Starting phenix.real_space_refine
on Wed Mar  4 04:59:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6t2c_10368/03_2026/6t2c_10368.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6t2c_10368/03_2026/6t2c_10368.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6t2c_10368/03_2026/6t2c_10368.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6t2c_10368/03_2026/6t2c_10368.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6t2c_10368/03_2026/6t2c_10368.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6t2c_10368/03_2026/6t2c_10368.cif"
  }
  resolution = 3.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
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
     P      29      5.49       5
     Mg      1      5.21       5
     S      65      5.16       5
     C    6670      2.51       5
     N    1853      2.21       5
     O    2082      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10700
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 513, 4145
          Classifications: {'peptide': 513}
          Link IDs: {'PTRANS': 21, 'TRANS': 491}
    Chain: "B"
      Number of atoms: 4996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 626, 4996
          Classifications: {'peptide': 626}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 599}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 941
          Classifications: {'peptide': 116}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 8, 'TRANS': 107}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "V"
      Number of atoms: 617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 617
          Classifications: {'RNA': 29}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 12, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 7, 'rna3p': 21}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.15, per 1000 atoms: 0.20
  Number of scatterers: 10700
  At special positions: 0
  Unit cell: (104.749, 116.281, 94.178, 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)
     S      65     16.00
     P      29     15.00
     Mg      1     11.99
     O    2082      8.00
     N    1853      7.00
     C    6670      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.91
  Conformation dependent library (CDL) restraints added in 480.7 milliseconds
  

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2356

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 13 sheets defined
      47.2% alpha, 13.5% beta
      5 base pairs and 14 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 208 through 216
    Processing helix  chain 'A' and resid 225 through 235
      removed outlier: 3.643A  pdb=" N   SER A 235 " --> pdb=" O   ALA A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 249
      removed outlier: 3.784A  pdb=" N   ALA A 244 " --> pdb=" O   GLY A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 312
    Processing helix  chain 'A' and resid 330 through 347
      removed outlier: 3.811A  pdb=" N   TYR A 334 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   LYS A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLU A 347 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 366
    Processing helix  chain 'A' and resid 401 through 409
    Processing helix  chain 'A' and resid 428 through 446
    Processing helix  chain 'A' and resid 448 through 471
      removed outlier: 3.752A  pdb=" N   GLU A 452 " --> pdb=" O   CYS A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 528
      removed outlier: 3.614A  pdb=" N   ASN A 527 " --> pdb=" O   ASP A 524 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLU A 528 " --> pdb=" O   PRO A 525 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 524 through 528'
    Processing helix  chain 'A' and resid 566 through 575
    Processing helix  chain 'A' and resid 577 through 596
      removed outlier: 4.078A  pdb=" N   LEU A 584 " --> pdb=" O   LEU A 580 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   SER A 589 " --> pdb=" O   GLN A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 608
      removed outlier: 3.553A  pdb=" N   PHE A 607 " --> pdb=" O   THR A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 645
    Processing helix  chain 'A' and resid 647 through 669
      removed outlier: 3.593A  pdb=" N   GLU A 651 " --> pdb=" O   SER A 647 " (cutoff:3.500A)
      removed outlier: 4.981A  pdb=" N   LYS A 659 " --> pdb=" O   ALA A 655 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   LEU A 660 " --> pdb=" O   GLU A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 687
      removed outlier: 3.617A  pdb=" N   LEU A 681 " --> pdb=" O   ASP A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 713
      removed outlier: 3.895A  pdb=" N   MET A 713 " --> pdb=" O   VAL A 709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 11
    Processing helix  chain 'B' and resid 17 through 22
      removed outlier: 3.762A  pdb=" N   PHE B  22 " --> pdb=" O   SER B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 47
    Processing helix  chain 'B' and resid 84 through 99
      removed outlier: 3.521A  pdb=" N   VAL B  88 " --> pdb=" O   GLN B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 115
      removed outlier: 3.787A  pdb=" N   GLN B 115 " --> pdb=" O   ILE B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 123
    Processing helix  chain 'B' and resid 138 through 153
    Processing helix  chain 'B' and resid 156 through 161
      removed outlier: 4.008A  pdb=" N   SER B 160 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLY B 161 " --> pdb=" O   ASN B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 163 through 173
    Processing helix  chain 'B' and resid 213 through 222
      removed outlier: 3.604A  pdb=" N   LEU B 222 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 264
      removed outlier: 3.614A  pdb=" N   VAL B 252 " --> pdb=" O   ILE B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 290
      removed outlier: 4.230A  pdb=" N   LYS B 279 " --> pdb=" O   GLY B 275 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ALA B 280 " --> pdb=" O   ASN B 276 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   LYS B 281 " --> pdb=" O   GLU B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 326
