Starting phenix.real_space_refine
on Wed Feb  4 10:52:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nyg_49934/02_2026/9nyg_49934.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nyg_49934/02_2026/9nyg_49934.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nyg_49934/02_2026/9nyg_49934.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nyg_49934/02_2026/9nyg_49934.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nyg_49934/02_2026/9nyg_49934.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nyg_49934/02_2026/9nyg_49934.cif"
  }
  resolution = 2.93
  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=   0.011
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      31      5.49       5
     S      27      5.16       5
     C    6285      2.51       5
     N    1758      2.21       5
     O    1960      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10061
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 1239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 153, 1239
          Classifications: {'peptide': 153}
          Link IDs: {'PTRANS': 8, 'TRANS': 144}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2256
          Classifications: {'peptide': 274}
          Link IDs: {'PTRANS': 5, 'TRANS': 268}
          Chain breaks: 3
    Chain: "G"
      Number of atoms: 1329
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 168, 1329
          Classifications: {'peptide': 168}
          Link IDs: {'PTRANS': 2, 'TRANS': 165}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 4601
          Classifications: {'peptide': 571}
          Link IDs: {'PTRANS': 22, 'TRANS': 548}
          Chain breaks: 5
    Chain: "E"
      Number of atoms: 313
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 313
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "F"
      Number of atoms: 323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 323
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
  Time building chain proxies: 1.67, per 1000 atoms: 0.17
  Number of scatterers: 10061
  At special positions: 0
  Unit cell: (81.2, 103.675, 165.3, 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      27     16.00
     P      31     15.00
     O    1960      8.00
     N    1758      7.00
     C    6285      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 315.0 milliseconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2244

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 2 sheets defined
      51.1% alpha, 3.5% beta
      10 base pairs and 21 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'C' and resid 34 through 44
      removed outlier: 3.910A  pdb=" N   LEU C  38 " --> pdb=" O   TRP C  34 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ALA C  39 " --> pdb=" O   ILE C  35 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   TYR C  40 " --> pdb=" O   ALA C  36 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLN C  44 " --> pdb=" O   TYR C  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 71
      removed outlier: 4.216A  pdb=" N   SER C  71 " --> pdb=" O   ASN C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 75 through 83
    Processing helix  chain 'C' and resid 92 through 94
      No H-bonds generated for 'chain 'C' and resid 92 through 94'
    Processing helix  chain 'C' and resid 95 through 100
      removed outlier: 3.867A  pdb=" N   PHE C  99 " --> pdb=" O   LEU C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 162
    Processing helix  chain 'C' and resid 166 through 174
      removed outlier: 3.619A  pdb=" N   LEU C 174 " --> pdb=" O   LEU C 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 28
      removed outlier: 4.134A  pdb=" N   ARG A  25 " --> pdb=" O   ARG A  21 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LEU A  26 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLU A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 179
      removed outlier: 3.936A  pdb=" N   TYR A 177 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LYS A 178 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 209
      removed outlier: 3.655A  pdb=" N   ILE A 192 " --> pdb=" O   HIS A 188 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   TRP A 199 " --> pdb=" O   GLU A 195 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL A 200 " --> pdb=" O   ILE A 196 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   GLU A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 238
    Processing helix  chain 'A' and resid 264 through 269
      removed outlier: 4.205A  pdb=" N   ILE A 268 " --> pdb=" O   GLN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 296
      removed outlier: 3.657A  pdb=" N   LEU A 283 " --> pdb=" O   ALA A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 302
    Processing helix  chain 'A' and resid 303 through 308
      removed outlier: 3.675A  pdb=" N   ARG A 308 " --> pdb=" O   ARG A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 313
    Processing helix  chain 'A' and resid 319 through 325
      removed outlier: 3.827A  pdb=" N   LEU A 323 " --> pdb=" O   GLN A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 333
      No H-bonds generated for 'chain 'A' and resid 331 through 333'
    Processing helix  chain 'A' and resid 334 through 342
      removed outlier: 3.769A  pdb=" N   TYR A 338 " --> pdb=" O   GLY A 334 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ILE A 339 " --> pdb=" O   GLN A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 368
      removed outlier: 3.787A  pdb=" N   ALA A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 230 through 234
    Processing helix  chain 'G' and resid 239 through 245
    Processing helix  chain 'G' and resid 278 through 314
    Processing helix  chain 'G' and resid 315 through 317
      No H-bonds generated for 'chain 'G' and resid 315 through 317'
    Processing helix  chain 'G' and resid 356 through 360
      removed outlier: 3.770A  pdb=" N   LEU G 360 " --> pdb=" O   GLU G 356 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 356 through 360'
    Processing helix  chain 'G' and resid 361 through 374
      removed outlier: 3.504A  pdb=" N   ARG G 367 " --> pdb=" O   GLU G 363 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   SER G 370 " --> pdb=" O   ALA G 366 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   ASN G 371 " --> pdb=" O   ARG G 367 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   LEU G 372 " --> pdb=" O   ALA G 368 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   GLU G 373 " --> pdb=" O   PHE G 369 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 386 through 416
    Processing helix  chain 'G' and resid 426 through 440
    Processing helix  chain 'B' and resid 39 through 41
      No H-bonds generated for 'chain 'B' and resid 39 through 41'
    Processing helix  chain 'B' and resid 42 through 52
      removed outlier: 3.586A  pdb=" N   GLY B  52 " --> pdb=" O   ASP B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 130
    Processing helix  chain 'B' and resid 152 through 156
