Starting phenix.real_space_refine
on Tue Jul 29 20:23:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zrk_14917/07_2025/7zrk_14917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zrk_14917/07_2025/7zrk_14917.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zrk_14917/07_2025/7zrk_14917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zrk_14917/07_2025/7zrk_14917.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zrk_14917/07_2025/7zrk_14917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zrk_14917/07_2025/7zrk_14917.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
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: 6
    Type Number    sf(0)   Gaussians
     K      12      8.98       5
     P       8      5.49       5
     S      62      5.16       5
     C    7133      2.51       5
     N    1826      2.21       5
     O    2009      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11050
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 557, 4155
          Classifications: {'peptide': 557}
          Link IDs: {'PTRANS': 25, 'TRANS': 531}
    Chain: "C"
      Number of atoms: 1431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1431
          Classifications: {'peptide': 190}
          Link IDs: {'PTRANS': 13, 'TRANS': 176}
    Chain: "D"
      Number of atoms: 200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 200
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "B"
      Number of atoms: 5025
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 676, 5025
          Classifications: {'peptide': 676}
          Link IDs: {'PTRANS': 26, 'TRANS': 649}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PHD:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 211
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 211
          Unusual residues: {'  K': 11, 'CDL': 2}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'  K': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.84, per 1000 atoms: 0.62
  Number of scatterers: 11050
  At special positions: 0
  Unit cell: (98.164, 116.38, 146.74, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     K      12     19.00
     S      62     16.00
     P       8     15.00
     O    2009      8.00
     N    1826      7.00
     C    7133      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: 3.09
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2638

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 8 sheets defined
      64.5% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 32
      removed outlier: 3.860A  pdb=" N   ARG A  21 " --> pdb=" O   MET A  17 " (cutoff:3.500A)
      Proline residue:  A  22  - end of helix
    Processing helix  chain 'A' and resid 41 through 51
    Processing helix  chain 'A' and resid 58 through 83
    Processing helix  chain 'A' and resid 98 through 111
    Processing helix  chain 'A' and resid 119 through 124
    Processing helix  chain 'A' and resid 125 through 132
    Processing helix  chain 'A' and resid 132 through 157
      removed outlier: 3.734A  pdb=" N   ALA A 141 " --> pdb=" O   ASN A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 177
    Processing helix  chain 'A' and resid 177 through 193
      removed outlier: 3.913A  pdb=" N   VAL A 181 " --> pdb=" O   VAL A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 229
      removed outlier: 3.835A  pdb=" N   GLN A 222 " --> pdb=" O   PRO A 218 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ILE A 225 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 242
    Processing helix  chain 'A' and resid 248 through 274
      removed outlier: 4.509A  pdb=" N   ILE A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
      Proline residue:  A 263  - end of helix
    Processing helix  chain 'A' and resid 276 through 305
      removed outlier: 4.290A  pdb=" N   GLY A 280 " --> pdb=" O   ASP A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 342
    Processing helix  chain 'A' and resid 350 through 354
    Processing helix  chain 'A' and resid 355 through 368
      Proline residue:  A 362  - end of helix
    Processing helix  chain 'A' and resid 377 through 399
    Processing helix  chain 'A' and resid 410 through 437
      removed outlier: 4.503A  pdb=" N   THR A 424 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
      Proline residue:  A 425  - end of helix
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 449 through 465
    Processing helix  chain 'A' and resid 478 through 509
      removed outlier: 4.691A  pdb=" N   VAL A 496 " --> pdb=" O   GLY A 492 " (cutoff:3.500A)
      Proline residue:  A 499  - end of helix
      removed outlier: 4.386A  pdb=" N   SER A 509 " --> pdb=" O   GLY A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 550
      removed outlier: 4.074A  pdb=" N   PHE A 527 " --> pdb=" O   HIS A 523 " (cutoff:3.500A)
      Proline residue:  A 545  - end of helix
    Processing helix  chain 'A' and resid 550 through 557
    Processing helix  chain 'C' and resid 3 through 21
      removed outlier: 3.764A  pdb=" N   ALA C   7 " --> pdb=" O   GLY C   3 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 34
    Processing helix  chain 'C' and resid 34 through 40
    Processing helix  chain 'C' and resid 78 through 82
      removed outlier: 3.997A  pdb=" N   SER C  82 " --> pdb=" O   PRO C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 109
      removed outlier: 3.661A  pdb=" N   ASP C  95 " --> pdb=" O   ASN C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 122
      removed outlier: 3.732A  pdb=" N   VAL C 121 " --> pdb=" O   PRO C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 133 through 149
      Proline residue:  C 142  - end of helix
    Processing helix  chain 'C' and resid 151 through 162
    Processing helix  chain 'C' and resid 178 through 190
    Processing helix  chain 'D' and resid 2 through 25
    Processing helix  chain 'B' and resid 11 through 25
      removed outlier: 3.656A  pdb=" N   GLU B  20 " --> pdb=" O   GLN B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 55
    Processing helix  chain 'B' and resid 61 through 99
    Processing helix  chain 'B' and resid 155 through 160
    Processing helix  chain 'B' and resid 198 through 208
