR cc_start: 0.8897 (p90) cc_final: 0.8579 (p90)
REVERT: C  182 SER cc_start: 0.8418 (t) cc_final: 0.7992 (m)
REVERT: C  473 MET cc_start: 0.8839 (mmm) cc_final: 0.8541 (mmt)
  outliers start: 23
  outliers final: 15
  residues processed: 102
  average time/residue: 0.1057
  time to fit residues: 15.3855
Evaluate side-chains
  93 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain C residue    8 THR
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  187 SER
Chi-restraints excluded: chain C residue  308 GLU
Chi-restraints excluded: chain C residue  375 ILE
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  504 THR
Chi-restraints excluded: chain C residue  560 VAL
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   61 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 93 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0000
   chunk 113 optimal weight:    0.9980
   chunk 97 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.6384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  78 HIS
** C 105 ASN ** 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 = 0.3630 r_free = 0.3630 target = 0.138777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.120348 restraints weight = 12542.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 1.23
r_work: 0.3346 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.6143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10686  Z= 0.106
  Angle     :  0.491   6.018  14496  Z= 0.259
  Chirality :  0.042   0.193   1652
  Planarity :  0.005   0.063   1823
  Dihedral  :  7.990 116.147   1669
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 14.05 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    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:  0.86 (0.24), residues: 1289
  helix:  2.47 (0.22), residues: 559
  sheet:  1.13 (0.43), residues: 135
  loop : -1.56 (0.23), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 456 
 TYR   0.016   0.001   TYR C 510 
 PHE   0.010   0.001   PHE B 256 
 TRP   0.008   0.001   TRP C 294 
 HIS   0.002   0.000   HIS A 122 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00233 /  0.11 (10685)
  covalent geometry    : angle       0.49079 /  0.26 (14496)
  hydrogen bonds       : bond        0.04622 /  3.09 (  461)
  hydrogen bonds       : angle       3.90024 /  2.85 ( 1338)
  Misc. bond           : bond        0.00015 /  0.01 (    1)

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

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

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  120 MET cc_start: 0.7937 (ttm) cc_final: 0.7590 (mtp)
REVERT: A  147 ASP cc_start: 0.8254 (t0) cc_final: 0.7735 (t0)
REVERT: B  273 GLU cc_start: 0.7447 (mm-30) cc_final: 0.6905 (mt-10)
REVERT: C  147 TYR cc_start: 0.8815 (p90) cc_final: 0.8554 (p90)
REVERT: C  182 SER cc_start: 0.8214 (t) cc_final: 0.7798 (m)
REVERT: C  473 MET cc_start: 0.8758 (mmm) cc_final: 0.8523 (mmt)
  outliers start: 18
  outliers final: 12
  residues processed: 93
  average time/residue: 0.0905
  time to fit residues: 11.9348
Evaluate side-chains
  87 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain C residue    8 THR
Chi-restraints excluded: chain C residue  187 SER
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  560 VAL
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   61 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0570
   chunk 118 optimal weight:    0.7980
   chunk 110 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 117 optimal weight:    0.6980
   chunk 112 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   overall best weight:    0.7100

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  78 HIS
** C 105 ASN ** 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 = 0.3704 r_free = 0.3704 target = 0.143847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.125743 restraints weight = 12400.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 1.24
r_work: 0.3423 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3317 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.6199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10686  Z= 0.110
  Angle     :  0.496   6.325  14496  Z= 0.261
  Chirality :  0.042   0.186   1652
  Planarity :  0.005   0.061   1823
  Dihedral  :  7.819 113.754   1669
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 14.22 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    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:  0.99 (0.24), residues: 1289
  helix:  2.58 (0.22), residues: 558
  sheet:  1.24 (0.46), residues: 124
  loop : -1.44 (0.23), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 547 
 TYR   0.017   0.001   TYR C 510 
 PHE   0.011   0.001   PHE B 185 
 TRP   0.009   0.001   TRP C 294 
 HIS   0.002   0.000   HIS C 514 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.11 (10685)
  covalent geometry    : angle       0.49624 /  0.26 (14496)
  hydrogen bonds       : bond        0.04827 /  3.23 (  461)
  hydrogen bonds       : angle       3.84697 /  2.81 ( 1338)
  Misc. bond           : bond        0.00029 /  0.02 (    1)

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

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

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8089 (ttm) cc_final: 0.7737 (mtp)
REVERT: A  147 ASP cc_start: 0.8235 (t0) cc_final: 0.7713 (t0)
REVERT: A  154 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7778 (m)
REVERT: B  273 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6996 (mt-10)
REVERT: C   97 ASP cc_start: 0.8368 (m-30) cc_final: 0.8035 (p0)
REVERT: C  147 TYR cc_start: 0.8819 (p90) cc_final: 0.8571 (p90)
REVERT: C  182 SER cc_start: 0.8301 (t) cc_final: 0.7899 (m)
  outliers start: 15
  outliers final: 11
  residues processed: 94
  average time/residue: 0.0955
  time to fit residues: 12.8618
Evaluate side-chains
  92 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain C residue    8 THR
Chi-restraints excluded: chain C residue  308 GLU
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  560 VAL
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   61 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 2 optimal weight:    0.1980
   chunk 97 optimal weight:    0.0770
   chunk 45 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.3980
   chunk 9 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 127 optimal weight:    7.9990
   overall best weight:    0.6940

