Starting phenix.real_space_refine
on Wed Sep 17 19:49:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n0z_48799/09_2025/9n0z_48799.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n0z_48799/09_2025/9n0z_48799.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n0z_48799/09_2025/9n0z_48799.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n0z_48799/09_2025/9n0z_48799.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n0z_48799/09_2025/9n0z_48799.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n0z_48799/09_2025/9n0z_48799.map"
  }
  resolution = 3.5
  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=   0.001 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      61      5.16       5
     C    6861      2.51       5
     N    1856      2.21       5
     O    2069      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10847
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 581, 4527
          Classifications: {'peptide': 581}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 554}
    Chain: "B"
      Number of atoms: 3529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 431, 3529
          Classifications: {'peptide': 431}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 415}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2496
          Classifications: {'peptide': 308}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 294}
    Chain: "D"
      Number of atoms: 295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 295
          Classifications: {'peptide': 35}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 32}
  Time building chain proxies: 2.72, per 1000 atoms: 0.25
  Number of scatterers: 10847
  At special positions: 0
  Unit cell: (105.165, 102.6, 129.105, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      61     16.00
     O    2069      8.00
     N    1856      7.00
     C    6861      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: 1.04
  Conformation dependent library (CDL) restraints added in 478.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2600

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 14 sheets defined
      48.4% alpha, 7.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 20
      removed outlier: 3.619A  pdb=" N   ASP A  18 " --> pdb=" O   ALA A  14 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU A  20 " --> pdb=" O   LEU A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 43
      removed outlier: 5.083A  pdb=" N   SER A  36 " --> pdb=" O   ILE A  32 " (cutoff:3.500A)
      removed outlier: 6.078A  pdb=" N   THR A  37 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ILE A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 56
      removed outlier: 4.214A  pdb=" N   LEU A  52 " --> pdb=" O   ARG A  48 " (cutoff:3.500A)
      Proline residue:  A  53  - end of helix
    Processing helix  chain 'A' and resid 62 through 74
      removed outlier: 3.861A  pdb=" N   ALA A  68 " --> pdb=" O   GLU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 89
    Processing helix  chain 'A' and resid 90 through 95
      removed outlier: 3.721A  pdb=" N   SER A  95 " --> pdb=" O   PRO A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 117
      removed outlier: 3.978A  pdb=" N   HIS A 117 " --> pdb=" O   ARG A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 128
    Processing helix  chain 'A' and resid 128 through 136
    Processing helix  chain 'A' and resid 142 through 148
    Processing helix  chain 'A' and resid 159 through 174
    Processing helix  chain 'A' and resid 178 through 194
      removed outlier: 3.596A  pdb=" N   ARG A 182 " --> pdb=" O   THR A 178 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   GLY A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   GLU A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 214
      removed outlier: 4.216A  pdb=" N   ILE A 206 " --> pdb=" O   LYS A 202 " (cutoff:3.500A)
      Proline residue:  A 207  - end of helix
    Processing helix  chain 'A' and resid 222 through 235
      removed outlier: 4.373A  pdb=" N   GLU A 226 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 253
      removed outlier: 3.596A  pdb=" N   GLU A 253 " --> pdb=" O   ARG A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 266
      removed outlier: 3.594A  pdb=" N   ARG A 260 " --> pdb=" O   SER A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 275
    Processing helix  chain 'A' and resid 275 through 292
      removed outlier: 4.935A  pdb=" N   VAL A 284 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
      Proline residue:  A 285  - end of helix
    Processing helix  chain 'A' and resid 296 through 305
      removed outlier: 3.658A  pdb=" N   LYS A 305 " --> pdb=" O   ALA A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 312
      removed outlier: 3.654A  pdb=" N   ASN A 312 " --> pdb=" O   GLU A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 325
    Processing helix  chain 'A' and resid 326 through 335
      removed outlier: 4.154A  pdb=" N   SER A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 349
      removed outlier: 3.953A  pdb=" N   LYS A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   VAL A 348 " --> pdb=" O   ALA A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 356
      removed outlier: 3.525A  pdb=" N   SER A 353 " --> pdb=" O   MET A 350 " (cutoff:3.500A)
      Proline residue:  A 354  - end of helix
      No H-bonds generated for 'chain 'A' and resid 350 through 356'
    Processing helix  chain 'A' and resid 358 through 375
      removed outlier: 4.346A  pdb=" N   LEU A 366 " --> pdb=" O   ILE A 362 " (cutoff:3.500A)
      Proline residue:  A 367  - end of helix
    Processing helix  chain 'A' and resid 379 through 387
      removed outlier: 3.662A  pdb=" N   ASN A 387 " --> pdb=" O   ASN A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 393
    Processing helix  chain 'A' and resid 400 through 413
      Proline residue:  A 406  - end of helix
      removed outlier: 4.020A  pdb=" N   GLU A 413 " --> pdb=" O   VAL A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 435
      removed outlier: 3.944A  pdb=" N   ARG A 420 " --> pdb=" O   LYS A 416 " (cutoff:3.500A)
      Proline residue:  A 428  - end of helix
      removed outlier: 3.829A  pdb=" N   GLY A 435 " --> pdb=" O   ALA A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 442
    Processing helix  chain 'A' and resid 443 through 452