    Processing helix  chain 'B' and resid 215 through 247
      removed outlier: 4.011A  pdb=" N   TRP B 240 " --> pdb=" O   THR B 236 " (cutoff:3.500A)
      Proline residue:  B 241  - end of helix
      removed outlier: 3.692A  pdb=" N   GLY B 246 " --> pdb=" O   PHE B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 263
    Processing helix  chain 'B' and resid 264 through 285
      removed outlier: 5.819A  pdb=" N   SER B 272 " --> pdb=" O   GLY B 268 " (cutoff:3.500A)
      removed outlier: 4.929A  pdb=" N   ALA B 273 " --> pdb=" O   GLY B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 299
      removed outlier: 3.989A  pdb=" N   VAL B 295 " --> pdb=" O   SER B 291 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLY B 299 " --> pdb=" O   VAL B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 342
    Processing helix  chain 'B' and resid 346 through 361
      removed outlier: 3.834A  pdb=" N   LYS B 357 " --> pdb=" O   VAL B 353 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   GLN B 358 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 408
    Processing helix  chain 'B' and resid 413 through 426
      removed outlier: 4.171A  pdb=" N   ASP B 417 " --> pdb=" O   PRO B 413 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   GLN B 426 " --> pdb=" O   GLN B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 463
    Processing helix  chain 'B' and resid 474 through 486
    Processing helix  chain 'B' and resid 495 through 509
      removed outlier: 3.799A  pdb=" N   LYS B 499 " --> pdb=" O   THR B 495 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LEU B 500 " --> pdb=" O   PRO B 496 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLU B 509 " --> pdb=" O   GLN B 505 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 519 through 521
      No H-bonds generated for 'chain 'B' and resid 519 through 521'
    Processing helix  chain 'B' and resid 522 through 529
    Processing helix  chain 'B' and resid 539 through 546
    Processing helix  chain 'B' and resid 554 through 556
      No H-bonds generated for 'chain 'B' and resid 554 through 556'
    Processing helix  chain 'B' and resid 557 through 595
      removed outlier: 4.017A  pdb=" N   ASP B 583 " --> pdb=" O   SER B 579 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   VAL B 584 " --> pdb=" O   ILE B 580 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   ALA B 585 " --> pdb=" O   ALA B 581 " (cutoff:3.500A)
      Proline residue:  B 592  - end of helix
    Processing helix  chain 'B' and resid 599 through 606
      removed outlier: 3.971A  pdb=" N   ALA B 604 " --> pdb=" O   GLN B 601 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 631
      removed outlier: 4.337A  pdb=" N   ILE B 628 " --> pdb=" O   ASN B 624 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   VAL B 629 " --> pdb=" O   ALA B 625 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 631 through 638
    Processing helix  chain 'B' and resid 645 through 680
      removed outlier: 4.244A  pdb=" N   LEU B 659 " --> pdb=" O   TRP B 655 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLY B 660 " --> pdb=" O   ILE B 656 " (cutoff:3.500A)
      Proline residue:  B 665  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205
    Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 45
      removed outlier: 3.845A  pdb=" N   GLY C  51 " --> pdb=" O   ILE C  43 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   GLU C  45 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 5.625A  pdb=" N   VAL C  49 " --> pdb=" O   GLU C  45 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132
      removed outlier: 3.638A  pdb=" N   ILE C 132 " --> pdb=" O   VAL C 176 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 108
      removed outlier: 3.837A  pdb=" N   ARG B 107 " --> pdb=" O   LEU B 133 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   VAL B 134 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   LEU B 187 " --> pdb=" O   VAL B 134 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   GLU B 190 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 5.577A  pdb=" N   VAL B 146 " --> pdb=" O   GLU B 190 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   GLY B 144 " --> pdb=" O   VAL B 176 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 166
      removed outlier: 3.791A  pdb=" N   SER B 152 " --> pdb=" O   LEU B 183 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 287 through 289
      removed outlier: 5.597A  pdb=" N   ALA B 532 " --> pdb=" O   MET B 548 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   ASP B 550 " --> pdb=" O   ALA B 532 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   ALA B 534 " --> pdb=" O   ASP B 550 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL B 531 " --> pdb=" O   VAL B 513 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   MET B 535 " --> pdb=" O   GLY B 517 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   VAL B 303 " --> pdb=" O   ALA B 514 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   THR B 516 " --> pdb=" O   VAL B 303 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   LEU B 305 " --> pdb=" O   THR B 516 " (cutoff:3.500A)
      removed outlier: 5.649A  pdb=" N   LEU B 304 " --> pdb=" O   VAL B 468 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ILE B 470 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 5.687A  pdb=" N   LEU B 306 " --> pdb=" O   ILE B 470 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   GLY B 472 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASP B 489 " --> pdb=" O   THR B 467 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 383 through 384
      removed outlier: 3.768A  pdb=" N   ARG B 394 " --> pdb=" O   VAL B 434 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL B 434 " --> pdb=" O   ARG B 394 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLY B 396 " --> pdb=" O   VAL B 432 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   VAL B 432 " --> pdb=" O   GLY B 396 " (cutoff:3.500A)
      removed outlier: 5.162A  pdb=" N   VAL B 433 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)

    674 hydrogen bonds defined for protein.