      removed outlier: 4.159A  pdb=" N   ALA B 156 " --> pdb=" O   ASP B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 166
      removed outlier: 3.555A  pdb=" N   ILE B 165 " --> pdb=" O   PRO B 161 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   ALA B 166 " --> pdb=" O   GLN B 162 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 161 through 166'
    Processing helix  chain 'B' and resid 181 through 186
    Processing helix  chain 'B' and resid 187 through 192
    Processing helix  chain 'B' and resid 196 through 201
      removed outlier: 3.700A  pdb=" N   GLU B 201 " --> pdb=" O   ASN B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 217
      removed outlier: 4.286A  pdb=" N   LYS B 207 " --> pdb=" O   GLN B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 233
    Processing helix  chain 'B' and resid 237 through 244
      removed outlier: 3.624A  pdb=" N   ALA B 241 " --> pdb=" O   TYR B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 256
      removed outlier: 3.641A  pdb=" N   GLN B 255 " --> pdb=" O   ASP B 252 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LEU B 256 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 252 through 256'
    Processing helix  chain 'B' and resid 257 through 267
      removed outlier: 3.690A  pdb=" N   ASN B 267 " --> pdb=" O   ASN B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 305
      removed outlier: 6.116A  pdb=" N   ASN B 302 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   LEU B 303 " --> pdb=" O   ILE B 299 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   LYS B 305 " --> pdb=" O   ASN B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 333
      removed outlier: 3.730A  pdb=" N   LEU B 319 " --> pdb=" O   SER B 315 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ALA B 320 " --> pdb=" O   MET B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 370
    Processing helix  chain 'B' and resid 379 through 408
      removed outlier: 4.404A  pdb=" N   GLN B 383 " --> pdb=" O   PRO B 379 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   GLU B 389 " --> pdb=" O   ALA B 385 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   LYS B 390 " --> pdb=" O   LEU B 386 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   GLY B 395 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   GLU B 396 " --> pdb=" O   TYR B 392 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ARG B 399 " --> pdb=" O   GLY B 395 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   LEU B 400 " --> pdb=" O   GLU B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 432
    Processing helix  chain 'B' and resid 433 through 442
    Processing helix  chain 'B' and resid 451 through 456
      removed outlier: 3.529A  pdb=" N   TYR B 455 " --> pdb=" O   LEU B 451 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LYS B 456 " --> pdb=" O   SER B 452 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 451 through 456'
    Processing helix  chain 'B' and resid 461 through 469
      removed outlier: 4.067A  pdb=" N   ILE B 469 " --> pdb=" O   LEU B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 488
    Processing helix  chain 'B' and resid 489 through 492
      removed outlier: 3.602A  pdb=" N   TRP B 492 " --> pdb=" O   ALA B 489 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 489 through 492'
    Processing helix  chain 'B' and resid 532 through 552
    Processing helix  chain 'B' and resid 566 through 569
      removed outlier: 4.240A  pdb=" N   VAL B 569 " --> pdb=" O   PRO B 566 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 566 through 569'
    Processing helix  chain 'B' and resid 595 through 610
      removed outlier: 3.828A  pdb=" N   ILE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   GLU B 610 " --> pdb=" O   ASN B 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 625 through 629
      removed outlier: 3.534A  pdb=" N   LEU B 628 " --> pdb=" O   PRO B 625 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   VAL B 629 " --> pdb=" O   SER B 626 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 625 through 629'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 23
      removed outlier: 5.589A  pdb=" N   ILE B   5 " --> pdb=" O   LYS B  75 " (cutoff:3.500A)
      removed outlier: 5.927A  pdb=" N   LYS B  75 " --> pdb=" O   ILE B   5 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LYS B   7 " --> pdb=" O   GLN B  73 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   TRP B  69 " --> pdb=" O   TRP B  11 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 159 through 160
      removed outlier: 6.104A  pdb=" N   ASN B  30 " --> pdb=" O   VAL B 620 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   ASP B 622 " --> pdb=" O   ASN B  30 " (cutoff:3.500A)
      removed outlier: 5.520A  pdb=" N   ILE B  32 " --> pdb=" O   ASP B 622 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   VAL B  29 " --> pdb=" O   HIS B 636 " (cutoff:3.500A)

    349 hydrogen bonds defined for protein.
    1032 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      24 hydrogen bonds
      48 hydrogen bond angles
      0 basepair planarities
      10 basepair parallelities
      21 stacking parallelities
  Total time for adding SS restraints: 1.07

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.11 -     1.25: 1613
        1.25 -     1.39: 2441
        1.39 -     1.53: 5743
        1.53 -     1.68: 457
        1.68 -     1.82: 43
  Bond restraints: 10297
  Sorted by residual:
  bond pdb=" CG  PRO B 558 "
       pdb=" CD  PRO B 558 "
    ideal  model  delta    sigma   weight residual
    1.503  1.110  0.393 3.40e-02 8.65e+02 1.33e+02
  bond pdb=" CG  PRO B  19 "
       pdb=" CD  PRO B  19 "
    ideal  model  delta    sigma   weight residual
    1.503  1.140  0.363 3.40e-02 8.65e+02 1.14e+02
  bond pdb=" CB  PRO B 558 "
       pdb=" CG  PRO B 558 "
    ideal  model  delta    sigma   weight residual
    1.492  1.193  0.299 5.00e-02 4.00e+02 3.58e+01
  bond pdb=" C   ILE C  93 "
       pdb=" N   PRO C  94 "
    ideal  model  delta    sigma   weight residual
    1.333  1.402 -0.069 1.44e-02 4.82e+03 2.29e+01
  bond pdb=" C   HIS C  49 "
       pdb=" N   PRO C  50 "
    ideal  model  delta    sigma   weight residual
    1.336  1.388 -0.052 1.20e-02 6.94e+03 1.87e+01
  ... (remaining 10292 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.87: 13958
        6.87 -    13.74: 53
       13.74 -    20.62: 1
       20.62 -    27.49: 1
       27.49 -    34.36: 3
  Bond angle restraints: 14016
  Sorted by residual:
  angle pdb=" N   PRO B 558 "
        pdb=" CD  PRO B 558 "
        pdb=" CG  PRO B 558 "
      ideal   model   delta    sigma   weight residual
     103.20   73.13   30.07 1.50e+00 4.44e-01 4.02e+02
  angle pdb=" CA  PRO B 558 "
        pdb=" CB  PRO B 558 "
        pdb=" CG  PRO B 558 "
      ideal   model   delta    sigma   weight residual
     104.50   70.14   34.36 1.90e+00 2.77e-01 3.27e+02
  angle pdb=" N   PRO B  19 "
        pdb=" CD  PRO B  19 "
        pdb=" CG  PRO B  19 "