      removed outlier: 3.653A  pdb=" N   VAL A 452 " --> pdb=" O   MET A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 480
      removed outlier: 7.217A  pdb=" N   LYS A 475 " --> pdb=" O   GLU A 471 " (cutoff:3.500A)
      removed outlier: 9.046A  pdb=" N   GLU A 476 " --> pdb=" O   LYS A 472 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   TRP A 477 " --> pdb=" O   PHE A 473 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ALA A 478 " --> pdb=" O   GLY A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 489
      removed outlier: 4.509A  pdb=" N   LYS A 485 " --> pdb=" O   THR A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 492
      No H-bonds generated for 'chain 'A' and resid 490 through 492'
    Processing helix  chain 'A' and resid 494 through 513
      removed outlier: 3.712A  pdb=" N   ARG A 498 " --> pdb=" O   ASN A 494 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   GLU A 510 " --> pdb=" O   ASN A 506 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   VAL A 511 " --> pdb=" O   VAL A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 529
      removed outlier: 4.344A  pdb=" N   LYS A 519 " --> pdb=" O   ASP A 515 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   LEU A 522 " --> pdb=" O   THR A 518 " (cutoff:3.500A)
      Proline residue:  A 523  - end of helix
    Processing helix  chain 'A' and resid 533 through 548
      removed outlier: 3.679A  pdb=" N   ASN A 539 " --> pdb=" O   ASN A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 551
      No H-bonds generated for 'chain 'A' and resid 549 through 551'
    Processing helix  chain 'A' and resid 552 through 568
      removed outlier: 3.920A  pdb=" N   SER A 558 " --> pdb=" O   SER A 554 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   LYS A 561 " --> pdb=" O   GLN A 557 " (cutoff:3.500A)
      Proline residue:  A 562  - end of helix
    Processing helix  chain 'A' and resid 572 through 586
      removed outlier: 3.801A  pdb=" N   LYS A 576 " --> pdb=" O   ASP A 572 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 30
      removed outlier: 3.794A  pdb=" N   ILE B  30 " --> pdb=" O   GLU B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 330
    Processing helix  chain 'B' and resid 334 through 338
      removed outlier: 3.853A  pdb=" N   GLU B 338 " --> pdb=" O   SER B 335 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 19
    Processing helix  chain 'C' and resid 24 through 41
      removed outlier: 3.938A  pdb=" N   VAL C  28 " --> pdb=" O   SER C  24 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   LYS C  41 " --> pdb=" O   GLU C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 73
    Processing helix  chain 'C' and resid 92 through 107
    Processing helix  chain 'C' and resid 120 through 127
    Processing helix  chain 'C' and resid 128 through 137
    Processing helix  chain 'C' and resid 140 through 153
      removed outlier: 3.623A  pdb=" N   TYR C 152 " --> pdb=" O   ASP C 148 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 182
    Processing helix  chain 'C' and resid 193 through 201
    Processing helix  chain 'C' and resid 221 through 233
      removed outlier: 3.665A  pdb=" N   SER C 225 " --> pdb=" O   GLY C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 264 through 268
      removed outlier: 3.833A  pdb=" N   ARG C 268 " --> pdb=" O   TYR C 265 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 8
      removed outlier: 4.195A  pdb=" N   LYS D   7 " --> pdb=" O   GLU D   3 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 8 through 13
    Processing helix  chain 'D' and resid 20 through 32
      removed outlier: 4.221A  pdb=" N   LYS D  24 " --> pdb=" O   ASP D  20 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE D  31 " --> pdb=" O   VAL D  27 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LYS D  32 " --> pdb=" O   ARG D  28 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 13
    Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 36
    Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 52
      removed outlier: 3.584A  pdb=" N   VAL B  52 " --> pdb=" O   PHE B  77 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 109 through 114
      removed outlier: 3.552A  pdb=" N   LEU B 111 " --> pdb=" O   TRP B 122 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   SER B 125 " --> pdb=" O   GLU B 165 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 109 through 114
      removed outlier: 3.552A  pdb=" N   LEU B 111 " --> pdb=" O   TRP B 122 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ARG B 170 " --> pdb=" O   LEU B 121 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 129 through 132
    Processing sheet with id=AA7, first strand: chain 'B' and resid 184 through 185
      removed outlier: 3.653A  pdb=" N   TYR B 192 " --> pdb=" O   TRP B 203 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   ILE B 200 " --> pdb=" O   ILE B 214 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   PHE B 212 " --> pdb=" O   LEU B 202 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   THR C 301 " --> pdb=" O   SER B 211 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASN B 213 " --> pdb=" O   THR C 301 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 251 through 252
    Processing sheet with id=AA9, first strand: chain 'B' and resid 302 through 303
      removed outlier: 3.706A  pdb=" N   GLU B 321 " --> pdb=" O   ILE B 310 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 350
      removed outlier: 3.801A  pdb=" N   LEU B 379 " --> pdb=" O   PHE B 366 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 421 through 424
      removed outlier: 4.249A  pdb=" N   HIS B 421 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ALA B 432 " --> pdb=" O   ALA B 423 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 48
      removed outlier: 3.771A  pdb=" N   VAL C  48 " --> pdb=" O   LEU C 158 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   PHE C 164 " --> pdb=" O   SER C 238 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   VAL C 257 " --> pdb=" O   VAL C 237 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   CYS C 251 " --> pdb=" O   VAL C 256 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 80 through 81
      removed outlier: 6.658A  pdb=" N   TYR C  80 " --> pdb=" O   THR C 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'C' and resid 276 through 278
      removed outlier: 3.575A  pdb=" N   SER C 285 " --> pdb=" O   GLU C 277 " (cutoff:3.500A)

    412 hydrogen bonds defined for protein.