    1980 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.33

  Time building geometry restraints manager: 3.64 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1785
        1.32 -     1.45: 2749
        1.45 -     1.57: 6576
        1.57 -     1.70: 16
        1.70 -     1.82: 112
  Bond restraints: 11238
  Sorted by residual:
  bond pdb=" OD1 PHD B 307 "
       pdb=" P   PHD B 307 "
    ideal  model  delta    sigma   weight residual
    1.816  1.606  0.210 2.00e-02 2.50e+03 1.10e+02
  bond pdb=" C   ILE C 141 "
       pdb=" N   PRO C 142 "
    ideal  model  delta    sigma   weight residual
    1.335  1.383 -0.047 1.36e-02 5.41e+03 1.21e+01
  bond pdb=" C51 CDL A 613 "
       pdb=" C52 CDL A 613 "
    ideal  model  delta    sigma   weight residual
    1.523  1.479  0.044 1.50e-02 4.44e+03 8.66e+00
  bond pdb=" OB3 CDL A 613 "
       pdb=" PB2 CDL A 613 "
    ideal  model  delta    sigma   weight residual
    1.529  1.502  0.027 1.00e-02 1.00e+04 7.34e+00
  bond pdb=" OA3 CDL A 612 "
       pdb=" PA1 CDL A 612 "
    ideal  model  delta    sigma   weight residual
    1.529  1.504  0.025 1.00e-02 1.00e+04 6.15e+00
  ... (remaining 11233 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 14776
        1.88 -     3.77: 360
        3.77 -     5.65: 82
        5.65 -     7.53: 32
        7.53 -     9.41: 6
  Bond angle restraints: 15256
  Sorted by residual:
  angle pdb=" N   VAL A 496 "
        pdb=" CA  VAL A 496 "
        pdb=" C   VAL A 496 "
      ideal   model   delta    sigma   weight residual
     112.96  107.91    5.05 1.00e+00 1.00e+00 2.55e+01
  angle pdb=" CA  TYR A 381 "
        pdb=" CB  TYR A 381 "
        pdb=" CG  TYR A 381 "
      ideal   model   delta    sigma   weight residual
     113.90  121.13   -7.23 1.80e+00 3.09e-01 1.61e+01
  angle pdb=" C   MET B 392 "
        pdb=" N   ILE B 393 "
        pdb=" CA  ILE B 393 "
      ideal   model   delta    sigma   weight residual
     120.69  126.14   -5.45 1.46e+00 4.69e-01 1.40e+01
  angle pdb=" C   ARG B 391 "
        pdb=" N   MET B 392 "
        pdb=" CA  MET B 392 "
      ideal   model   delta    sigma   weight residual
     121.54  128.23   -6.69 1.91e+00 2.74e-01 1.23e+01
  angle pdb=" C   LEU A 380 "
        pdb=" N   TYR A 381 "
        pdb=" CA  TYR A 381 "
      ideal   model   delta    sigma   weight residual
     121.14  115.60    5.54 1.75e+00 3.27e-01 1.00e+01
  ... (remaining 15251 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.31: 6373
       28.31 -    56.61: 336
       56.61 -    84.92: 33
       84.92 -   113.23: 2
      113.23 -   141.53: 2
  Dihedral angle restraints: 6746
    sinusoidal: 2640
      harmonic: 4106
  Sorted by residual:
  dihedral pdb=" O1B ADP B 701 "
           pdb=" O3A ADP B 701 "
           pdb=" PB  ADP B 701 "
           pdb=" PA  ADP B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   63.98 -123.98     1      2.00e+01 2.50e-03 3.74e+01
  dihedral pdb=" CA5 CDL A 612 "
           pdb=" CA4 CDL A 612 "
           pdb=" OA6 CDL A 612 "
           pdb=" CA6 CDL A 612 "
      ideal   model   delta sinusoidal    sigma   weight residual
     168.24   26.71  141.53     1      3.00e+01 1.11e-03 1.90e+01
  dihedral pdb=" CA  ALA A 470 "
           pdb=" C   ALA A 470 "
           pdb=" N   PHE A 471 "
           pdb=" CA  PHE A 471 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.25   21.75     0      5.00e+00 4.00e-02 1.89e+01
  ... (remaining 6743 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1394
       0.051 -    0.101: 337
       0.101 -    0.152: 70
       0.152 -    0.203: 10
       0.203 -    0.253: 4
  Chirality restraints: 1815
  Sorted by residual:
  chirality pdb=" CB4 CDL A 613 "
            pdb=" CB3 CDL A 613 "
            pdb=" CB6 CDL A 613 "
            pdb=" OB6 CDL A 613 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.57   -2.32   -0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CA4 CDL A 612 "
            pdb=" CA3 CDL A 612 "
            pdb=" CA6 CDL A 612 "
            pdb=" OA6 CDL A 612 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.57   -2.34   -0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CA4 CDL A 613 "
            pdb=" CA3 CDL A 613 "
            pdb=" CA6 CDL A 613 "
            pdb=" OA6 CDL A 613 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.57   -2.35   -0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 1812 not shown)

  Planarity restraints: 1910
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 163 "   -0.055 5.00e-02 4.00e+02   8.38e-02 1.12e+01
        pdb=" N   PRO B 164 "    0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO B 164 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO B 164 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 495 "   -0.042 5.00e-02 4.00e+02   6.33e-02 6.42e+00
        pdb=" N   PRO B 496 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO B 496 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 496 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B  58 "   -0.039 5.00e-02 4.00e+02   5.89e-02 5.55e+00