      removed outlier: 3.602A  pdb=" N   PHE B 318 " --> pdb=" O   ASN B 314 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   THR B 326 " --> pdb=" O   VAL B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 345
      removed outlier: 4.747A  pdb=" N   ALA B 340 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      Proline residue:  B 341  - end of helix
    Processing helix  chain 'B' and resid 369 through 376
      removed outlier: 3.698A  pdb=" N   ASN B 372 " --> pdb=" O   SER B 369 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   SER B 374 " --> pdb=" O   GLU B 371 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   ILE B 376 " --> pdb=" O   LEU B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 381
      removed outlier: 4.124A  pdb=" N   TYR B 380 " --> pdb=" O   ASN B 377 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   PHE B 381 " --> pdb=" O   LEU B 378 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 377 through 381'
    Processing helix  chain 'B' and resid 382 through 393
      removed outlier: 3.513A  pdb=" N   LYS B 386 " --> pdb=" O   ASN B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 425
    Processing helix  chain 'B' and resid 428 through 433
    Processing helix  chain 'B' and resid 455 through 471
    Processing helix  chain 'B' and resid 518 through 536
      removed outlier: 3.605A  pdb=" N   ASP B 522 " --> pdb=" O   ASN B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 559
    Processing helix  chain 'B' and resid 572 through 583
    Processing helix  chain 'B' and resid 585 through 589
      removed outlier: 3.886A  pdb=" N   LEU B 589 " --> pdb=" O   LYS B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 594
    Processing helix  chain 'B' and resid 600 through 604
      removed outlier: 3.651A  pdb=" N   ASN B 603 " --> pdb=" O   ASN B 600 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   LEU B 604 " --> pdb=" O   LEU B 601 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 600 through 604'
    Processing helix  chain 'B' and resid 607 through 612
      removed outlier: 3.570A  pdb=" N   LYS B 612 " --> pdb=" O   GLU B 608 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 617 through 625
    Processing helix  chain 'C' and resid 43 through 53
      removed outlier: 3.645A  pdb=" N   ALA C  52 " --> pdb=" O   LYS C  48 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   MET C  53 " --> pdb=" O   TRP C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 66
      removed outlier: 3.835A  pdb=" N   GLU C  65 " --> pdb=" O   ARG C  62 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   MET C  66 " --> pdb=" O   ILE C  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 62 through 66'
    Processing helix  chain 'C' and resid 92 through 103
      removed outlier: 4.077A  pdb=" N   VAL C  96 " --> pdb=" O   SER C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 115
    Processing helix  chain 'C' and resid 115 through 127
      removed outlier: 3.756A  pdb=" N   PHE C 119 " --> pdb=" O   TYR C 115 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 258 through 259
    Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 275
      removed outlier: 6.001A  pdb=" N   LYS A 274 " --> pdb=" O   LYS A 397 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 293
      removed outlier: 7.390A  pdb=" N   TYR A 496 " --> pdb=" O   PHE A 520 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   LEU A 558 " --> pdb=" O   GLU A 539 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   GLU A 539 " --> pdb=" O   LEU A 558 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   VAL A 560 " --> pdb=" O   VAL A 537 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   VAL A 537 " --> pdb=" O   VAL A 560 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   VAL A 537 " --> pdb=" O   ILE A 323 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   THR A 321 " --> pdb=" O   GLU A 539 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   GLY A 541 " --> pdb=" O   LYS A 319 " (cutoff:3.500A)
      removed outlier: 8.195A  pdb=" N   LYS A 319 " --> pdb=" O   GLY A 541 " (cutoff:3.500A)
      removed outlier: 10.386A  pdb=" N   MET A 543 " --> pdb=" O   TRP A 317 " (cutoff:3.500A)
      removed outlier: 10.766A  pdb=" N   TRP A 317 " --> pdb=" O   MET A 543 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293
      removed outlier: 5.219A  pdb=" N   THR A 493 " --> pdb=" O   CYS A 484 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   CYS A 484 " --> pdb=" O   THR A 493 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   LEU A 495 " --> pdb=" O   THR A 482 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   THR A 482 " --> pdb=" O   LEU A 495 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   GLY A 497 " --> pdb=" O   ILE A 480 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   GLN A 476 " --> pdb=" O   LYS A 501 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   TYR A 475 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 373
      removed outlier: 5.872A  pdb=" N   GLU A 372 " --> pdb=" O   ARG B 365 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   GLN B 367 " --> pdb=" O   GLU A 372 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 622 through 626
      removed outlier: 6.544A  pdb=" N   GLY A 622 " --> pdb=" O   GLU A 618 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   GLU A 618 " --> pdb=" O   GLY A 622 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   GLU A 624 " --> pdb=" O   ILE A 616 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 55 through 57
    Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130
    Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 183
      removed outlier: 3.630A  pdb=" N   THR B 183 " --> pdb=" O   LYS B 208 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LYS B 208 " --> pdb=" O   THR B 183 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243
      removed outlier: 6.948A  pdb=" N   LEU B 224 " --> pdb=" O   ARG B 350 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492
    Processing sheet with id=AB3, first strand: chain 'C' and resid 57 through 58
    Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 130

    457 hydrogen bonds defined for protein.