    1173 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.67

  Time building geometry restraints manager: 1.37 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3557
        1.34 -     1.46: 1463
        1.46 -     1.57: 5951
        1.57 -     1.69: 0
        1.69 -     1.81: 89
  Bond restraints: 11060
  Sorted by residual:
  bond pdb=" N   VAL A 394 "
       pdb=" CA  VAL A 394 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 9.00e-03 1.23e+04 1.68e+01
  bond pdb=" N   PRO A 285 "
       pdb=" CD  PRO A 285 "
    ideal  model  delta    sigma   weight residual
    1.473  1.524 -0.051 1.40e-02 5.10e+03 1.33e+01
  bond pdb=" N   ILE A 355 "
       pdb=" CA  ILE A 355 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 1.09e-02 8.42e+03 1.12e+01
  bond pdb=" N   ILE A 483 "
       pdb=" CA  ILE A 483 "
    ideal  model  delta    sigma   weight residual
    1.461  1.502 -0.041 1.23e-02 6.61e+03 1.10e+01
  bond pdb=" N   ILE A 482 "
       pdb=" CA  ILE A 482 "
    ideal  model  delta    sigma   weight residual
    1.460  1.498 -0.038 1.21e-02 6.83e+03 9.98e+00
  ... (remaining 11055 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 14327
        1.81 -     3.62: 584
        3.62 -     5.43: 61
        5.43 -     7.24: 7
        7.24 -     9.05: 2
  Bond angle restraints: 14981
  Sorted by residual:
  angle pdb=" N   LYS B  88 "
        pdb=" CA  LYS B  88 "
        pdb=" C   LYS B  88 "
      ideal   model   delta    sigma   weight residual
     113.01  107.65    5.36 1.20e+00 6.94e-01 2.00e+01
  angle pdb=" N   GLU A 471 "
        pdb=" CA  GLU A 471 "
        pdb=" C   GLU A 471 "
      ideal   model   delta    sigma   weight residual
     112.89  107.75    5.14 1.24e+00 6.50e-01 1.72e+01
  angle pdb=" N   LEU A 466 "
        pdb=" CA  LEU A 466 "
        pdb=" C   LEU A 466 "
      ideal   model   delta    sigma   weight residual
     111.07  106.66    4.41 1.07e+00 8.73e-01 1.70e+01
  angle pdb=" N   ILE B 285 "
        pdb=" CA  ILE B 285 "
        pdb=" C   ILE B 285 "
      ideal   model   delta    sigma   weight residual
     111.77  107.77    4.00 1.04e+00 9.25e-01 1.48e+01
  angle pdb=" C   GLU A 363 "
        pdb=" N   HIS A 364 "
        pdb=" CA  HIS A 364 "
      ideal   model   delta    sigma   weight residual
     122.08  116.22    5.86 1.53e+00 4.27e-01 1.46e+01
  ... (remaining 14976 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 5983
       17.98 -    35.96: 561
       35.96 -    53.94: 158
       53.94 -    71.92: 31
       71.92 -    89.90: 23
  Dihedral angle restraints: 6756
    sinusoidal: 2764
      harmonic: 3992
  Sorted by residual:
  dihedral pdb=" CD  ARG A 420 "
           pdb=" NE  ARG A 420 "
           pdb=" CZ  ARG A 420 "
           pdb=" NH1 ARG A 420 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   59.29  -59.29     1      1.00e+01 1.00e-02 4.70e+01
  dihedral pdb=" CD  ARG A 527 "
           pdb=" NE  ARG A 527 "
           pdb=" CZ  ARG A 527 "
           pdb=" NH1 ARG A 527 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   56.23  -56.23     1      1.00e+01 1.00e-02 4.26e+01
  dihedral pdb=" CD  ARG A 134 "
           pdb=" NE  ARG A 134 "
           pdb=" CZ  ARG A 134 "
           pdb=" NH1 ARG A 134 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   55.93  -55.93     1      1.00e+01 1.00e-02 4.22e+01
  ... (remaining 6753 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1244
       0.050 -    0.100: 336
       0.100 -    0.151: 94
       0.151 -    0.201: 17
       0.201 -    0.251: 3
  Chirality restraints: 1694
  Sorted by residual:
  chirality pdb=" CA  VAL A 533 "
            pdb=" N   VAL A 533 "
            pdb=" C   VAL A 533 "
            pdb=" CB  VAL A 533 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.69   -0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CA  ILE A 355 "
            pdb=" N   ILE A 355 "
            pdb=" C   ILE A 355 "
            pdb=" CB  ILE A 355 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CG  LEU A 411 "
            pdb=" CB  LEU A 411 "
            pdb=" CD1 LEU A 411 "
            pdb=" CD2 LEU A 411 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 1691 not shown)

  Planarity restraints: 1938
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 420 "   -0.943 9.50e-02 1.11e+02   4.23e-01 1.08e+02
        pdb=" NE  ARG A 420 "    0.057 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 420 "    0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 420 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 420 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 527 "    0.920 9.50e-02 1.11e+02   4.12e-01 1.03e+02
        pdb=" NE  ARG A 527 "   -0.055 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 527 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 527 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 527 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 134 "   -0.913 9.50e-02 1.11e+02   4.09e-01 1.01e+02
        pdb=" NE  ARG A 134 "    0.055 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 134 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 134 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 134 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 1935 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.23: 3
        2.23 -     2.90: 4452
        2.90 -     3.56: 14983
        3.56 -     4.23: 23565
        4.23 -     4.90: 41109
  Nonbonded interactions: 84112
  Sorted by model distance:
  nonbonded pdb=" CE  MET B 301 "
            pdb=" CG2 VAL B 308 "
     model   vdw
     1.559 3.880
  nonbonded pdb=" O   MET C  83 "
            pdb=" ND1 HIS C 167 "
     model   vdw
     1.917 3.120
  nonbonded pdb=" OD2 ASP C  57 "
            pdb=" OD2 ASP C  85 "
     model   vdw
     2.110 3.040
  nonbonded pdb=" O   SER B  15 "
            pdb=" OE1 GLN B  16 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OH  TYR B  74 "
            pdb=" OE2 GLU B 126 "
     model   vdw
     2.312 3.040
  ... (remaining 84107 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.800
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
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      :  0.006   0.055  11060  Z= 0.357
  Angle     :  0.778   9.048  14981  Z= 0.502
  Chirality :  0.051   0.251   1694
  Planarity :  0.018   0.423   1938
  Dihedral  : 16.264  89.895   4156
  Min Nonbonded Distance : 1.559

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.81 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 19.95 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.66 (0.23), residues: 1345
  helix: -0.20 (0.23), residues: 568
  sheet: -4.97 (0.28), residues: 164
  loop : -2.30 (0.25), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 185 
 TYR   0.020   0.001   TYR B  74 
 PHE   0.021   0.001   PHE B 242 
 TRP   0.020   0.002   TRP C 143 
 HIS   0.006   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00614 (11060)
  covalent geometry    : angle       0.77849 (14981)
  hydrogen bonds       : bond        0.17048 (  407)