        pdb=" N   PRO B  59 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO B  59 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B  59 "   -0.033 5.00e-02 4.00e+02
  ... (remaining 1907 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.83: 3302
        2.83 -     3.41: 12547
        3.41 -     3.98: 22053
        3.98 -     4.56: 31145
        4.56 -     5.14: 44819
  Nonbonded interactions: 113866
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU C 119 "
            pdb=" OG1 THR C 133 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   GLY B 149 "
            pdb=" OG  SER B 169 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG1 THR B  47 "
            pdb=" OG  SER B  69 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" OG  SER B 615 "
            pdb=" OD1 ASP B 673 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" O   LEU A 541 "
            pdb=" OH  TYR B 587 "
     model   vdw
     2.324 3.040
  ... (remaining 113861 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.820
  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:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     28.520
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.210  11238  Z= 0.231
  Angle     :  0.773   9.415  15256  Z= 0.390
  Chirality :  0.047   0.253   1815
  Planarity :  0.006   0.084   1910
  Dihedral  : 16.226 141.532   4108
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.21), residues: 1436
  helix:  0.67 (0.16), residues: 854
  sheet: -0.82 (0.78), residues: 49
  loop : -1.43 (0.25), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  31 
 HIS   0.007   0.001   HIS B 563 
 PHE   0.021   0.002   PHE B   9 
 TYR   0.021   0.002   TYR A 381 
 ARG   0.008   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09223 (  674)
  hydrogen bonds       : angle       5.18855 ( 1980)
  covalent geometry    : bond        0.00466 (11238)
  covalent geometry    : angle       0.77345 (15256)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 1.184 
Fit side-chains
REVERT: A    6 PHE cc_start: 0.7967 (t80) cc_final: 0.7690 (t80)
REVERT: A  414 MET cc_start: 0.7693 (mmm) cc_final: 0.7469 (mmp)
REVERT: B  609 CYS cc_start: 0.7899 (m) cc_final: 0.7645 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2268
  time to fit residues: 53.0419
Evaluate side-chains
  134 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 120 optimal weight:    8.9990
   chunk 108 optimal weight:    0.0270
   chunk 60 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 112 optimal weight:    5.9990
   chunk 43 optimal weight:    0.6980
   chunk 68 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 129 optimal weight:    3.9990
   overall best weight:    1.5442

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

Flipped N/Q/H residues before XYZ refinement:
D  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.146718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.102468 restraints weight = 12952.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 1.45
r_work: 0.2937 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.0937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11238  Z= 0.161
  Angle     :  0.575   6.284  15256  Z= 0.288
  Chirality :  0.041   0.171   1815
  Planarity :  0.005   0.056   1910
  Dihedral  : 12.198 128.941   1728
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  7.23 %
    Favored  : 92.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.22), residues: 1436
  helix:  1.39 (0.18), residues: 867
  sheet: -1.09 (0.69), residues: 55
  loop : -1.43 (0.25), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  31 
 HIS   0.005   0.001   HIS B 563 
 PHE   0.022   0.002   PHE B 377 
 TYR   0.031   0.002   TYR A 381 
 ARG   0.002   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04381 (  674)
  hydrogen bonds       : angle       4.45273 ( 1980)
  covalent geometry    : bond        0.00372 (11238)
  covalent geometry    : angle       0.57484 (15256)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 140
  time to evaluate  : 1.098 
Fit side-chains
REVERT: A  211 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7661 (mm-40)
REVERT: A  408 LYS cc_start: 0.8406 (mptt) cc_final: 0.8123 (mptt)
REVERT: A  414 MET cc_start: 0.8369 (mmm) cc_final: 0.8120 (mmp)
REVERT: C   48 THR cc_start: 0.8314 (t) cc_final: 0.7908 (m)
REVERT: B  279 MET cc_start: 0.8223 (mmp) cc_final: 0.7955 (mmp)
REVERT: B  318 GLN cc_start: 0.6322 (pt0) cc_final: 0.5886 (mt0)
  outliers start: 4
  outliers final: 4
  residues processed: 143
  average time/residue: 0.2078
  time to fit residues: 44.6670
Evaluate side-chains
  134 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 130
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  156 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 97 optimal weight:    0.5980
   chunk 91 optimal weight:    9.9990
   chunk 79 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 109 optimal weight:    9.9990