    1266 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      12 hydrogen bonds
      24 hydrogen bond angles
      0 basepair planarities
      5 basepair parallelities
      14 stacking parallelities
  Total time for adding SS restraints: 1.82

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2892
        1.33 -     1.45: 2066
        1.45 -     1.57: 5864
        1.57 -     1.69: 55
        1.69 -     1.80: 112
  Bond restraints: 10989
  Sorted by residual:
  bond pdb=" C   SER A 206 "
       pdb=" N   TYR A 207 "
    ideal  model  delta    sigma   weight residual
    1.331  1.265  0.066 2.07e-02 2.33e+03 1.01e+01
  bond pdb=" N   ASP B 445 "
       pdb=" CA  ASP B 445 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.00e-02 1.00e+04 9.21e+00
  bond pdb=" N   SER B 444 "
       pdb=" CA  SER B 444 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.030 1.29e-02 6.01e+03 5.49e+00
  bond pdb=" N   SER B 443 "
       pdb=" CA  SER B 443 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 1.19e-02 7.06e+03 5.49e+00
  bond pdb=" CA  SER B 443 "
       pdb=" CB  SER B 443 "
    ideal  model  delta    sigma   weight residual
    1.532  1.504  0.028 1.58e-02 4.01e+03 3.04e+00
  ... (remaining 10984 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 14400
        1.71 -     3.42: 504
        3.42 -     5.12: 61
        5.12 -     6.83: 8
        6.83 -     8.54: 5
  Bond angle restraints: 14978
  Sorted by residual:
  angle pdb=" N   ASP B 445 "
        pdb=" CA  ASP B 445 "
        pdb=" C   ASP B 445 "
      ideal   model   delta    sigma   weight residual
     112.54  104.50    8.04 1.51e+00 4.39e-01 2.83e+01
  angle pdb=" N   VAL C 109 "
        pdb=" CA  VAL C 109 "
        pdb=" C   VAL C 109 "
      ideal   model   delta    sigma   weight residual
     113.71  109.15    4.56 9.50e-01 1.11e+00 2.31e+01
  angle pdb=" N   ASP B 446 "
        pdb=" CA  ASP B 446 "
        pdb=" C   ASP B 446 "
      ideal   model   delta    sigma   weight residual
     109.07  116.34   -7.27 1.61e+00 3.86e-01 2.04e+01
  angle pdb=" C   ILE A 540 "
        pdb=" N   GLY A 541 "
        pdb=" CA  GLY A 541 "
      ideal   model   delta    sigma   weight residual
     121.15  115.20    5.95 1.80e+00 3.09e-01 1.09e+01
  angle pdb=" N   ILE B 248 "
        pdb=" CA  ILE B 248 "
        pdb=" CB  ILE B 248 "
      ideal   model   delta    sigma   weight residual
     112.15  107.32    4.83 1.47e+00 4.63e-01 1.08e+01
  ... (remaining 14973 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 5954
       17.68 -    35.36: 509
       35.36 -    53.04: 135
       53.04 -    70.73: 57
       70.73 -    88.41: 12
  Dihedral angle restraints: 6667
    sinusoidal: 3018
      harmonic: 3649
  Sorted by residual:
  dihedral pdb=" CA  ILE A 481 "
           pdb=" C   ILE A 481 "
           pdb=" N   THR A 482 "
           pdb=" CA  THR A 482 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.47   20.53     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  MET B 408 "
           pdb=" C   MET B 408 "
           pdb=" N   MET B 409 "
           pdb=" CA  MET B 409 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.72  -20.28     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  LEU A 581 "
           pdb=" C   LEU A 581 "
           pdb=" N   GLN A 582 "
           pdb=" CA  GLN A 582 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.33  -19.67     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 6664 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1296
       0.059 -    0.118: 311
       0.118 -    0.177: 42
       0.177 -    0.236: 4
       0.236 -    0.294: 1
  Chirality restraints: 1654
  Sorted by residual:
  chirality pdb=" CA  PHE B 447 "
            pdb=" N   PHE B 447 "
            pdb=" C   PHE B 447 "
            pdb=" CB  PHE B 447 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.17e+00
  chirality pdb=" CB  ILE A 418 "
            pdb=" CA  ILE A 418 "
            pdb=" CG1 ILE A 418 "
            pdb=" CG2 ILE A 418 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.72e-01
  chirality pdb=" CG  LEU B 258 "
            pdb=" CB  LEU B 258 "
            pdb=" CD1 LEU B 258 "
            pdb=" CD2 LEU B 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.71e-01
  ... (remaining 1651 not shown)

  Planarity restraints: 1818
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 111 "    0.052 5.00e-02 4.00e+02   7.71e-02 9.52e+00
        pdb=" N   PRO C 112 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO C 112 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO C 112 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 619 "   -0.044 5.00e-02 4.00e+02   6.63e-02 7.04e+00
        pdb=" N   PRO A 620 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 620 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 620 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 584 "    0.012 2.00e-02 2.50e+03   2.33e-02 5.44e+00
        pdb=" C   LEU A 584 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   LEU A 584 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLN A 585 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1815 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 221
        2.66 -     3.22: 9032
        3.22 -     3.78: 16295
        3.78 -     4.34: 22418
        4.34 -     4.90: 37425
  Nonbonded interactions: 85391
  Sorted by model distance:
  nonbonded pdb=" O   ASP B  48 "
            pdb=" OD1 ASP B  48 "
     model   vdw
     2.097 3.040
  nonbonded pdb=" OG  SER B 374 "
            pdb=" OD1 ASP B 375 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OD2 ASP B 446 "
            pdb="MG    MG B 801 "
     model   vdw
     2.278 2.170
  nonbonded pdb=" O   LYS A 380 "
            pdb=" OH  TYR B 380 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   ASP B 120 "
            pdb=" OG1 THR B 123 "
     model   vdw
     2.295 3.040
  ... (remaining 85386 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:             2.090