  hydrogen bonds       : angle       6.68013 ( 1173)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  134 TYR cc_start: 0.7088 (m-80) cc_final: 0.6767 (m-80)
REVERT: B  396 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8199 (mmtm)
REVERT: C   92 TYR cc_start: 0.5415 (m-80) cc_final: 0.5039 (m-80)
REVERT: C  144 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7844 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 250
  average time/residue: 0.1281
  time to fit residues: 43.5729
Evaluate side-chains
  155 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0980
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 465 ASN
C  63 HIS
** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 222 GLN
** C 241 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 = 0.4041 r_free = 0.4041 target = 0.179738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.112581 restraints weight = 13557.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.111787 restraints weight = 9861.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.112411 restraints weight = 8433.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.113003 restraints weight = 7667.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.113253 restraints weight = 7361.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11060  Z= 0.144
  Angle     :  0.646   8.586  14981  Z= 0.333
  Chirality :  0.043   0.185   1694
  Planarity :  0.005   0.055   1938
  Dihedral  :  5.183  69.398   1472
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.17 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 20.77 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.87 (0.24), residues: 1345
  helix:  0.49 (0.23), residues: 574
  sheet: -4.02 (0.30), residues: 193
  loop : -1.97 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 121 
 TYR   0.021   0.001   TYR A 577 
 PHE   0.026   0.002   PHE A 503 
 TRP   0.014   0.002   TRP C 143 
 HIS   0.008   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (11060)
  covalent geometry    : angle       0.64570 (14981)
  hydrogen bonds       : bond        0.04043 (  407)
  hydrogen bonds       : angle       4.98716 ( 1173)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 168
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7317 (t-90)
REVERT: A  389 ASP cc_start: 0.7984 (p0) cc_final: 0.7737 (p0)
REVERT: A  433 GLN cc_start: 0.7441 (mt0) cc_final: 0.6945 (mm-40)
REVERT: A  453 ASP cc_start: 0.8529 (t0) cc_final: 0.7956 (t0)
REVERT: A  537 ARG cc_start: 0.8667 (ttm-80) cc_final: 0.8289 (ttm-80)
REVERT: B   58 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6938 (mt-10)
REVERT: B  129 LYS cc_start: 0.8610 (mttt) cc_final: 0.8355 (mtmm)
REVERT: B  214 ILE cc_start: 0.8839 (tp) cc_final: 0.8551 (pt)
REVERT: B  234 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8543 (m-80)
REVERT: C   92 TYR cc_start: 0.4612 (m-80) cc_final: 0.4257 (m-80)
REVERT: C  144 LYS cc_start: 0.8333 (mtpp) cc_final: 0.7847 (mmmt)
REVERT: C  195 MET cc_start: 0.5583 (ttt) cc_final: 0.5181 (tmm)
REVERT: C  260 PHE cc_start: 0.6302 (t80) cc_final: 0.5541 (m-80)
  outliers start: 37
  outliers final: 20
  residues processed: 200
  average time/residue: 0.1170
  time to fit residues: 32.6444
Evaluate side-chains
  160 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 137
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  304 HIS
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  465 ASN
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  295 HIS
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  355 SER
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue  238 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 104 optimal weight:    5.9990
   chunk 106 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 38 optimal weight:    6.9990
   chunk 107 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 46 optimal weight:   10.0000
   chunk 102 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 465 ASN
B 174 ASN
** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 241 HIS ** 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 = 0.4130 r_free = 0.4130 target = 0.187493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.143595 restraints weight = 13451.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.136646 restraints weight = 20239.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.131245 restraints weight = 21827.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.132187 restraints weight = 19836.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.132740 restraints weight = 14001.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11060  Z= 0.177
  Angle     :  0.647  10.772  14981  Z= 0.329
  Chirality :  0.044   0.249   1694
  Planarity :  0.005   0.041   1938
  Dihedral  :  5.116  66.829   1472
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.54 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 19.95 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.68 (0.24), residues: 1345
  helix:  0.57 (0.23), residues: 581
  sheet: -3.74 (0.32), residues: 201
  loop : -1.84 (0.27), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 185 
 TYR   0.018   0.001   TYR A 577 
 PHE   0.029   0.002   PHE B 442 
 TRP   0.017   0.002   TRP C 143 
 HIS   0.005   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (11060)
  covalent geometry    : angle       0.64672 (14981)
  hydrogen bonds       : bond        0.03885 (  407)
  hydrogen bonds       : angle       4.85069 ( 1173)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 153
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7285 (t-90)
REVERT: A  433 GLN cc_start: 0.7139 (mt0) cc_final: 0.6803 (mm-40)
REVERT: A  453 ASP cc_start: 0.8441 (t0) cc_final: 0.8099 (t0)
REVERT: A  528 MET cc_start: 0.7008 (ttm) cc_final: 0.6755 (ttm)
REVERT: A  537 ARG cc_start: 0.8903 (ttm-80) cc_final: 0.8652 (ttm-80)
REVERT: B   58 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6989 (mt-10)
REVERT: B  214 ILE cc_start: 0.8953 (tp) cc_final: 0.8554 (pt)
REVERT: B  234 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8510 (m-80)
REVERT: C   92 TYR cc_start: 0.5243 (m-80) cc_final: 0.4803 (m-80)
REVERT: C  144 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7855 (mmmt)
REVERT: C  195 MET cc_start: 0.5612 (ttt) cc_final: 0.5364 (tmm)
REVERT: C  234 LEU cc_start: 0.6242 (mp) cc_final: 0.5989 (mt)
REVERT: C  260 PHE cc_start: 0.6229 (t80) cc_final: 0.5837 (m-80)
REVERT: C  268 ARG cc_start: 0.6892 (mmm160) cc_final: 0.5774 (mtm110)
  outliers start: 52
  outliers final: 34
  residues processed: 196
  average time/residue: 0.1140
  time to fit residues: 31.5268
Evaluate side-chains
  171 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 134
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  304 HIS
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain B residue   13 CYS
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   37 ASN
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  340 ASP