      ideal   model   delta    sigma   weight residual
     103.20   82.54   20.66 1.50e+00 4.44e-01 1.90e+02
  angle pdb=" CB  PRO B 558 "
        pdb=" CG  PRO B 558 "
        pdb=" CD  PRO B 558 "
      ideal   model   delta    sigma   weight residual
     106.10  135.45  -29.35 3.20e+00 9.77e-02 8.41e+01
  angle pdb=" CA  PRO B  19 "
        pdb=" N   PRO B  19 "
        pdb=" CD  PRO B  19 "
      ideal   model   delta    sigma   weight residual
     112.00  101.43   10.57 1.40e+00 5.10e-01 5.71e+01
  ... (remaining 14011 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.46: 5685
       32.46 -    64.92: 508
       64.92 -    97.39: 40
       97.39 -   129.85: 0
      129.85 -   162.31: 1
  Dihedral angle restraints: 6234
    sinusoidal: 2798
      harmonic: 3436
  Sorted by residual:
  dihedral pdb=" CA  PHE C  59 "
           pdb=" C   PHE C  59 "
           pdb=" N   ILE C  60 "
           pdb=" CA  ILE C  60 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.96   27.04     0      5.00e+00 4.00e-02 2.93e+01
  dihedral pdb=" CA  GLU C  22 "
           pdb=" C   GLU C  22 "
           pdb=" N   ILE C  23 "
           pdb=" CA  ILE C  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.29   25.71     0      5.00e+00 4.00e-02 2.64e+01
  dihedral pdb=" CA  ARG C  52 "
           pdb=" C   ARG C  52 "
           pdb=" N   LEU C  53 "
           pdb=" CA  LEU C  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.75  -24.25     0      5.00e+00 4.00e-02 2.35e+01
  ... (remaining 6231 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1382
       0.078 -    0.156: 179
       0.156 -    0.234: 14
       0.234 -    0.312: 5
       0.312 -    0.390: 3
  Chirality restraints: 1583
  Sorted by residual:
  chirality pdb=" CB  ILE C  93 "
            pdb=" CA  ILE C  93 "
            pdb=" CG1 ILE C  93 "
            pdb=" CG2 ILE C  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.25    0.39 2.00e-01 2.50e+01 3.80e+00
  chirality pdb=" CG  LEU B 362 "
            pdb=" CB  LEU B 362 "
            pdb=" CD1 LEU B 362 "
            pdb=" CD2 LEU B 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.92    0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" CB  ILE B 111 "
            pdb=" CA  ILE B 111 "
            pdb=" CG1 ILE B 111 "
            pdb=" CG2 ILE B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.33 2.00e-01 2.50e+01 2.71e+00
  ... (remaining 1580 not shown)

  Planarity restraints: 1673
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  18 "    0.082 5.00e-02 4.00e+02   1.15e-01 2.12e+01
        pdb=" N   PRO B  19 "   -0.199 5.00e-02 4.00e+02
        pdb=" CA  PRO B  19 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO B  19 "    0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 557 "   -0.049 5.00e-02 4.00e+02   6.87e-02 7.56e+00
        pdb=" N   PRO B 558 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO B 558 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 558 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 470 "    0.044 5.00e-02 4.00e+02   6.59e-02 6.94e+00
        pdb=" N   PRO B 471 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO B 471 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 471 "    0.037 5.00e-02 4.00e+02
  ... (remaining 1670 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2492
        2.80 -     3.32: 8712
        3.32 -     3.85: 17684
        3.85 -     4.37: 19772
        4.37 -     4.90: 32417
  Nonbonded interactions: 81077
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  79 "
            pdb=" O   ALA B 102 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   THR B 515 "
            pdb=" OG1 THR B 515 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   GLN B  91 "
            pdb=" OG1 THR B  94 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" O   GLY A 226 "
            pdb=" OG  SER A 230 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" O   THR A 214 "
            pdb=" OG1 THR A 214 "
     model   vdw
     2.344 3.040
  ... (remaining 81072 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:             6.750
  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:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.340
  Find NCS groups from input model:        0.030
  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:5.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5620
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      :  0.008   0.393  10297  Z= 0.282
  Angle     :  1.129  34.359  14016  Z= 0.600
  Chirality :  0.055   0.390   1583
  Planarity :  0.007   0.115   1673
  Dihedral  : 21.924 162.309   3990
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.67 %
    Favored  : 89.24 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 40.72 %
    Favored  : 56.52 %
  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: -3.66 (0.21), residues: 1134
  helix: -2.08 (0.18), residues: 552
  sheet: -1.94 (0.78), residues: 51
  loop : -2.85 (0.23), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG G 358 
 TYR   0.021   0.002   TYR C  79 
 PHE   0.028   0.002   PHE B 172 
 TRP   0.018   0.002   TRP A  80 
 HIS   0.007   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00754 (10297)
  covalent geometry    : angle       1.12935 (14016)
  hydrogen bonds       : bond        0.15892 (  373)
  hydrogen bonds       : angle       7.06020 ( 1080)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 92
  time to evaluate  : 0.484 
Fit side-chains
REVERT: C  105 LYS cc_start: 0.2453 (OUTLIER) cc_final: 0.2119 (pttm)
  outliers start: 29
  outliers final: 17
  residues processed: 115
  average time/residue: 0.3660
  time to fit residues: 46.5467
Evaluate side-chains
  100 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   66 ARG
Chi-restraints excluded: chain C residue   85 ASN
Chi-restraints excluded: chain C residue  105 LYS
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain G residue  238 VAL
Chi-restraints excluded: chain G residue  293 THR
Chi-restraints excluded: chain G residue  347 ASN
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  145 ASP
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  180 HIS
Chi-restraints excluded: chain B residue  470 ASP
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  648 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** C  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  93 ASN
** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 HIS
G 410 GLN
B 312 ASN
B 321 ASN
** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 623 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4992 r_free = 0.4992 target = 0.255966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4794 r_free = 0.4794 target = 0.231796 restraints weight = 12785.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.4802 rms_B_bonded: 1.55
r_work: 0.4703 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.4593 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.4593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5957