  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:          0.200
  Check model and map are aligned:         0.010
  Set scattering table:                    0.040
  Process input model:                     11.710
  Find NCS groups from input model:        0.050
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.069  10989  Z= 0.323
  Angle     :  0.756   8.541  14978  Z= 0.427
  Chirality :  0.051   0.294   1654
  Planarity :  0.007   0.077   1818
  Dihedral  : 15.430  88.408   4311
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.71 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  :  8.06 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.65 (0.19), residues: 1243
  helix: -2.33 (0.16), residues: 537
  sheet: -1.15 (0.45), residues: 119
  loop : -2.76 (0.21), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 279 
 TYR   0.017   0.002   TYR B 155 
 PHE   0.023   0.002   PHE B 490 
 TRP   0.021   0.002   TRP B 438 
 HIS   0.005   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00754 (10989)
  covalent geometry    : angle       0.75563 (14978)
  hydrogen bonds       : bond        0.16559 (  465)
  hydrogen bonds       : angle       6.38672 ( 1290)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 223
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 SER cc_start: 0.9446 (m) cc_final: 0.9077 (t)
REVERT: A  288 MET cc_start: 0.8489 (ttp) cc_final: 0.8280 (ttt)
REVERT: A  356 LYS cc_start: 0.8287 (mttt) cc_final: 0.8037 (ttpp)
REVERT: A  388 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8486 (m-10)
REVERT: A  414 ASN cc_start: 0.7936 (m110) cc_final: 0.7701 (p0)
REVERT: A  474 GLU cc_start: 0.7910 (mp0) cc_final: 0.7532 (mm-30)
REVERT: A  585 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7916 (tp40)
REVERT: A  598 LYS cc_start: 0.8753 (mmtt) cc_final: 0.7819 (tptm)
REVERT: A  679 LYS cc_start: 0.8836 (mttt) cc_final: 0.8613 (mmtt)
REVERT: A  707 LYS cc_start: 0.8569 (tttt) cc_final: 0.8367 (tptp)
REVERT: B   15 GLN cc_start: 0.9417 (OUTLIER) cc_final: 0.8256 (mp10)
REVERT: B   54 ILE cc_start: 0.9299 (mt) cc_final: 0.8956 (pt)
REVERT: B  120 ASP cc_start: 0.7326 (p0) cc_final: 0.7071 (p0)
REVERT: B  157 LEU cc_start: 0.8417 (mt) cc_final: 0.7961 (mp)
REVERT: B  169 ASP cc_start: 0.8008 (m-30) cc_final: 0.7660 (m-30)
REVERT: B  171 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8913 (mm)
REVERT: B  175 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6205 (mp0)
REVERT: B  248 ILE cc_start: 0.9148 (tt) cc_final: 0.8783 (tp)
REVERT: B  249 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.6950 (mpt90)
REVERT: B  256 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7892 (mm-30)
REVERT: B  353 ARG cc_start: 0.8398 (ptp-170) cc_final: 0.7949 (ptm-80)
REVERT: B  411 MET cc_start: 0.6755 (mtt) cc_final: 0.6541 (mtm)
REVERT: B  468 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7700 (mtt180)
REVERT: B  481 LYS cc_start: 0.8700 (mttt) cc_final: 0.8247 (mtmt)
REVERT: C   47 MET cc_start: 0.8288 (tpp) cc_final: 0.7696 (tpt)
REVERT: C   71 ASP cc_start: 0.7781 (m-30) cc_final: 0.7379 (m-30)
REVERT: C   83 ASP cc_start: 0.8266 (t70) cc_final: 0.7300 (t70)
REVERT: C  113 ARG cc_start: 0.4380 (OUTLIER) cc_final: 0.3862 (mpt180)
  outliers start: 69
  outliers final: 35
  residues processed: 278
  average time/residue: 0.1244
  time to fit residues: 46.3855
Evaluate side-chains
  203 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 160
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 THR
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  315 TRP
Chi-restraints excluded: chain A residue  388 TYR
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  476 GLN
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain B residue   15 GLN
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  108 GLN
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  175 GLU
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  177 ASP
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  249 ARG
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  435 THR
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  468 ARG
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  583 THR
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  597 ASN
Chi-restraints excluded: chain B residue  619 ASP
Chi-restraints excluded: chain B residue  632 VAL
Chi-restraints excluded: chain B residue  658 ASP
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  245 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 123 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 414 ASN
A 461 ASN
A 476 GLN
B  47 HIS
B  65 GLN
B 276 ASN
B 346 ASN
B 425 ASN
B 567 ASN
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.128937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.105125 restraints weight = 16297.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.108179 restraints weight = 8279.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.110174 restraints weight = 5338.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.111435 restraints weight = 4034.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.112064 restraints weight = 3385.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10989  Z= 0.114
  Angle     :  0.537   7.547  14978  Z= 0.281
  Chirality :  0.039   0.171   1654
  Planarity :  0.005   0.045   1818
  Dihedral  : 13.512  81.121   1879
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.74 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 12.05 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.64 (0.22), residues: 1243
  helix: -0.02 (0.22), residues: 535
  sheet: -1.03 (0.46), residues: 116
  loop : -2.14 (0.23), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 260 
 TYR   0.010   0.001   TYR B 555 
 PHE   0.018   0.001   PHE A 352 
 TRP   0.011   0.001   TRP C  49 
 HIS   0.005   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (10989)
  covalent geometry    : angle       0.53663 (14978)
  hydrogen bonds       : bond        0.04254 (  465)