Chi-restraints excluded: chain B residue  355 SER
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   chunk 84 optimal weight:    0.3980
   chunk 128 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 114 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 119 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 174 ASN
** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 125 GLN
** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 264 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.175870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.112125 restraints weight = 13649.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.109234 restraints weight = 10072.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.108863 restraints weight = 8565.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.109097 restraints weight = 8605.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.109465 restraints weight = 8082.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  11060  Z= 0.239
  Angle     :  0.694  12.644  14981  Z= 0.352
  Chirality :  0.046   0.279   1694
  Planarity :  0.005   0.041   1938
  Dihedral  :  5.271  63.802   1472
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.66 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 20.20 %
    Favored  : 74.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.82 (0.24), residues: 1345
  helix:  0.43 (0.23), residues: 581
  sheet: -3.90 (0.33), residues: 183
  loop : -1.94 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 185 
 TYR   0.020   0.001   TYR B  74 
 PHE   0.024   0.002   PHE B  14 
 TRP   0.017   0.002   TRP C 143 
 HIS   0.005   0.001   HIS B 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00588 (11060)
  covalent geometry    : angle       0.69400 (14981)
  hydrogen bonds       : bond        0.04119 (  407)
  hydrogen bonds       : angle       4.86951 ( 1173)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 147
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7581 (tp30)
REVERT: A  304 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7230 (t-90)
REVERT: A  389 ASP cc_start: 0.7825 (p0) cc_final: 0.7564 (p0)
REVERT: A  433 GLN cc_start: 0.7392 (mt0) cc_final: 0.6921 (mm-40)
REVERT: A  453 ASP cc_start: 0.8631 (t0) cc_final: 0.8114 (t0)
REVERT: A  528 MET cc_start: 0.6763 (ttm) cc_final: 0.6523 (ttm)
REVERT: A  537 ARG cc_start: 0.8798 (ttm-80) cc_final: 0.8545 (ttm-80)
REVERT: B   37 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8305 (p0)
REVERT: B   58 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7198 (mt-10)
REVERT: B  234 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8599 (m-80)
REVERT: B  280 PHE cc_start: 0.8175 (t80) cc_final: 0.7607 (t80)
REVERT: C   92 TYR cc_start: 0.4853 (m-80) cc_final: 0.4405 (m-80)
REVERT: C  144 LYS cc_start: 0.8432 (mtpp) cc_final: 0.7967 (mmmt)
REVERT: C  185 ARG cc_start: 0.6681 (ttp-110) cc_final: 0.6160 (ptm-80)
REVERT: C  195 MET cc_start: 0.5673 (ttt) cc_final: 0.5426 (tmm)
REVERT: C  260 PHE cc_start: 0.6470 (t80) cc_final: 0.5872 (m-80)
  outliers start: 62
  outliers final: 42
  residues processed: 190
  average time/residue: 0.0997
  time to fit residues: 27.7276
Evaluate side-chains
  182 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 136
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  294 CYS
Chi-restraints excluded: chain A residue  304 HIS
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain B residue   13 CYS
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   37 ASN
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  355 SER
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  163 ILE
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 108 optimal weight:    0.9980
   chunk 115 optimal weight:    2.9990
   chunk 117 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 89 optimal weight:    0.5980
   chunk 93 optimal weight:    0.5980
   chunk 118 optimal weight:    7.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 465 ASN
B 174 ASN
** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 141 ASN
** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 271 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 = 0.4032 r_free = 0.4032 target = 0.178650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.115372 restraints weight = 13576.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.113850 restraints weight = 9577.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.112388 restraints weight = 8499.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.112813 restraints weight = 9050.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.112974 restraints weight = 7936.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11060  Z= 0.129
  Angle     :  0.603   9.687  14981  Z= 0.307
  Chirality :  0.042   0.197   1694
  Planarity :  0.004   0.039   1938
  Dihedral  :  5.012  60.563   1472
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.39 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 22.01 %
    Favored  : 74.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.48 (0.24), residues: 1345
  helix:  0.71 (0.23), residues: 575
  sheet: -3.24 (0.33), residues: 207
  loop : -1.81 (0.26), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 239 
 TYR   0.020   0.001   TYR A 577 
 PHE   0.021   0.001   PHE B 442 
 TRP   0.020   0.001   TRP C 143 
 HIS   0.003   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (11060)
  covalent geometry    : angle       0.60331 (14981)
  hydrogen bonds       : bond        0.03272 (  407)
  hydrogen bonds       : angle       4.60714 ( 1173)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 138
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 MET cc_start: 0.8649 (tpp) cc_final: 0.8429 (tpt)
REVERT: A  304 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7294 (t-90)
REVERT: A  389 ASP cc_start: 0.7870 (p0) cc_final: 0.7568 (p0)
REVERT: A  433 GLN cc_start: 0.7362 (mt0) cc_final: 0.6937 (mm-40)
REVERT: A  453 ASP cc_start: 0.8583 (t0) cc_final: 0.8030 (t0)
REVERT: A  528 MET cc_start: 0.6669 (ttm) cc_final: 0.6466 (ttm)
REVERT: A  537 ARG cc_start: 0.8695 (ttm-80) cc_final: 0.8326 (ttm-80)
REVERT: B   37 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8155 (p0)
REVERT: B   58 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7106 (mt-10)
REVERT: B  234 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8570 (m-80)
REVERT: B  280 PHE cc_start: 0.8172 (t80) cc_final: 0.7547 (t80)
REVERT: C   92 TYR cc_start: 0.4581 (m-80) cc_final: 0.4175 (m-80)
REVERT: C  144 LYS cc_start: 0.8482 (mtpp) cc_final: 0.8019 (mmmt)
REVERT: C  185 ARG cc_start: 0.6966 (ttp-110) cc_final: 0.6453 (ptm-80)
REVERT: C  195 MET cc_start: 0.6130 (ttt) cc_final: 0.5627 (tmm)
REVERT: C  260 PHE cc_start: 0.6451 (t80) cc_final: 0.5827 (m-80)
REVERT: C  268 ARG cc_start: 0.6699 (mmm160) cc_final: 0.5579 (ttp-110)
  outliers start: 48
  outliers final: 35
  residues processed: 171
  average time/residue: 0.1074
  time to fit residues: 26.4868
Evaluate side-chains