moved from start:          0.1363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10297  Z= 0.156
  Angle     :  0.640  11.075  14016  Z= 0.338
  Chirality :  0.042   0.195   1583
  Planarity :  0.005   0.053   1673
  Dihedral  : 17.309 162.365   1640
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.23 %
    Favored  : 89.68 %
  Rotamer:
    Outliers :  9.42 %
    Allowed  : 33.78 %
    Favored  : 56.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.83 (0.23), residues: 1134
  helix: -1.04 (0.21), residues: 556
  sheet: -2.34 (0.66), residues: 52
  loop : -2.78 (0.25), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 457 
 TYR   0.016   0.001   TYR A 232 
 PHE   0.012   0.002   PHE B 157 
 TRP   0.011   0.002   TRP C 161 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (10297)
  covalent geometry    : angle       0.64018 (14016)
  hydrogen bonds       : bond        0.04216 (  373)
  hydrogen bonds       : angle       5.07902 ( 1080)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 99
    poor density    : 87
  time to evaluate  : 0.275 
Fit side-chains
REVERT: C  105 LYS cc_start: 0.2730 (OUTLIER) cc_final: -0.0045 (tttp)
REVERT: C  112 LEU cc_start: 0.5788 (OUTLIER) cc_final: 0.5460 (mp)
REVERT: A  359 PHE cc_start: 0.5819 (OUTLIER) cc_final: 0.5094 (m-80)
REVERT: B  321 ASN cc_start: 0.5157 (OUTLIER) cc_final: 0.4394 (p0)
REVERT: B  621 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.5940 (mt)
  outliers start: 99
  outliers final: 41
  residues processed: 180
  average time/residue: 0.3376
  time to fit residues: 66.8384
Evaluate side-chains
  124 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 78
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   63 SER
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  105 LYS
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain G residue  238 VAL
Chi-restraints excluded: chain G residue  300 SER
Chi-restraints excluded: chain G residue  336 LEU
Chi-restraints excluded: chain G residue  343 GLN
Chi-restraints excluded: chain G residue  372 LEU
Chi-restraints excluded: chain G residue  402 SER
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  321 ASN
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  596 VAL
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  621 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0870
   chunk 65 optimal weight:    0.5980
   chunk 98 optimal weight:    0.7980
   chunk 112 optimal weight:    2.9990
   chunk 113 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 106 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
A 212 GLN
A 322 HIS
** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4977 r_free = 0.4977 target = 0.254286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4777 r_free = 0.4777 target = 0.230015 restraints weight = 12852.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.4791 rms_B_bonded: 1.57
r_work: 0.4689 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.4578 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.4578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5992
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10297  Z= 0.144
  Angle     :  0.609   6.934  14016  Z= 0.323
  Chirality :  0.042   0.204   1583
  Planarity :  0.004   0.046   1673
  Dihedral  : 17.070 164.848   1613
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.41 %
    Favored  : 89.51 %
  Rotamer:
    Outliers :  8.75 %
    Allowed  : 34.44 %
    Favored  : 56.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.46 (0.24), residues: 1134
  helix: -0.70 (0.22), residues: 550
  sheet: -2.23 (0.68), residues: 51
  loop : -2.61 (0.25), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 297 
 TYR   0.015   0.001   TYR A 232 
 PHE   0.017   0.001   PHE B 172 
 TRP   0.015   0.001   TRP C 161 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (10297)
  covalent geometry    : angle       0.60873 (14016)
  hydrogen bonds       : bond        0.03921 (  373)
  hydrogen bonds       : angle       4.82058 ( 1080)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 92
    poor density    : 84
  time to evaluate  : 0.331 
Fit side-chains
REVERT: C   43 LYS cc_start: 0.6855 (OUTLIER) cc_final: 0.6265 (tttm)
REVERT: C  105 LYS cc_start: 0.3029 (OUTLIER) cc_final: 0.0075 (tttp)
REVERT: C  106 ASN cc_start: 0.5813 (OUTLIER) cc_final: 0.4603 (m-40)
REVERT: C  112 LEU cc_start: 0.5856 (OUTLIER) cc_final: 0.5538 (mp)
REVERT: A   24 GLN cc_start: 0.6756 (OUTLIER) cc_final: 0.6546 (tt0)
REVERT: A  156 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6639 (tp)
REVERT: A  193 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6100 (mpp)
REVERT: A  359 PHE cc_start: 0.5814 (OUTLIER) cc_final: 0.5127 (m-80)
REVERT: G  367 ARG cc_start: 0.4930 (ptt-90) cc_final: 0.4640 (ptt90)
REVERT: B  505 ILE cc_start: 0.3777 (OUTLIER) cc_final: 0.2022 (tt)
REVERT: B  621 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.5938 (mt)
  outliers start: 92
  outliers final: 45
  residues processed: 169
  average time/residue: 0.3292
  time to fit residues: 61.4465
Evaluate side-chains
  132 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 77
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain C residue   29 CYS
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  105 LYS
Chi-restraints excluded: chain C residue  106 ASN
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  212 GLN
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain G residue  238 VAL
Chi-restraints excluded: chain G residue  336 LEU
Chi-restraints excluded: chain G residue  343 GLN
Chi-restraints excluded: chain G residue  372 LEU
Chi-restraints excluded: chain G residue  402 SER
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   83 ILE
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  596 VAL
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  621 LEU
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  648 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 11 optimal weight:    0.4980
   chunk 89 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   chunk 113 optimal weight:    0.7980
   chunk 52 optimal weight:    0.3980
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0050
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 408 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4976 r_free = 0.4976 target = 0.254173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4775 r_free = 0.4775 target = 0.229838 restraints weight = 12885.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.4792 rms_B_bonded: 1.57
r_work: 0.4689 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.4579 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.4579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5990
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10297  Z= 0.136
  Angle     :  0.599   7.220  14016  Z= 0.317
  Chirality :  0.041   0.203   1583
  Planarity :  0.004   0.044   1673
  Dihedral  : 17.006 166.567   1613
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.85 %
    Favored  : 89.07 %
  Rotamer:
    Outliers :  8.37 %
    Allowed  : 35.11 %
    Favored  : 56.52 %
  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: -2.22 (0.24), residues: 1134
  helix: -0.48 (0.22), residues: 550
  sheet: -2.23 (0.69), residues: 52
  loop : -2.50 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 297 
 TYR   0.016   0.001   TYR A 232 
 PHE   0.023   0.001   PHE B 157 
 TRP   0.011   0.001   TRP B 641 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (10297)
  covalent geometry    : angle       0.59897 (14016)
  hydrogen bonds       : bond        0.03713 (  373)
  hydrogen bonds       : angle       4.65265 ( 1080)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 84
  time to evaluate  : 0.319 
Fit side-chains
REVERT: C   43 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.6221 (tttm)
REVERT: C  105 LYS cc_start: 0.2947 (OUTLIER) cc_final: -0.0151 (tmtm)
REVERT: C  106 ASN cc_start: 0.5778 (OUTLIER) cc_final: 0.4677 (m-40)
REVERT: C  112 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5458 (mp)
REVERT: A   37 PHE cc_start: 0.5063 (OUTLIER) cc_final: 0.4852 (m-10)
REVERT: A  156 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6632 (tp)
REVERT: A  193 MET cc_start: 0.6580 (OUTLIER) cc_final: 0.6268 (mpp)
REVERT: A  359 PHE cc_start: 0.5861 (OUTLIER) cc_final: 0.5107 (m-80)
REVERT: G  367 ARG cc_start: 0.4935 (ptt-90) cc_final: 0.4605 (ptt90)
REVERT: B  505 ILE cc_start: 0.3846 (OUTLIER) cc_final: 0.2064 (tt)
REVERT: B  621 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.5983 (mt)
  outliers start: 88
  outliers final: 41
  residues processed: 163
  average time/residue: 0.3257
  time to fit residues: 58.9822
Evaluate side-chains
  129 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 78
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  105 LYS
Chi-restraints excluded: chain C residue  106 ASN
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  172 ASP
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain G residue  238 VAL
Chi-restraints excluded: chain G residue  343 GLN
Chi-restraints excluded: chain G residue  372 LEU
Chi-restraints excluded: chain G residue  402 SER
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   83 ILE
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  147 LYS
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  596 VAL
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  621 LEU
Chi-restraints excluded: chain B residue  626 SER
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  648 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0010
   chunk 53 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   chunk 110 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 59 optimal weight:    0.3980
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
A 212 GLN
A 239 ASN
** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4973 r_free = 0.4973 target = 0.253909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4771 r_free = 0.4771 target = 0.229565 restraints weight = 12911.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.4787 rms_B_bonded: 1.57
r_work: 0.4683 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.4572 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.4572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6002
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10297  Z= 0.135
  Angle     :  0.603   8.262  14016  Z= 0.316
  Chirality :  0.042   0.197   1583
  Planarity :  0.004   0.044   1673
  Dihedral  : 16.955 168.528   1613
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.49 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  9.32 %
    Allowed  : 34.35 %
    Favored  : 56.33 %
  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: -2.14 (0.25), residues: 1134
  helix: -0.40 (0.22), residues: 551
  sheet: -2.28 (0.68), residues: 52
  loop : -2.47 (0.26), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 297 
 TYR   0.016   0.001   TYR A 232 
 PHE   0.021   0.001   PHE B 157 
 TRP   0.011   0.001   TRP B 641 
 HIS   0.004   0.001   HIS B 546 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10297)
  covalent geometry    : angle       0.60275 (14016)
  hydrogen bonds       : bond        0.03642 (  373)
  hydrogen bonds       : angle       4.55948 ( 1080)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 98
    poor density    : 87
  time to evaluate  : 0.295 
Fit side-chains
REVERT: C   43 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6220 (tttm)
REVERT: C  105 LYS cc_start: 0.2882 (OUTLIER) cc_final: -0.0170 (tmtm)
REVERT: C  106 ASN cc_start: 0.5790 (OUTLIER) cc_final: 0.4744 (m-40)
REVERT: A   37 PHE cc_start: 0.5140 (OUTLIER) cc_final: 0.4939 (m-10)
REVERT: A  156 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6476 (tp)
REVERT: A  193 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.6288 (mpp)
REVERT: A  359 PHE cc_start: 0.5832 (OUTLIER) cc_final: 0.5063 (m-80)
REVERT: B  309 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6162 (ptm160)
REVERT: B  372 LEU cc_start: 0.3829 (OUTLIER) cc_final: 0.3378 (pp)
REVERT: B  505 ILE cc_start: 0.3756 (OUTLIER) cc_final: 0.2026 (tt)
REVERT: B  621 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.5982 (mt)
  outliers start: 98
  outliers final: 46
  residues processed: 175
  average time/residue: 0.3252
  time to fit residues: 63.0712
Evaluate side-chains
  138 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 81
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain C residue   29 CYS
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   63 SER
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  105 LYS
Chi-restraints excluded: chain C residue  106 ASN
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain G residue  238 VAL
Chi-restraints excluded: chain G residue  343 GLN
Chi-restraints excluded: chain G residue  372 LEU
Chi-restraints excluded: chain G residue  402 SER
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   83 ILE
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  561 ILE
Chi-restraints excluded: chain B residue  596 VAL
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  621 LEU
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  648 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 39 optimal weight:    0.3980
   chunk 32 optimal weight:    0.6980
   chunk 108 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 81 optimal weight:    0.8980
   chunk 1 optimal weight:    0.2980
   chunk 91 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 212 GLN
G 288 GLN
B 109 GLN
** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4957 r_free = 0.4957 target = 0.251845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4755 r_free = 0.4755 target = 0.227479 restraints weight = 12815.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.4770 rms_B_bonded: 1.55
r_work: 0.4666 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.4555 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.4555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6048