   chunk 84 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 139 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
A  85 HIS
A 222 GLN
D  25 ASN
** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.141392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.099376 restraints weight = 13433.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 1.88
r_work: 0.2856 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2732 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.1220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11238  Z= 0.155
  Angle     :  0.560   7.064  15256  Z= 0.279
  Chirality :  0.041   0.174   1815
  Planarity :  0.004   0.049   1910
  Dihedral  : 11.551 125.051   1728
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 10.23 %
    Favored  : 89.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.22), residues: 1436
  helix:  1.61 (0.18), residues: 867
  sheet: -0.95 (0.62), residues: 63
  loop : -1.33 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  71 
 HIS   0.005   0.001   HIS B 563 
 PHE   0.016   0.002   PHE A 471 
 TYR   0.029   0.002   TYR A 381 
 ARG   0.004   0.000   ARG A  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04328 (  674)
  hydrogen bonds       : angle       4.38279 ( 1980)
  covalent geometry    : bond        0.00357 (11238)
  covalent geometry    : angle       0.56005 (15256)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 138
  time to evaluate  : 1.154 
Fit side-chains
REVERT: A  414 MET cc_start: 0.8393 (mmm) cc_final: 0.8090 (mmp)
REVERT: C   93 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7362 (tp30)
REVERT: B   58 MET cc_start: 0.6239 (OUTLIER) cc_final: 0.4759 (tpt)
REVERT: B  279 MET cc_start: 0.8301 (mmp) cc_final: 0.8051 (mmp)
REVERT: B  524 PRO cc_start: 0.6496 (Cg_endo) cc_final: 0.6242 (Cg_exo)
  outliers start: 7
  outliers final: 5
  residues processed: 143
  average time/residue: 0.2049
  time to fit residues: 43.9396
Evaluate side-chains
  138 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 132
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue  156 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 87 optimal weight:    9.9990
   chunk 104 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   chunk 112 optimal weight:    6.9990
   chunk 117 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0770
   chunk 124 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.1740

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

Flipped N/Q/H residues before XYZ refinement:
B  30 GLN
B 528 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.141476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.096144 restraints weight = 13233.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 1.46
r_work: 0.2895 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11238  Z= 0.134
  Angle     :  0.536   5.957  15256  Z= 0.267
  Chirality :  0.040   0.170   1815
  Planarity :  0.004   0.047   1910
  Dihedral  : 11.213 122.966   1728
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 11.38 %
    Favored  : 87.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.22), residues: 1436
  helix:  1.76 (0.18), residues: 867
  sheet: -0.94 (0.63), residues: 62
  loop : -1.25 (0.26), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  71 
 HIS   0.004   0.001   HIS B 563 
 PHE   0.014   0.001   PHE A 109 
 TYR   0.027   0.001   TYR A 381 
 ARG   0.002   0.000   ARG A  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04137 (  674)
  hydrogen bonds       : angle       4.31036 ( 1980)
  covalent geometry    : bond        0.00305 (11238)
  covalent geometry    : angle       0.53575 (15256)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 137
  time to evaluate  : 1.274 
Fit side-chains
REVERT: A    6 PHE cc_start: 0.8339 (t80) cc_final: 0.8025 (t80)
REVERT: A  414 MET cc_start: 0.8369 (mmm) cc_final: 0.8125 (mmp)
REVERT: C   93 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7430 (tp30)
REVERT: B   58 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.4917 (tpp)
REVERT: B  111 GLU cc_start: 0.2296 (pm20) cc_final: 0.1887 (tt0)
REVERT: B  318 GLN cc_start: 0.6316 (pt0) cc_final: 0.5886 (pp30)
  outliers start: 9
  outliers final: 6
  residues processed: 143
  average time/residue: 0.2057
  time to fit residues: 44.0373
Evaluate side-chains
  140 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 133
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue  156 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 113 optimal weight:    6.9990
   chunk 131 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 66 optimal weight:    0.3980
   chunk 141 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.142927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.097865 restraints weight = 13127.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 1.45
r_work: 0.2925 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2807 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11238  Z= 0.114