  169 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 130
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  304 HIS
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain B residue   13 CYS
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   37 ASN
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  355 SER
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain B residue  411 ASP
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  163 ILE
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain D residue   31 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 110 optimal weight:    6.9990
   chunk 132 optimal weight:    0.9980
   chunk 98 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 133 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 465 ASN
B 174 ASN
** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 271 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 = 0.4105 r_free = 0.4105 target = 0.185215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 151)---------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.128621 restraints weight = 13502.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 96)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.117759 restraints weight = 15509.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.117722 restraints weight = 13675.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.119249 restraints weight = 12348.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.120810 restraints weight = 9963.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11060  Z= 0.154
  Angle     :  0.616   9.168  14981  Z= 0.312
  Chirality :  0.043   0.210   1694
  Planarity :  0.004   0.038   1938
  Dihedral  :  4.941  57.169   1472
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.54 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 21.27 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.47 (0.24), residues: 1345
  helix:  0.66 (0.23), residues: 587
  sheet: -3.28 (0.35), residues: 188
  loop : -1.86 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 239 
 TYR   0.017   0.001   TYR A 577 
 PHE   0.022   0.002   PHE A 503 
 TRP   0.022   0.001   TRP C 143 
 HIS   0.004   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (11060)
  covalent geometry    : angle       0.61623 (14981)
  hydrogen bonds       : bond        0.03396 (  407)
  hydrogen bonds       : angle       4.58850 ( 1173)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 138
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 MET cc_start: 0.8607 (tpp) cc_final: 0.8367 (tpt)
REVERT: A  304 HIS cc_start: 0.8113 (OUTLIER) cc_final: 0.7239 (t-90)
REVERT: A  389 ASP cc_start: 0.7875 (p0) cc_final: 0.7580 (p0)
REVERT: A  414 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7896 (m-30)
REVERT: A  433 GLN cc_start: 0.7392 (mt0) cc_final: 0.6974 (mm-40)
REVERT: A  453 ASP cc_start: 0.8603 (t0) cc_final: 0.7940 (t0)
REVERT: A  521 MET cc_start: 0.7837 (ptt) cc_final: 0.7538 (ptt)
REVERT: A  537 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8279 (ttm-80)
REVERT: B   37 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8240 (p0)
REVERT: B   58 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7108 (mt-10)
REVERT: B  234 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8541 (m-80)
REVERT: B  280 PHE cc_start: 0.8101 (t80) cc_final: 0.7742 (t80)
REVERT: C   92 TYR cc_start: 0.4433 (m-80) cc_final: 0.4056 (m-80)
REVERT: C  144 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8044 (mmmt)
REVERT: C  185 ARG cc_start: 0.7015 (ttp-110) cc_final: 0.4845 (ttp80)
REVERT: C  195 MET cc_start: 0.6147 (OUTLIER) cc_final: 0.5705 (tmm)
REVERT: C  260 PHE cc_start: 0.6429 (t80) cc_final: 0.5804 (m-80)
REVERT: C  268 ARG cc_start: 0.6699 (mmm160) cc_final: 0.5585 (ttp-110)
  outliers start: 58
  outliers final: 44
  residues processed: 181
  average time/residue: 0.1057
  time to fit residues: 27.9079
Evaluate side-chains
  183 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 133
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  304 HIS
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  465 ASN
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain B residue   13 CYS
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   37 ASN
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  355 SER
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain B residue  411 ASP
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  163 ILE
Chi-restraints excluded: chain C residue  195 MET
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 113 optimal weight:    9.9990
   chunk 56 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0000
   chunk 15 optimal weight:    0.7980
   chunk 94 optimal weight:    4.9990
   chunk 99 optimal weight:    0.7980
   chunk 122 optimal weight:    0.3980
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 387 ASN
** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 ASN
B 174 ASN
** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 271 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 = 0.4147 r_free = 0.4147 target = 0.189410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 113)---------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.137962 restraints weight = 13419.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.135680 restraints weight = 17938.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.134530 restraints weight = 17674.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.132730 restraints weight = 17161.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.134194 restraints weight = 15485.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.3216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11060  Z= 0.116
  Angle     :  0.599  12.756  14981  Z= 0.301
  Chirality :  0.042   0.244   1694
  Planarity :  0.004   0.038   1938
  Dihedral  :  4.791  54.022   1472
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.87 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 22.67 %
    Favored  : 73.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.29 (0.24), residues: 1345
  helix:  0.78 (0.23), residues: 587
  sheet: -2.99 (0.34), residues: 210
  loop : -1.72 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 171 
 TYR   0.020   0.001   TYR A 577 
 PHE   0.020   0.001   PHE B 442 
 TRP   0.024   0.001   TRP C 143 
 HIS   0.003   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (11060)
  covalent geometry    : angle       0.59859 (14981)
  hydrogen bonds       : bond        0.03048 (  407)
  hydrogen bonds       : angle       4.50296 ( 1173)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 137
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7337 (mtm-85)
REVERT: A  262 MET cc_start: 0.8619 (tpp) cc_final: 0.8364 (tpt)
REVERT: A  304 HIS cc_start: 0.8188 (OUTLIER) cc_final: 0.7393 (t-90)
REVERT: A  383 ASN cc_start: 0.8485 (m-40) cc_final: 0.8273 (m-40)
REVERT: A  440 ASP cc_start: 0.6868 (t0) cc_final: 0.6645 (t0)