  hydrogen bonds       : angle       4.39745 ( 1290)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 187
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A  218 SER cc_start: 0.9380 (m) cc_final: 0.9018 (t)
REVERT: A  388 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.8455 (m-10)
REVERT: A  414 ASN cc_start: 0.7994 (m-40) cc_final: 0.7758 (p0)
REVERT: A  568 ILE cc_start: 0.9025 (tp) cc_final: 0.8545 (pt)
REVERT: A  585 GLN cc_start: 0.8321 (tt0) cc_final: 0.7895 (tp40)
REVERT: A  597 VAL cc_start: 0.8384 (m) cc_final: 0.7963 (t)
REVERT: A  598 LYS cc_start: 0.8794 (mmtt) cc_final: 0.7830 (tptm)
REVERT: A  707 LYS cc_start: 0.8534 (tttt) cc_final: 0.8310 (tptp)
REVERT: B   15 GLN cc_start: 0.9431 (OUTLIER) cc_final: 0.8245 (mp10)
REVERT: B  157 LEU cc_start: 0.8441 (mt) cc_final: 0.8118 (mp)
REVERT: B  169 ASP cc_start: 0.7939 (m-30) cc_final: 0.7726 (m-30)
REVERT: B  175 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.5997 (mp0)
REVERT: B  256 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7774 (mm-30)
REVERT: B  287 LYS cc_start: 0.8033 (tmtt) cc_final: 0.7546 (mtmt)
REVERT: B  353 ARG cc_start: 0.8269 (ptp-170) cc_final: 0.7864 (ptm-80)
REVERT: B  468 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7939 (mtt180)
REVERT: B  481 LYS cc_start: 0.8561 (mttt) cc_final: 0.8134 (mtmt)
REVERT: B  577 LYS cc_start: 0.8365 (tptt) cc_final: 0.7976 (tppt)
REVERT: C   47 MET cc_start: 0.8134 (tpp) cc_final: 0.7465 (tpt)
REVERT: C   77 LEU cc_start: 0.8597 (mp) cc_final: 0.8193 (mp)
REVERT: C  113 ARG cc_start: 0.4360 (OUTLIER) cc_final: 0.3763 (mpt180)
  outliers start: 43
  outliers final: 24
  residues processed: 222
  average time/residue: 0.1235
  time to fit residues: 36.8553
Evaluate side-chains
  186 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 157
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 THR
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  315 TRP
Chi-restraints excluded: chain A residue  388 TYR
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain B residue   15 GLN
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue   32 HIS
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  175 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  468 ARG
Chi-restraints excluded: chain B residue  632 VAL
Chi-restraints excluded: chain B residue  658 ASP
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  245 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 106 optimal weight:    3.9990
   chunk 103 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0000
   chunk 124 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    2.5992

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN
B 276 ASN
B 310 ASN
C  80 ASN
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.125469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.101844 restraints weight = 16580.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.104771 restraints weight = 8562.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.106719 restraints weight = 5586.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.107915 restraints weight = 4249.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.108742 restraints weight = 3585.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  10989  Z= 0.199
  Angle     :  0.570   7.231  14978  Z= 0.296
  Chirality :  0.041   0.160   1654
  Planarity :  0.004   0.043   1818
  Dihedral  : 12.830  80.620   1841
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.10 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 12.77 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.23), residues: 1243
  helix:  0.61 (0.23), residues: 539
  sheet: -0.77 (0.47), residues: 119
  loop : -1.99 (0.24), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  64 
 TYR   0.013   0.001   TYR A 475 
 PHE   0.015   0.001   PHE A 352 
 TRP   0.012   0.001   TRP B 438 
 HIS   0.003   0.001   HIS B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (10989)
  covalent geometry    : angle       0.56994 (14978)
  hydrogen bonds       : bond        0.04762 (  465)
  hydrogen bonds       : angle       4.34280 ( 1290)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 164
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A  218 SER cc_start: 0.9360 (m) cc_final: 0.9049 (t)
REVERT: A  414 ASN cc_start: 0.7993 (m-40) cc_final: 0.7759 (p0)
REVERT: A  568 ILE cc_start: 0.9115 (tp) cc_final: 0.8578 (pt)
REVERT: A  585 GLN cc_start: 0.8447 (tt0) cc_final: 0.8001 (tp40)
REVERT: A  598 LYS cc_start: 0.8767 (mmtt) cc_final: 0.7746 (tptm)
REVERT: A  707 LYS cc_start: 0.8556 (tttt) cc_final: 0.8338 (tptp)
REVERT: B   15 GLN cc_start: 0.9429 (OUTLIER) cc_final: 0.8087 (mp10)
REVERT: B  157 LEU cc_start: 0.8529 (mt) cc_final: 0.8160 (mp)
REVERT: B  169 ASP cc_start: 0.7889 (m-30) cc_final: 0.7647 (m-30)
REVERT: B  175 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.5934 (mp0)
REVERT: B  287 LYS cc_start: 0.8063 (tmtt) cc_final: 0.7580 (mtmt)
REVERT: B  353 ARG cc_start: 0.8386 (ptp-170) cc_final: 0.7933 (ptm-80)
REVERT: B  442 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8628 (tp40)
REVERT: B  468 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8026 (mtt180)
REVERT: B  481 LYS cc_start: 0.8655 (mttt) cc_final: 0.8106 (ptpt)
REVERT: B  577 LYS cc_start: 0.8434 (tptt) cc_final: 0.8056 (tppt)
REVERT: C   47 MET cc_start: 0.8108 (tpp) cc_final: 0.7394 (tpt)
REVERT: C  113 ARG cc_start: 0.4246 (OUTLIER) cc_final: 0.3614 (mpt180)
  outliers start: 50
  outliers final: 34
  residues processed: 205
  average time/residue: 0.1127
  time to fit residues: 31.8387
Evaluate side-chains
  192 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 153
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 THR
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain A residue  315 TRP
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain B residue   15 GLN
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue   32 HIS