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10297  Z= 0.152
  Angle     :  0.623   7.529  14016  Z= 0.326
  Chirality :  0.042   0.195   1583
  Planarity :  0.004   0.043   1673
  Dihedral  : 16.992 169.974   1613
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.93 %
    Favored  : 88.98 %
  Rotamer:
    Outliers :  8.94 %
    Allowed  : 35.20 %
    Favored  : 55.85 %
  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: -2.13 (0.25), residues: 1134
  helix: -0.43 (0.22), residues: 551
  sheet: -2.24 (0.67), residues: 52
  loop : -2.42 (0.27), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 217 
 TYR   0.017   0.001   TYR A 232 
 PHE   0.020   0.002   PHE B 157 
 TRP   0.010   0.001   TRP B 641 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (10297)
  covalent geometry    : angle       0.62281 (14016)
  hydrogen bonds       : bond        0.03778 (  373)
  hydrogen bonds       : angle       4.60477 ( 1080)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 94
    poor density    : 92
  time to evaluate  : 0.281 
Fit side-chains
REVERT: C   43 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6228 (tttm)
REVERT: C  105 LYS cc_start: 0.2943 (OUTLIER) cc_final: -0.0172 (tmtm)
REVERT: C  106 ASN cc_start: 0.5820 (OUTLIER) cc_final: 0.4777 (m-40)
REVERT: A   37 PHE cc_start: 0.5205 (OUTLIER) cc_final: 0.4997 (m-10)
REVERT: A  156 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6495 (tp)
REVERT: A  193 MET cc_start: 0.6695 (OUTLIER) cc_final: 0.6268 (mpp)
REVERT: A  195 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7506 (mp0)
REVERT: A  359 PHE cc_start: 0.5862 (OUTLIER) cc_final: 0.5107 (m-80)
REVERT: B  309 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.6119 (ptm160)
REVERT: B  372 LEU cc_start: 0.3865 (OUTLIER) cc_final: 0.3410 (pp)
REVERT: B  505 ILE cc_start: 0.3879 (OUTLIER) cc_final: 0.2175 (tt)
REVERT: B  621 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.5984 (mt)
  outliers start: 94
  outliers final: 47
  residues processed: 175
  average time/residue: 0.3182
  time to fit residues: 61.9373
Evaluate side-chains
  147 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 88
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain C residue   29 CYS
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   85 ASN
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  105 LYS
Chi-restraints excluded: chain C residue  106 ASN
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  212 GLN
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain G residue  238 VAL
Chi-restraints excluded: chain G residue  308 SER
Chi-restraints excluded: chain G residue  343 GLN
Chi-restraints excluded: chain G residue  372 LEU
Chi-restraints excluded: chain G residue  402 SER
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  163 ASN
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  561 ILE
Chi-restraints excluded: chain B residue  596 VAL
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  621 LEU
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  648 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    0.1980
   chunk 62 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0040
   chunk 37 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    0.8396

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
A 110 GLN
B  91 GLN
** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 208 ASN
** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4942 r_free = 0.4942 target = 0.249740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4736 r_free = 0.4736 target = 0.225257 restraints weight = 12760.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.4751 rms_B_bonded: 1.55
r_work: 0.4647 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.4536 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.4536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6104
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10297  Z= 0.173
  Angle     :  0.655   7.719  14016  Z= 0.342
  Chirality :  0.043   0.196   1583
  Planarity :  0.004   0.042   1673
  Dihedral  : 17.075 171.202   1613
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.46 %
    Favored  : 88.45 %
  Rotamer:
    Outliers :  8.37 %
    Allowed  : 35.97 %
    Favored  : 55.66 %
  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: -2.19 (0.25), residues: 1134
  helix: -0.55 (0.22), residues: 556
  sheet: -2.27 (0.65), residues: 52
  loop : -2.37 (0.27), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 211 
 TYR   0.015   0.002   TYR C  31 
 PHE   0.023   0.002   PHE B 172 
 TRP   0.011   0.002   TRP B 641 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (10297)
  covalent geometry    : angle       0.65451 (14016)
  hydrogen bonds       : bond        0.03955 (  373)
  hydrogen bonds       : angle       4.75621 ( 1080)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 90
  time to evaluate  : 0.235 
Fit side-chains
REVERT: C   43 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6241 (tttm)
REVERT: C  105 LYS cc_start: 0.2934 (OUTLIER) cc_final: -0.0310 (tmtm)
REVERT: C  106 ASN cc_start: 0.5787 (OUTLIER) cc_final: 0.4801 (m-40)
REVERT: A  156 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6481 (tp)
REVERT: A  193 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6286 (mpp)
REVERT: A  340 GLU cc_start: 0.5950 (OUTLIER) cc_final: 0.5087 (tp30)
REVERT: A  359 PHE cc_start: 0.5893 (OUTLIER) cc_final: 0.5119 (m-80)
REVERT: B   78 HIS cc_start: 0.5973 (OUTLIER) cc_final: 0.5516 (m-70)
REVERT: B  209 LEU cc_start: 0.6211 (mt) cc_final: 0.5873 (mp)
REVERT: B  309 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6076 (ptm160)
REVERT: B  372 LEU cc_start: 0.3875 (OUTLIER) cc_final: 0.3416 (pp)
REVERT: B  505 ILE cc_start: 0.4008 (OUTLIER) cc_final: 0.2321 (tt)
REVERT: B  621 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.5990 (mt)
  outliers start: 88
  outliers final: 49
  residues processed: 169
  average time/residue: 0.3113
  time to fit residues: 58.3244
Evaluate side-chains
  146 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 85
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain C residue   29 CYS
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  105 LYS
Chi-restraints excluded: chain C residue  106 ASN
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  340 GLU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain G residue  238 VAL
Chi-restraints excluded: chain G residue  308 SER
Chi-restraints excluded: chain G residue  343 GLN
Chi-restraints excluded: chain G residue  345 ASP
Chi-restraints excluded: chain G residue  370 SER
Chi-restraints excluded: chain G residue  372 LEU
Chi-restraints excluded: chain G residue  402 SER
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   78 HIS
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  163 ASN
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  596 VAL
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  621 LEU
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  648 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 106 optimal weight:    0.5980