  Angle     :  0.518   6.188  15256  Z= 0.257
  Chirality :  0.039   0.163   1815
  Planarity :  0.004   0.048   1910
  Dihedral  : 10.839 119.041   1728
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 12.61 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.22), residues: 1436
  helix:  1.91 (0.18), residues: 869
  sheet: -0.83 (0.64), residues: 62
  loop : -1.19 (0.26), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  71 
 HIS   0.002   0.001   HIS B 563 
 PHE   0.012   0.001   PHE A 373 
 TYR   0.026   0.001   TYR A 381 
 ARG   0.003   0.000   ARG A  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03897 (  674)
  hydrogen bonds       : angle       4.22027 ( 1980)
  covalent geometry    : bond        0.00249 (11238)
  covalent geometry    : angle       0.51806 (15256)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 1.878 
Fit side-chains
REVERT: A    6 PHE cc_start: 0.8286 (t80) cc_final: 0.7984 (t80)
REVERT: A  414 MET cc_start: 0.8352 (mmm) cc_final: 0.8129 (mmp)
REVERT: A  544 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8192 (mm)
REVERT: C   93 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7459 (tp30)
REVERT: B   58 MET cc_start: 0.6075 (OUTLIER) cc_final: 0.5001 (tpp)
REVERT: B  114 TYR cc_start: 0.5294 (t80) cc_final: 0.5008 (t80)
REVERT: B  318 GLN cc_start: 0.6253 (pt0) cc_final: 0.5817 (pp30)
  outliers start: 11
  outliers final: 7
  residues processed: 142
  average time/residue: 0.3004
  time to fit residues: 64.4957
Evaluate side-chains
  141 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 1.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  662 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 95 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 85 optimal weight:    9.9990
   chunk 10 optimal weight:    0.8980
   chunk 125 optimal weight:    3.9990
   chunk 106 optimal weight:    0.0270
   chunk 117 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 102 optimal weight:    0.6980
   overall best weight:    0.7240

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.147762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.102013 restraints weight = 13163.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 1.49
r_work: 0.2917 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11238  Z= 0.111
  Angle     :  0.515   7.874  15256  Z= 0.254
  Chirality :  0.039   0.160   1815
  Planarity :  0.004   0.048   1910
  Dihedral  : 10.556 116.669   1728
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 13.32 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.23), residues: 1436
  helix:  1.98 (0.18), residues: 875
  sheet: -0.94 (0.64), residues: 64
  loop : -1.19 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 245 
 HIS   0.002   0.000   HIS A 451 
 PHE   0.012   0.001   PHE A 373 
 TYR   0.026   0.001   TYR A 381 
 ARG   0.004   0.000   ARG A  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03832 (  674)
  hydrogen bonds       : angle       4.17196 ( 1980)
  covalent geometry    : bond        0.00241 (11238)
  covalent geometry    : angle       0.51490 (15256)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 1.472 
Fit side-chains
REVERT: A    6 PHE cc_start: 0.8259 (t80) cc_final: 0.7960 (t80)
REVERT: A  414 MET cc_start: 0.8363 (mmm) cc_final: 0.8147 (mmp)
REVERT: A  544 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8148 (mm)
REVERT: C   93 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7378 (tp30)
REVERT: B   58 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.4882 (tpp)
REVERT: B  114 TYR cc_start: 0.5299 (t80) cc_final: 0.4951 (t80)
REVERT: B  318 GLN cc_start: 0.6197 (pt0) cc_final: 0.5740 (pp30)
REVERT: B  467 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7901 (t)
  outliers start: 15
  outliers final: 9
  residues processed: 142
  average time/residue: 0.2276
  time to fit residues: 48.4734
Evaluate side-chains
  143 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  399 ASP
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  662 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 109 optimal weight:   10.0000
   chunk 91 optimal weight:    0.7980
   chunk 137 optimal weight:    6.9990
   chunk 111 optimal weight:    6.9990
   chunk 129 optimal weight:    5.9990
   chunk 81 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   chunk 132 optimal weight:    5.9990
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
D  25 ASN
** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.138714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.095469 restraints weight = 13452.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 1.83
r_work: 0.2812 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2684 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11238  Z= 0.191
  Angle     :  0.588   9.790  15256  Z= 0.292
  Chirality :  0.042   0.175   1815
  Planarity :  0.004   0.047   1910
  Dihedral  : 10.800 125.561   1728
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 14.02 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.22), residues: 1436