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  175 GLU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  263 CYS
Chi-restraints excluded: chain B residue  290 MET
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  442 GLN
Chi-restraints excluded: chain B residue  468 ARG
Chi-restraints excluded: chain B residue  597 ASN
Chi-restraints excluded: chain B residue  617 ASP
Chi-restraints excluded: chain B residue  632 VAL
Chi-restraints excluded: chain B residue  658 ASP
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  133 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 104 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 69 optimal weight:    8.9990
   chunk 40 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   chunk 22 optimal weight:    0.0670
   chunk 109 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    1.8124

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

Flipped N/Q/H residues before XYZ refinement:
B 108 GLN
** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 242 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.123387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.099149 restraints weight = 16693.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.102043 restraints weight = 8667.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.103871 restraints weight = 5717.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.105162 restraints weight = 4400.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.105794 restraints weight = 3718.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10989  Z= 0.149
  Angle     :  0.516   7.677  14978  Z= 0.269
  Chirality :  0.040   0.150   1654
  Planarity :  0.004   0.042   1818
  Dihedral  : 12.606  78.690   1836
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 15.13 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.24), residues: 1243
  helix:  1.03 (0.23), residues: 542
  sheet: -0.74 (0.46), residues: 121
  loop : -1.79 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 396 
 TYR   0.013   0.001   TYR A 475 
 PHE   0.018   0.001   PHE A 352 
 TRP   0.010   0.001   TRP B 438 
 HIS   0.003   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (10989)
  covalent geometry    : angle       0.51571 (14978)
  hydrogen bonds       : bond        0.04180 (  465)
  hydrogen bonds       : angle       4.17127 ( 1290)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 169
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 SER cc_start: 0.9367 (m) cc_final: 0.9038 (t)
REVERT: A  414 ASN cc_start: 0.8008 (m-40) cc_final: 0.7768 (p0)
REVERT: A  568 ILE cc_start: 0.9074 (tp) cc_final: 0.8558 (pt)
REVERT: A  585 GLN cc_start: 0.8409 (tt0) cc_final: 0.8012 (tp40)
REVERT: A  597 VAL cc_start: 0.8531 (m) cc_final: 0.8136 (t)
REVERT: A  598 LYS cc_start: 0.8815 (mmtt) cc_final: 0.7746 (tptm)
REVERT: A  707 LYS cc_start: 0.8555 (tttt) cc_final: 0.8319 (tptp)
REVERT: B  118 ARG cc_start: 0.7894 (mmm-85) cc_final: 0.7568 (tpp80)
REVERT: B  157 LEU cc_start: 0.8536 (mt) cc_final: 0.8111 (mp)
REVERT: B  169 ASP cc_start: 0.7922 (m-30) cc_final: 0.7647 (m-30)
REVERT: B  175 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.5927 (mp0)
REVERT: B  256 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7802 (mm-30)
REVERT: B  287 LYS cc_start: 0.8050 (tmtt) cc_final: 0.7545 (mtmt)
REVERT: B  442 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8536 (tp40)
REVERT: B  468 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7799 (mtt-85)
REVERT: B  481 LYS cc_start: 0.8624 (mttt) cc_final: 0.8192 (mtmt)
REVERT: C   47 MET cc_start: 0.8071 (tpp) cc_final: 0.7394 (tpt)
REVERT: C  113 ARG cc_start: 0.4174 (OUTLIER) cc_final: 0.3645 (mpt180)
  outliers start: 42
  outliers final: 31
  residues processed: 202
  average time/residue: 0.1171
  time to fit residues: 32.6971
Evaluate side-chains
  191 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 156
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 THR
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain A residue  315 TRP
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue   32 HIS
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  175 GLU
Chi-restraints excluded: chain B residue  263 CYS
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  442 GLN
Chi-restraints excluded: chain B residue  468 ARG
Chi-restraints excluded: chain B residue  610 CYS
Chi-restraints excluded: chain B residue  617 ASP
Chi-restraints excluded: chain B residue  632 VAL
Chi-restraints excluded: chain B residue  658 ASP
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  133 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 78 optimal weight:    8.9990
   chunk 11 optimal weight:    5.9990
   chunk 85 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 95 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.127564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.103667 restraints weight = 16570.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.106662 restraints weight = 8561.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.108626 restraints weight = 5595.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.109920 restraints weight = 4257.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.110707 restraints weight = 3572.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10989  Z= 0.118
  Angle     :  0.494   8.195  14978  Z= 0.256
  Chirality :  0.039   0.151   1654
  Planarity :  0.004   0.041   1818
  Dihedral  : 12.387  77.023   1831
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 15.58 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.24), residues: 1243
  helix:  1.37 (0.23), residues: 539
  sheet: -0.30 (0.47), residues: 117
  loop : -1.73 (0.24), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 396 
 TYR   0.011   0.001   TYR A 475 
 PHE   0.019   0.001   PHE A 352 
 TRP   0.009   0.001   TRP A 363 
 HIS   0.003   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (10989)
  covalent geometry    : angle       0.49375 (14978)
  hydrogen bonds       : bond        0.03808 (  465)