   chunk 96 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 82 optimal weight:    4.9990
   chunk 19 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 116 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
A 322 HIS
B  91 GLN
** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4954 r_free = 0.4954 target = 0.251210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4755 r_free = 0.4755 target = 0.227118 restraints weight = 12802.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.4755 rms_B_bonded: 1.53
r_work: 0.4653 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.4545 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.4545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6072
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10297  Z= 0.159
  Angle     :  0.660   8.453  14016  Z= 0.343
  Chirality :  0.043   0.193   1583
  Planarity :  0.004   0.042   1673
  Dihedral  : 17.053 171.196   1613
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.20 %
    Favored  : 88.71 %
  Rotamer:
    Outliers :  7.52 %
    Allowed  : 36.54 %
    Favored  : 55.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.08 (0.25), residues: 1134
  helix: -0.47 (0.22), residues: 551
  sheet: -1.61 (0.70), residues: 47
  loop : -2.37 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 297 
 TYR   0.014   0.001   TYR C  31 
 PHE   0.023   0.002   PHE B 172 
 TRP   0.013   0.002   TRP B 641 
 HIS   0.005   0.001   HIS B 546 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (10297)
  covalent geometry    : angle       0.65987 (14016)
  hydrogen bonds       : bond        0.03801 (  373)
  hydrogen bonds       : angle       4.68488 ( 1080)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 93
  time to evaluate  : 0.368 
Fit side-chains
REVERT: C   43 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6250 (tttm)
REVERT: C  105 LYS cc_start: 0.2915 (OUTLIER) cc_final: -0.0272 (tmtm)
REVERT: C  106 ASN cc_start: 0.5702 (OUTLIER) cc_final: 0.4791 (m-40)
REVERT: A   37 PHE cc_start: 0.5367 (OUTLIER) cc_final: 0.5041 (m-10)
REVERT: A  156 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6506 (tp)
REVERT: A  193 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6369 (mpp)
REVERT: A  219 LYS cc_start: 0.7618 (tmmt) cc_final: 0.6908 (tttp)
REVERT: A  340 GLU cc_start: 0.5932 (OUTLIER) cc_final: 0.5087 (tp30)
REVERT: A  359 PHE cc_start: 0.5865 (OUTLIER) cc_final: 0.5084 (m-80)
REVERT: B   78 HIS cc_start: 0.5993 (OUTLIER) cc_final: 0.5434 (m-70)
REVERT: B  183 LYS cc_start: 0.5286 (mmtt) cc_final: 0.4849 (tptp)
REVERT: B  309 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6042 (ptm160)
REVERT: B  372 LEU cc_start: 0.3788 (OUTLIER) cc_final: 0.3310 (pp)
REVERT: B  505 ILE cc_start: 0.3923 (OUTLIER) cc_final: 0.2249 (tt)
REVERT: B  621 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.5859 (mt)
  outliers start: 79
  outliers final: 45
  residues processed: 162
  average time/residue: 0.3317
  time to fit residues: 59.6408
Evaluate side-chains
  145 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 87
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain C residue   29 CYS
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  105 LYS
Chi-restraints excluded: chain C residue  106 ASN
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  340 GLU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain G residue  238 VAL
Chi-restraints excluded: chain G residue  308 SER
Chi-restraints excluded: chain G residue  343 GLN
Chi-restraints excluded: chain G residue  345 ASP
Chi-restraints excluded: chain G residue  370 SER
Chi-restraints excluded: chain G residue  402 SER
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   78 HIS
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  163 ASN
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  596 VAL
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  621 LEU
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  648 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 75 optimal weight:    0.0370
   chunk 111 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0980
   chunk 4 optimal weight:    0.5980
   chunk 20 optimal weight:   10.0000
   chunk 54 optimal weight:    1.9990
   chunk 31 optimal weight:    0.3980
   chunk 94 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.3458

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

Flipped N/Q/H residues before XYZ refinement:
** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 GLN
** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 321 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 = 0.4974 r_free = 0.4974 target = 0.253869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4783 r_free = 0.4783 target = 0.230409 restraints weight = 12802.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.4797 rms_B_bonded: 1.53
r_work: 0.4696 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.4586 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.4586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5975
moved from start:          0.2587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10297  Z= 0.131
  Angle     :  0.639   8.528  14016  Z= 0.331
  Chirality :  0.042   0.191   1583
  Planarity :  0.004   0.042   1673
  Dihedral  : 16.953 170.262   1613
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.41 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 38.15 %
    Favored  : 55.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.01 (0.25), residues: 1134
  helix: -0.40 (0.22), residues: 560
  sheet: -1.55 (0.72), residues: 47
  loop : -2.38 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 297 
 TYR   0.011   0.001   TYR C  40 
 PHE   0.025   0.002   PHE B 157 
 TRP   0.014   0.001   TRP B  69 
 HIS   0.005   0.001   HIS B 546 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (10297)
  covalent geometry    : angle       0.63936 (14016)
  hydrogen bonds       : bond        0.03515 (  373)
  hydrogen bonds       : angle       4.49898 ( 1080)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 95
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
REVERT: C   43 LYS cc_start: 0.6847 (OUTLIER) cc_final: 0.6352 (tttm)
REVERT: C  105 LYS cc_start: 0.2753 (OUTLIER) cc_final: 0.1003 (ptpt)
REVERT: C  106 ASN cc_start: 0.5689 (OUTLIER) cc_final: 0.4697 (m-40)
REVERT: A   37 PHE cc_start: 0.5221 (OUTLIER) cc_final: 0.4875 (m-10)
REVERT: A  156 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6450 (tp)
REVERT: A  193 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.6423 (mpp)
REVERT: A  219 LYS cc_start: 0.7624 (tmmt) cc_final: 0.6908 (tttp)
REVERT: A  359 PHE cc_start: 0.5722 (OUTLIER) cc_final: 0.5009 (m-80)
REVERT: G  388 ARG cc_start: 0.5835 (OUTLIER) cc_final: 0.5191 (ttp-170)
REVERT: B   78 HIS cc_start: 0.5940 (OUTLIER) cc_final: 0.5375 (m-70)
REVERT: B  183 LYS cc_start: 0.5204 (mmtt) cc_final: 0.4912 (tptp)
REVERT: B  372 LEU cc_start: 0.3672 (OUTLIER) cc_final: 0.3206 (pp)