REVERT: A  453 ASP cc_start: 0.8432 (t0) cc_final: 0.8017 (t0)
REVERT: A  537 ARG cc_start: 0.8863 (ttm-80) cc_final: 0.8467 (ttm-80)
REVERT: B  234 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8535 (m-80)
REVERT: B  396 LYS cc_start: 0.8366 (mmtt) cc_final: 0.7850 (ptpt)
REVERT: C   92 TYR cc_start: 0.5249 (m-80) cc_final: 0.4745 (m-80)
REVERT: C  144 LYS cc_start: 0.8388 (mtpp) cc_final: 0.7974 (mmmt)
REVERT: C  195 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.5825 (tmm)
REVERT: C  260 PHE cc_start: 0.6281 (t80) cc_final: 0.5949 (m-80)
REVERT: C  268 ARG cc_start: 0.6758 (mmm160) cc_final: 0.5753 (mtm110)
  outliers start: 50
  outliers final: 37
  residues processed: 173
  average time/residue: 0.1107
  time to fit residues: 27.4090
Evaluate side-chains
  172 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 131
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ARG
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  304 HIS
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  539 ASN
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain B residue   13 CYS
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  355 SER
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  163 ILE
Chi-restraints excluded: chain C residue  195 MET
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain D residue   31 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   chunk 105 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 89 optimal weight:    0.2980
   chunk 57 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 174 ASN
B 372 ASN
** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 271 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 = 0.4117 r_free = 0.4117 target = 0.186420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.134021 restraints weight = 13378.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.132049 restraints weight = 17885.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.132157 restraints weight = 17300.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.130524 restraints weight = 12837.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.130160 restraints weight = 13199.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.3346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11060  Z= 0.125
  Angle     :  0.610  12.251  14981  Z= 0.304
  Chirality :  0.042   0.219   1694
  Planarity :  0.004   0.039   1938
  Dihedral  :  4.702  50.720   1472
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.58 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 22.67 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.18 (0.24), residues: 1345
  helix:  0.86 (0.23), residues: 580
  sheet: -2.86 (0.35), residues: 205
  loop : -1.67 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 537 
 TYR   0.019   0.001   TYR A 577 
 PHE   0.019   0.001   PHE B 442 
 TRP   0.026   0.001   TRP C 143 
 HIS   0.003   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (11060)
  covalent geometry    : angle       0.61017 (14981)
  hydrogen bonds       : bond        0.03050 (  407)
  hydrogen bonds       : angle       4.51451 ( 1173)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 138
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7322 (mtm-85)
REVERT: A  262 MET cc_start: 0.8617 (tpp) cc_final: 0.8368 (tpt)
REVERT: A  304 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7395 (t-90)
REVERT: A  379 GLU cc_start: 0.6978 (tp30) cc_final: 0.6485 (tp30)
REVERT: A  453 ASP cc_start: 0.8446 (t0) cc_final: 0.8015 (t0)
REVERT: A  537 ARG cc_start: 0.8837 (ttm-80) cc_final: 0.8470 (ttm-80)
REVERT: B  234 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8580 (m-80)
REVERT: C   92 TYR cc_start: 0.5274 (m-80) cc_final: 0.4770 (m-80)
REVERT: C  144 LYS cc_start: 0.8383 (mtpp) cc_final: 0.7970 (mmmt)
REVERT: C  195 MET cc_start: 0.6274 (ttt) cc_final: 0.5754 (tmm)
REVERT: C  251 CYS cc_start: 0.6120 (p) cc_final: 0.5915 (p)
REVERT: C  260 PHE cc_start: 0.6206 (t80) cc_final: 0.5891 (m-80)
REVERT: C  268 ARG cc_start: 0.6727 (mmm160) cc_final: 0.5725 (mtm110)
  outliers start: 43
  outliers final: 35
  residues processed: 171
  average time/residue: 0.1095
  time to fit residues: 26.7746
Evaluate side-chains
  168 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 130
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ARG
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  304 HIS
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain B residue   13 CYS
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  355 SER
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  163 ILE
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 56 optimal weight:    7.9990
   chunk 127 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 112 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 79 optimal weight:    0.5980
   chunk 75 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 ASN
B 174 ASN
B 372 ASN
** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 271 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 = 0.4060 r_free = 0.4060 target = 0.181366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.112100 restraints weight = 13483.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.115145 restraints weight = 10444.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.115476 restraints weight = 7639.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.115655 restraints weight = 7328.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.115752 restraints weight = 6993.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.3454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11060  Z= 0.130
  Angle     :  0.613  11.591  14981  Z= 0.309
  Chirality :  0.042   0.217   1694
  Planarity :  0.004   0.052   1938
  Dihedral  :  4.657  47.161   1472
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.17 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 23.00 %
    Favored  : 73.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.15 (0.24), residues: 1345
  helix:  0.84 (0.23), residues: 582
  sheet: -2.75 (0.36), residues: 205
  loop : -1.66 (0.26), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 171 
 TYR   0.020   0.001   TYR A 577 
 PHE   0.022   0.001   PHE A 538 
 TRP   0.028   0.001   TRP C 143 
 HIS   0.003   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (11060)
  covalent geometry    : angle       0.61346 (14981)
  hydrogen bonds       : bond        0.03078 (  407)
  hydrogen bonds       : angle       4.50923 ( 1173)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 130
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7283 (mtm-85)
REVERT: A  262 MET cc_start: 0.8610 (tpp) cc_final: 0.8345 (tpt)
REVERT: A  304 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7370 (t-90)
REVERT: A  453 ASP cc_start: 0.8485 (t0) cc_final: 0.7929 (t0)
REVERT: A  521 MET cc_start: 0.7692 (ptt) cc_final: 0.7440 (ptm)
REVERT: A  537 ARG cc_start: 0.8696 (ttm-80) cc_final: 0.8358 (ttm-80)
REVERT: B  234 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8546 (m-80)