  helix:  1.68 (0.17), residues: 880
  sheet: -0.66 (0.63), residues: 67
  loop : -1.21 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 115 
 HIS   0.004   0.001   HIS B 563 
 PHE   0.015   0.002   PHE A 373 
 TYR   0.024   0.002   TYR A 381 
 ARG   0.003   0.000   ARG A 326 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04572 (  674)
  hydrogen bonds       : angle       4.41079 ( 1980)
  covalent geometry    : bond        0.00448 (11238)
  covalent geometry    : angle       0.58824 (15256)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 1.082 
Fit side-chains
REVERT: A  414 MET cc_start: 0.8482 (mmm) cc_final: 0.8142 (mmp)
REVERT: A  544 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8305 (mm)
REVERT: B   58 MET cc_start: 0.6401 (OUTLIER) cc_final: 0.5042 (tpt)
REVERT: B  114 TYR cc_start: 0.5294 (t80) cc_final: 0.4880 (t80)
REVERT: B  318 GLN cc_start: 0.6335 (pt0) cc_final: 0.5866 (pp30)
  outliers start: 15
  outliers final: 10
  residues processed: 143
  average time/residue: 0.2022
  time to fit residues: 43.5175
Evaluate side-chains
  143 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  399 ASP
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  662 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0970
   chunk 44 optimal weight:    0.0570
   chunk 88 optimal weight:    0.0870
   chunk 12 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 128 optimal weight:    4.9990
   chunk 125 optimal weight:    0.5980
   chunk 78 optimal weight:    3.9990
   chunk 93 optimal weight:    0.0770
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.1832

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

Flipped N/Q/H residues before XYZ refinement:
** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.145048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.100277 restraints weight = 13109.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 1.45
r_work: 0.2938 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11238  Z= 0.101
  Angle     :  0.523  10.247  15256  Z= 0.257
  Chirality :  0.038   0.157   1815
  Planarity :  0.004   0.047   1910
  Dihedral  : 10.279 114.376   1728
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 14.99 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.23), residues: 1436
  helix:  2.05 (0.18), residues: 879
  sheet: -0.81 (0.66), residues: 63
  loop : -1.12 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 176 
 HIS   0.002   0.000   HIS A 451 
 PHE   0.011   0.001   PHE A 494 
 TYR   0.024   0.001   TYR A 381 
 ARG   0.004   0.000   ARG A  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03653 (  674)
  hydrogen bonds       : angle       4.16729 ( 1980)
  covalent geometry    : bond        0.00209 (11238)
  covalent geometry    : angle       0.52291 (15256)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 137
  time to evaluate  : 1.104 
Fit side-chains
REVERT: A    6 PHE cc_start: 0.8231 (t80) cc_final: 0.7943 (t80)
REVERT: A  544 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8170 (mm)
REVERT: C   93 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7422 (tp30)
REVERT: B   58 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.4852 (tpp)
REVERT: B  318 GLN cc_start: 0.6196 (pt0) cc_final: 0.5744 (pp30)
  outliers start: 8
  outliers final: 4
  residues processed: 141
  average time/residue: 0.2104
  time to fit residues: 44.3145
Evaluate side-chains
  139 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 133
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue  662 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 136 optimal weight:    1.9990
   chunk 134 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 128 optimal weight:    1.9990
   chunk 114 optimal weight:    9.9990
   chunk 10 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 99 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   overall best weight:    1.2986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.145544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.099459 restraints weight = 13174.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 1.49
r_work: 0.2887 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2766 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11238  Z= 0.144
  Angle     :  0.559  11.035  15256  Z= 0.274
  Chirality :  0.040   0.168   1815
  Planarity :  0.004   0.046   1910
  Dihedral  : 10.446 118.464   1728
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 14.64 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.22), residues: 1436
  helix:  1.98 (0.18), residues: 874
  sheet: -0.74 (0.65), residues: 64
  loop : -1.17 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  71 
 HIS   0.004   0.001   HIS B 563 
 PHE   0.013   0.001   PHE A 373 
 TYR   0.027   0.001   TYR A 381 
 ARG   0.003   0.000   ARG A  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04118 (  674)
  hydrogen bonds       : angle       4.25870 ( 1980)