  hydrogen bonds       : angle       4.04624 ( 1290)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 168
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 SER cc_start: 0.9353 (m) cc_final: 0.9042 (t)
REVERT: A  414 ASN cc_start: 0.8025 (m-40) cc_final: 0.7788 (p0)
REVERT: A  568 ILE cc_start: 0.9054 (tp) cc_final: 0.8553 (pt)
REVERT: A  585 GLN cc_start: 0.8359 (tt0) cc_final: 0.8032 (tp40)
REVERT: A  598 LYS cc_start: 0.8779 (mmtt) cc_final: 0.7725 (tptm)
REVERT: A  707 LYS cc_start: 0.8536 (tttt) cc_final: 0.8328 (tptp)
REVERT: B  118 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7478 (tpp80)
REVERT: B  157 LEU cc_start: 0.8563 (mt) cc_final: 0.8122 (mp)
REVERT: B  169 ASP cc_start: 0.7916 (m-30) cc_final: 0.7615 (m-30)
REVERT: B  175 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.5937 (mp0)
REVERT: B  256 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7707 (mm-30)
REVERT: B  287 LYS cc_start: 0.7990 (tmtt) cc_final: 0.7494 (mtmt)
REVERT: B  302 ILE cc_start: 0.9173 (mt) cc_final: 0.8956 (tt)
REVERT: B  353 ARG cc_start: 0.8242 (ptp-170) cc_final: 0.7827 (ptm160)
REVERT: B  442 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8423 (tp40)
REVERT: B  481 LYS cc_start: 0.8583 (mttt) cc_final: 0.7987 (ptpt)
REVERT: C   47 MET cc_start: 0.8061 (tpp) cc_final: 0.7381 (tpt)
REVERT: C  113 ARG cc_start: 0.4218 (OUTLIER) cc_final: 0.3678 (mpt180)
  outliers start: 40
  outliers final: 30
  residues processed: 198
  average time/residue: 0.1150
  time to fit residues: 31.3016
Evaluate side-chains
  192 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 159
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 THR
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain A residue  315 TRP
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain B residue   32 HIS
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  175 GLU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  263 CYS
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  442 GLN
Chi-restraints excluded: chain B residue  610 CYS
Chi-restraints excluded: chain B residue  617 ASP
Chi-restraints excluded: chain B residue  632 VAL
Chi-restraints excluded: chain B residue  658 ASP
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  133 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 104 optimal weight:    0.0050
   chunk 103 optimal weight:    0.9980
   chunk 98 optimal weight:    4.9990
   chunk 23 optimal weight:    8.9990
   chunk 3 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 48 optimal weight:    7.9990
   chunk 85 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9980
   overall best weight:    0.7796

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

Flipped N/Q/H residues before XYZ refinement:
A 439 ASN
B 136 ASN
** C 242 GLN ** 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 = 0.3471 r_free = 0.3471 target = 0.130475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.107005 restraints weight = 16514.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.109980 restraints weight = 8437.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.111987 restraints weight = 5517.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.113283 restraints weight = 4180.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.114042 restraints weight = 3498.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  10989  Z= 0.094
  Angle     :  0.468   7.863  14978  Z= 0.243
  Chirality :  0.038   0.155   1654
  Planarity :  0.003   0.041   1818
  Dihedral  : 12.116  73.576   1826
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 15.85 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.24), residues: 1243
  helix:  1.64 (0.23), residues: 540
  sheet: -0.14 (0.49), residues: 114
  loop : -1.57 (0.25), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 468 
 TYR   0.011   0.001   TYR B 555 
 PHE   0.021   0.001   PHE A 352 
 TRP   0.008   0.001   TRP B 437 
 HIS   0.002   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 (10989)
  covalent geometry    : angle       0.46794 (14978)
  hydrogen bonds       : bond        0.03360 (  465)
  hydrogen bonds       : angle       3.89142 ( 1290)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 176
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 SER cc_start: 0.9311 (m) cc_final: 0.9039 (t)
REVERT: A  414 ASN cc_start: 0.8016 (m-40) cc_final: 0.7801 (p0)
REVERT: A  568 ILE cc_start: 0.8992 (tp) cc_final: 0.8541 (pt)
REVERT: A  585 GLN cc_start: 0.8293 (tt0) cc_final: 0.7990 (tp40)
REVERT: A  598 LYS cc_start: 0.8718 (mmtt) cc_final: 0.7630 (tptm)
REVERT: A  656 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6872 (mm-30)
REVERT: A  707 LYS cc_start: 0.8528 (tttt) cc_final: 0.8325 (tptm)
REVERT: B  118 ARG cc_start: 0.7816 (mmm-85) cc_final: 0.7428 (tpp80)
REVERT: B  157 LEU cc_start: 0.8456 (mt) cc_final: 0.8017 (mp)
REVERT: B  169 ASP cc_start: 0.7852 (m-30) cc_final: 0.7516 (m-30)
REVERT: B  175 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.5920 (mp0)
REVERT: B  287 LYS cc_start: 0.7956 (tmtt) cc_final: 0.7479 (mtmt)
REVERT: B  353 ARG cc_start: 0.8083 (ptp-170) cc_final: 0.7550 (ptm-80)
REVERT: B  442 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8370 (tp40)
REVERT: B  481 LYS cc_start: 0.8544 (mttt) cc_final: 0.7912 (ptpt)
REVERT: C   47 MET cc_start: 0.8055 (tpp) cc_final: 0.7403 (tpt)
  outliers start: 36
  outliers final: 25
  residues processed: 199
  average time/residue: 0.1141
  time to fit residues: 31.5634
Evaluate side-chains
  190 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 163
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain A residue  315 TRP
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  175 GLU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  263 CYS
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  442 GLN
Chi-restraints excluded: chain B residue  610 CYS
Chi-restraints excluded: chain B residue  670 ARG