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  78 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.139243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.120859 restraints weight = 12567.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 1.23
r_work: 0.3405 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3296 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8585
moved from start:          0.6230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10686  Z= 0.107
  Angle     :  0.486   6.001  14496  Z= 0.256
  Chirality :  0.042   0.187   1652
  Planarity :  0.005   0.059   1823
  Dihedral  :  7.695 112.260   1669
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.49 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    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:  1.01 (0.24), residues: 1289
  helix:  2.52 (0.22), residues: 565
  sheet:  1.33 (0.46), residues: 123
  loop : -1.40 (0.24), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 456 
 TYR   0.017   0.001   TYR C 510 
 PHE   0.010   0.001   PHE B 256 
 TRP   0.009   0.001   TRP C 294 
 HIS   0.002   0.000   HIS C 514 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.11 (10685)
  covalent geometry    : angle       0.48563 /  0.26 (14496)
  hydrogen bonds       : bond        0.04623 /  3.08 (  461)
  hydrogen bonds       : angle       3.81668 /  2.78 ( 1338)
  Misc. bond           : bond        0.00024 /  0.02 (    1)

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

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

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8224 (ttm) cc_final: 0.7855 (mtp)
REVERT: A  147 ASP cc_start: 0.8235 (t0) cc_final: 0.7715 (t0)
REVERT: A  154 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7751 (m)
REVERT: B   92 GLU cc_start: 0.6831 (pt0) cc_final: 0.6242 (pm20)
REVERT: C  182 SER cc_start: 0.8386 (t) cc_final: 0.8019 (m)
  outliers start: 16
  outliers final: 13
  residues processed: 94
  average time/residue: 0.0916
  time to fit residues: 12.4758
Evaluate side-chains
  91 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain C residue    8 THR
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  308 GLU
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  560 VAL
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   61 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 103 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 114 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  78 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.139472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.121392 restraints weight = 12394.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 1.23
r_work: 0.3344 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.6328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10686  Z= 0.169
  Angle     :  0.567   7.119  14496  Z= 0.299
  Chirality :  0.045   0.205   1652
  Planarity :  0.005   0.061   1823
  Dihedral  :  8.009 110.322   1669
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 2.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 14.40 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    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:  0.80 (0.24), residues: 1289
  helix:  2.40 (0.22), residues: 559
  sheet:  1.04 (0.44), residues: 133
  loop : -1.54 (0.24), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 547 
 TYR   0.018   0.002   TYR C 510 
 PHE   0.012   0.001   PHE B 318 
 TRP   0.010   0.001   TRP A 104 
 HIS   0.003   0.001   HIS B 446 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00416 /  0.17 (10685)
  covalent geometry    : angle       0.56737 /  0.30 (14496)
  hydrogen bonds       : bond        0.06583 /  4.39 (  461)
  hydrogen bonds       : angle       3.97450 /  2.89 ( 1338)
  Misc. bond           : bond        0.00055 /  0.04 (    1)

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

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

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2578 Ramachandran restraints generated.
    1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8360 (ttm) cc_final: 0.7996 (mtp)
REVERT: A  147 ASP cc_start: 0.8258 (t0) cc_final: 0.7758 (t0)
REVERT: B   92 GLU cc_start: 0.6875 (pt0) cc_final: 0.6255 (pm20)
REVERT: C  182 SER cc_start: 0.8439 (t) cc_final: 0.8017 (m)
  outliers start: 17
  outliers final: 16
  residues processed: 96
  average time/residue: 0.1049
  time to fit residues: 14.4383
Evaluate side-chains
  96 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain C residue    8 THR
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  187 SER
Chi-restraints excluded: chain C residue  199 THR
Chi-restraints excluded: chain C residue  308 GLU
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  560 VAL
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   61 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 120 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 105 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 126 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 23 optimal weight:    0.2980
   chunk 22 optimal weight:    1.9990
   chunk 6 optimal weight:    0.4980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  64 GLN
C  78 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.143410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.125379 restraints weight = 12465.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 1.24
r_work: 0.3428 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3320 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.6320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10686  Z= 0.111
  Angle     :  0.495   6.033  14496  Z= 0.261
  Chirality :  0.042   0.184   1652
  Planarity :  0.005   0.060   1823
  Dihedral  :  7.736 110.639   1669
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 14.75 %
    Favored  : 84.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    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:  0.97 (0.24), residues: 1289
  helix:  2.49 (0.22), residues: 565
  sheet:  1.20 (0.45), residues: 127
  loop : -1.42 (0.24), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 547 
 TYR   0.017   0.001   TYR C 510 
 PHE   0.010   0.001   PHE B 256 
 TRP   0.009   0.001   TRP C 294 
 HIS   0.002   0.000   HIS A 122 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.11 (10685)
  covalent geometry    : angle       0.49500 /  0.26 (14496)
  hydrogen bonds       : bond        0.04814 /  3.21 (  461)
  hydrogen bonds       : angle       3.85439 /  2.80 ( 1338)
  Misc. bond           : bond        0.00024 /  0.02 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2292.17 seconds
wall clock time: 39 minutes 57.52 seconds (2397.52 seconds total)