  covalent geometry    : bond        0.00334 (11238)
  covalent geometry    : angle       0.55943 (15256)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 1.113 
Fit side-chains
REVERT: A    6 PHE cc_start: 0.8328 (t80) cc_final: 0.8043 (t80)
REVERT: A  544 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8220 (mm)
REVERT: C   93 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7393 (tp30)
REVERT: B   58 MET cc_start: 0.6097 (OUTLIER) cc_final: 0.5001 (tpp)
REVERT: B  114 TYR cc_start: 0.5293 (t80) cc_final: 0.4877 (t80)
REVERT: B  318 GLN cc_start: 0.6301 (pt0) cc_final: 0.5769 (pp30)
REVERT: B  667 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8313 (mp)
  outliers start: 11
  outliers final: 6
  residues processed: 141
  average time/residue: 0.2078
  time to fit residues: 43.7811
Evaluate side-chains
  142 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue  399 ASP
Chi-restraints excluded: chain B residue  662 LEU
Chi-restraints excluded: chain B residue  667 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 117 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 127 optimal weight:    0.9990
   chunk 109 optimal weight:   10.0000
   chunk 114 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9990
   chunk 128 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 121 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.9384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.142150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.100330 restraints weight = 13118.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 1.79
r_work: 0.2940 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2815 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11238  Z= 0.125
  Angle     :  0.552  11.325  15256  Z= 0.270
  Chirality :  0.039   0.166   1815
  Planarity :  0.004   0.047   1910
  Dihedral  : 10.362 117.853   1728
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 14.73 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.22), residues: 1436
  helix:  1.96 (0.17), residues: 880
  sheet: -0.68 (0.66), residues: 64
  loop : -1.13 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  71 
 HIS   0.003   0.001   HIS B 563 
 PHE   0.012   0.001   PHE A 494 
 TYR   0.026   0.001   TYR A 381 
 ARG   0.003   0.000   ARG A  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04000 (  674)
  hydrogen bonds       : angle       4.24667 ( 1980)
  covalent geometry    : bond        0.00284 (11238)
  covalent geometry    : angle       0.55162 (15256)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 1.037 
Fit side-chains
REVERT: A    6 PHE cc_start: 0.8375 (t80) cc_final: 0.8098 (t80)
REVERT: A  544 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8296 (mm)
REVERT: C   93 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7483 (tp30)
REVERT: B   58 MET cc_start: 0.6117 (OUTLIER) cc_final: 0.4994 (tpp)
REVERT: B  114 TYR cc_start: 0.5304 (t80) cc_final: 0.4910 (t80)
REVERT: B  318 GLN cc_start: 0.6329 (pt0) cc_final: 0.5826 (pp30)
REVERT: B  392 MET cc_start: 0.5182 (ptt) cc_final: 0.4513 (ppp)
  outliers start: 13
  outliers final: 9
  residues processed: 140
  average time/residue: 0.2141
  time to fit residues: 44.5618
Evaluate side-chains
  143 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 1.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue  399 ASP
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  662 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 90 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 44 optimal weight:    5.9990
   chunk 111 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 95 optimal weight:    6.9990
   chunk 107 optimal weight:    9.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
D  25 ASN
** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.146369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.100354 restraints weight = 13095.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 1.49
r_work: 0.2888 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2768 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11238  Z= 0.136
  Angle     :  0.549  10.984  15256  Z= 0.271
  Chirality :  0.040   0.169   1815
  Planarity :  0.004   0.046   1910
  Dihedral  : 10.331 118.863   1728
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 14.73 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.22), residues: 1436
  helix:  1.94 (0.17), residues: 880
  sheet: -0.65 (0.66), residues: 64
  loop : -1.12 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  71 
 HIS   0.003   0.001   HIS B 563 
 PHE   0.012   0.001   PHE A 494 
 TYR   0.026   0.001   TYR A 381 
 ARG   0.003   0.000   ARG A  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04082 (  674)
  hydrogen bonds       : angle       4.26119 ( 1980)
  covalent geometry    : bond        0.00314 (11238)
  covalent geometry    : angle       0.54928 (15256)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6861.23 seconds
wall clock time: 121 minutes 36.88 seconds (7296.88 seconds total)