REVERT: B  621 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.5929 (mt)
  outliers start: 62
  outliers final: 41
  residues processed: 151
  average time/residue: 0.3278
  time to fit residues: 55.1350
Evaluate side-chains
  140 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 88
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain C residue   29 CYS
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   85 ASN
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  105 LYS
Chi-restraints excluded: chain C residue  106 ASN
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain G residue  343 GLN
Chi-restraints excluded: chain G residue  388 ARG
Chi-restraints excluded: chain G residue  402 SER
Chi-restraints excluded: chain B residue   12 SER
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   78 HIS
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  163 ASN
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  596 VAL
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  621 LEU
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  648 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 96 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 113 optimal weight:    0.0570
   chunk 98 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0770
   chunk 77 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.4056

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

Flipped N/Q/H residues before XYZ refinement:
** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 GLN
** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 321 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 = 0.4940 r_free = 0.4940 target = 0.254421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4746 r_free = 0.4746 target = 0.229414 restraints weight = 12650.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.4749 rms_B_bonded: 1.67
r_work: 0.4651 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.4536 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.4536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5987
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10297  Z= 0.134
  Angle     :  0.642   8.923  14016  Z= 0.333
  Chirality :  0.042   0.202   1583
  Planarity :  0.004   0.072   1673
  Dihedral  : 16.941 170.337   1612
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.58 %
    Favored  : 89.24 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 38.82 %
    Favored  : 55.85 %
  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: -1.90 (0.25), residues: 1134
  helix: -0.31 (0.22), residues: 553
  sheet: -1.45 (0.73), residues: 47
  loop : -2.31 (0.28), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG B 297 
 TYR   0.012   0.001   TYR C  31 
 PHE   0.024   0.001   PHE B 172 
 TRP   0.020   0.001   TRP C 161 
 HIS   0.005   0.001   HIS B 546 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10297)
  covalent geometry    : angle       0.64180 (14016)
  hydrogen bonds       : bond        0.03535 (  373)
  hydrogen bonds       : angle       4.50551 ( 1080)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 94
  time to evaluate  : 0.263 
Fit side-chains
REVERT: C   43 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6293 (tttm)
REVERT: C  105 LYS cc_start: 0.2590 (OUTLIER) cc_final: -0.0349 (tttm)
REVERT: C  106 ASN cc_start: 0.5645 (OUTLIER) cc_final: 0.4607 (m-40)
REVERT: A   37 PHE cc_start: 0.5156 (OUTLIER) cc_final: 0.4844 (m-10)
REVERT: A  193 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.6318 (mpp)
REVERT: A  219 LYS cc_start: 0.7571 (tmmt) cc_final: 0.6864 (tttp)
REVERT: A  340 GLU cc_start: 0.5858 (OUTLIER) cc_final: 0.4964 (tp30)
REVERT: A  359 PHE cc_start: 0.5802 (OUTLIER) cc_final: 0.5054 (m-80)
REVERT: G  388 ARG cc_start: 0.5880 (OUTLIER) cc_final: 0.5227 (ttp-170)
REVERT: B   78 HIS cc_start: 0.5925 (OUTLIER) cc_final: 0.5359 (m-70)
REVERT: B  183 LYS cc_start: 0.5126 (mmtt) cc_final: 0.4827 (tptp)
REVERT: B  372 LEU cc_start: 0.3746 (OUTLIER) cc_final: 0.3257 (pp)
REVERT: B  505 ILE cc_start: 0.3747 (OUTLIER) cc_final: 0.2034 (tt)
REVERT: B  621 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.5805 (mt)
  outliers start: 56
  outliers final: 39
  residues processed: 146
  average time/residue: 0.3129
  time to fit residues: 50.4372
Evaluate side-chains
  141 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 90
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain C residue   29 CYS
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   85 ASN
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  105 LYS
Chi-restraints excluded: chain C residue  106 ASN
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  340 GLU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain G residue  388 ARG
Chi-restraints excluded: chain G residue  402 SER
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   78 HIS
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  596 VAL
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  621 LEU
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  648 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 110 optimal weight:    0.5980
   chunk 1 optimal weight:    0.4980
   chunk 26 optimal weight:    8.9990
   chunk 37 optimal weight:    0.0570
   chunk 98 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 20 optimal weight:   10.0000
   chunk 57 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 38 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
A 212 GLN
B  91 GLN
** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4938 r_free = 0.4938 target = 0.254134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.229080 restraints weight = 12813.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.4744 rms_B_bonded: 1.68
r_work: 0.4644 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.4530 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.4530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5998
moved from start:          0.2644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10297  Z= 0.140
  Angle     :  0.654  11.092  14016  Z= 0.339
  Chirality :  0.042   0.218   1583
  Planarity :  0.004   0.071   1673
  Dihedral  : 16.931 170.649   1612
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.76 %
    Favored  : 89.07 %
  Rotamer:
    Outliers :  5.52 %
    Allowed  : 38.63 %
    Favored  : 55.85 %
  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: -1.92 (0.25), residues: 1134
  helix: -0.33 (0.22), residues: 553
  sheet: -1.46 (0.73), residues: 47
  loop : -2.31 (0.28), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG B 297 
 TYR   0.013   0.001   TYR C  79 
 PHE   0.025   0.002   PHE B 172 
 TRP   0.032   0.002   TRP C 161 
 HIS   0.010   0.001   HIS B 546 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (10297)
  covalent geometry    : angle       0.65371 (14016)
  hydrogen bonds       : bond        0.03608 (  373)
  hydrogen bonds       : angle       4.56657 ( 1080)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3122.79 seconds
wall clock time: 53 minutes 58.55 seconds (3238.55 seconds total)