REVERT: C   92 TYR cc_start: 0.4646 (m-80) cc_final: 0.4235 (m-80)
REVERT: C  144 LYS cc_start: 0.8467 (mtpp) cc_final: 0.8015 (mmmt)
REVERT: C  185 ARG cc_start: 0.6554 (ptm-80) cc_final: 0.6213 (ptm-80)
REVERT: C  195 MET cc_start: 0.6184 (ttt) cc_final: 0.5822 (tmm)
REVERT: C  239 ARG cc_start: 0.6410 (tmm160) cc_final: 0.5824 (tmm160)
REVERT: C  260 PHE cc_start: 0.6316 (t80) cc_final: 0.5742 (m-80)
REVERT: C  268 ARG cc_start: 0.6743 (mmm160) cc_final: 0.5613 (mtm110)
  outliers start: 43
  outliers final: 37
  residues processed: 164
  average time/residue: 0.1065
  time to fit residues: 25.4020
Evaluate side-chains
  167 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 127
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ARG
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  304 HIS
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  465 ASN
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  539 ASN
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain B residue   13 CYS
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  355 SER
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  163 ILE
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 127 optimal weight:    0.0570
   chunk 11 optimal weight:    1.9990
   chunk 109 optimal weight:    0.7980
   chunk 69 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 87 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.9100

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

Flipped N/Q/H residues before XYZ refinement:
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 ASN
B 174 ASN
B 372 ASN
** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 271 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 = 0.4118 r_free = 0.4118 target = 0.186548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.141945 restraints weight = 13358.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.131057 restraints weight = 21602.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.129193 restraints weight = 21775.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.129573 restraints weight = 18092.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.129867 restraints weight = 14186.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.3485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.154  11060  Z= 0.180
  Angle     :  0.882  59.200  14981  Z= 0.506
  Chirality :  0.043   0.223   1694
  Planarity :  0.004   0.049   1938
  Dihedral  :  4.655  47.129   1472
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.17 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 23.08 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.17 (0.24), residues: 1345
  helix:  0.82 (0.23), residues: 582
  sheet: -2.73 (0.36), residues: 205
  loop : -1.66 (0.26), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 239 
 TYR   0.020   0.001   TYR A 577 
 PHE   0.027   0.001   PHE A 538 
 TRP   0.025   0.001   TRP C 143 
 HIS   0.003   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (11060)
  covalent geometry    : angle       0.88210 (14981)
  hydrogen bonds       : bond        0.03106 (  407)
  hydrogen bonds       : angle       4.52164 ( 1173)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 127
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7332 (mtm-85)
REVERT: A  262 MET cc_start: 0.8618 (tpp) cc_final: 0.8362 (tpt)
REVERT: A  304 HIS cc_start: 0.8218 (OUTLIER) cc_final: 0.7353 (t-90)
REVERT: A  453 ASP cc_start: 0.8390 (t0) cc_final: 0.7989 (t0)
REVERT: A  537 ARG cc_start: 0.8874 (ttm-80) cc_final: 0.8595 (ttm-80)
REVERT: B  234 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8546 (m-80)
REVERT: C   92 TYR cc_start: 0.5280 (m-80) cc_final: 0.4764 (m-80)
REVERT: C  144 LYS cc_start: 0.8366 (mtpp) cc_final: 0.7959 (mmmt)
REVERT: C  185 ARG cc_start: 0.6015 (ptm-80) cc_final: 0.5799 (ptm-80)
REVERT: C  195 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.5992 (tmm)
REVERT: C  239 ARG cc_start: 0.6231 (tmm160) cc_final: 0.5910 (tmm160)
REVERT: C  260 PHE cc_start: 0.6140 (t80) cc_final: 0.5856 (m-80)
REVERT: C  268 ARG cc_start: 0.6823 (mmm160) cc_final: 0.5817 (mtm110)
  outliers start: 40
  outliers final: 36
  residues processed: 159
  average time/residue: 0.1074
  time to fit residues: 24.6109
Evaluate side-chains
  166 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 126
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ARG
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  304 HIS
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  465 ASN
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  575 VAL
Chi-restraints excluded: chain B residue   13 CYS
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  355 SER
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  163 ILE
Chi-restraints excluded: chain C residue  195 MET
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 114 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0970
   chunk 74 optimal weight:    0.1980
   chunk 130 optimal weight:    0.0270
   chunk 46 optimal weight:    7.9990
   chunk 44 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0870
   chunk 27 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.2214

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

Flipped N/Q/H residues before XYZ refinement:
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 174 ASN
B 372 ASN
** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 271 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 = 0.4119 r_free = 0.4119 target = 0.186551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.138886 restraints weight = 13398.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.125452 restraints weight = 20161.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.122813 restraints weight = 18094.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.123295 restraints weight = 15329.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.124030 restraints weight = 12949.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.154  11060  Z= 0.180
  Angle     :  0.882  59.200  14981  Z= 0.506
  Chirality :  0.043   0.223   1694
  Planarity :  0.004   0.049   1938
  Dihedral  :  4.655  47.129   1472
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.17 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 23.00 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.17 (0.24), residues: 1345
  helix:  0.82 (0.23), residues: 582
  sheet: -2.73 (0.36), residues: 205
  loop : -1.66 (0.26), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 239 
 TYR   0.020   0.001   TYR A 577 
 PHE   0.027   0.001   PHE A 538 
 TRP   0.025   0.001   TRP C 143 
 HIS   0.003   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (11060)
  covalent geometry    : angle       0.88210 (14981)
  hydrogen bonds       : bond        0.03106 (  407)
  hydrogen bonds       : angle       4.52164 ( 1173)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2248.43 seconds
wall clock time: 39 minutes 41.40 seconds (2381.40 seconds total)