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  133 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 104 optimal weight:    0.6980
   chunk 118 optimal weight:    0.7980
   chunk 60 optimal weight:    6.9990
   chunk 42 optimal weight:    8.9990
   chunk 99 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 87 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   chunk 25 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** C 242 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 = 0.3481 r_free = 0.3481 target = 0.131264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.107636 restraints weight = 16370.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.110560 restraints weight = 8500.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.112586 restraints weight = 5616.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.113853 restraints weight = 4263.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.114737 restraints weight = 3579.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  10989  Z= 0.095
  Angle     :  0.473   7.829  14978  Z= 0.245
  Chirality :  0.038   0.157   1654
  Planarity :  0.003   0.041   1818
  Dihedral  : 11.966  73.564   1816
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 17.21 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.25), residues: 1243
  helix:  1.77 (0.23), residues: 540
  sheet: -0.12 (0.50), residues: 115
  loop : -1.48 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 468 
 TYR   0.011   0.001   TYR B 555 
 PHE   0.020   0.001   PHE A 352 
 TRP   0.008   0.001   TRP B 438 
 HIS   0.002   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 (10989)
  covalent geometry    : angle       0.47329 (14978)
  hydrogen bonds       : bond        0.03309 (  465)
  hydrogen bonds       : angle       3.86124 ( 1290)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 169
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 SER cc_start: 0.9298 (m) cc_final: 0.9051 (t)
REVERT: A  414 ASN cc_start: 0.8031 (m-40) cc_final: 0.7810 (p0)
REVERT: A  568 ILE cc_start: 0.8958 (tp) cc_final: 0.8511 (pt)
REVERT: A  571 LYS cc_start: 0.8460 (tttt) cc_final: 0.8249 (tttp)
REVERT: A  585 GLN cc_start: 0.8236 (tt0) cc_final: 0.7989 (tp40)
REVERT: A  598 LYS cc_start: 0.8690 (mmtt) cc_final: 0.7589 (tptm)
REVERT: B  118 ARG cc_start: 0.7872 (mmm-85) cc_final: 0.7412 (tpp80)
REVERT: B  157 LEU cc_start: 0.8453 (mt) cc_final: 0.8000 (mp)
REVERT: B  169 ASP cc_start: 0.7844 (m-30) cc_final: 0.7465 (m-30)
REVERT: B  175 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5984 (mp0)
REVERT: B  287 LYS cc_start: 0.7956 (tmtt) cc_final: 0.7489 (mtmt)
REVERT: B  353 ARG cc_start: 0.7941 (ptp-170) cc_final: 0.7508 (ptm160)
REVERT: B  442 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8425 (tp40)
REVERT: B  481 LYS cc_start: 0.8511 (mttt) cc_final: 0.7938 (ptpt)
REVERT: C   47 MET cc_start: 0.8079 (tpp) cc_final: 0.7409 (tpt)
  outliers start: 31
  outliers final: 26
  residues processed: 189
  average time/residue: 0.1064
  time to fit residues: 28.2537
Evaluate side-chains
  189 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 161
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain A residue  315 TRP
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   32 HIS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  175 GLU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  263 CYS
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  442 GLN
Chi-restraints excluded: chain B residue  610 CYS
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  133 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 114 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 123 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0000
   chunk 81 optimal weight:    6.9990
   chunk 64 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 112 optimal weight:    9.9990
   overall best weight:    2.1790

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

Flipped N/Q/H residues before XYZ refinement:
B 247 GLN
** C 242 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 = 0.3432 r_free = 0.3432 target = 0.127407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.103631 restraints weight = 16641.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.106541 restraints weight = 8659.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.108510 restraints weight = 5696.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.109734 restraints weight = 4337.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.110556 restraints weight = 3655.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10989  Z= 0.171
  Angle     :  0.520   7.562  14978  Z= 0.269
  Chirality :  0.041   0.151   1654
  Planarity :  0.004   0.039   1818
  Dihedral  : 12.053  76.494   1816
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 16.67 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.24), residues: 1243
  helix:  1.65 (0.23), residues: 540
  sheet: -0.14 (0.48), residues: 122
  loop : -1.51 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 260 
 TYR   0.015   0.001   TYR A 475 
 PHE   0.021   0.001   PHE A 352 
 TRP   0.011   0.001   TRP C  49 
 HIS   0.003   0.001   HIS B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (10989)
  covalent geometry    : angle       0.52027 (14978)
  hydrogen bonds       : bond        0.04069 (  465)
  hydrogen bonds       : angle       4.04917 ( 1290)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 158
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 SER cc_start: 0.9325 (m) cc_final: 0.9066 (t)
REVERT: A  414 ASN cc_start: 0.8007 (m-40) cc_final: 0.7758 (p0)
REVERT: A  568 ILE cc_start: 0.9041 (tp) cc_final: 0.8545 (pt)
REVERT: A  585 GLN cc_start: 0.8246 (tt0) cc_final: 0.8000 (tp40)
REVERT: A  598 LYS cc_start: 0.8702 (mmtt) cc_final: 0.7619 (tptm)
REVERT: B  118 ARG cc_start: 0.7891 (mmm-85) cc_final: 0.7448 (tpp80)
REVERT: B  157 LEU cc_start: 0.8575 (mt) cc_final: 0.8057 (mp)
REVERT: B  169 ASP cc_start: 0.7883 (m-30) cc_final: 0.7491 (m-30)
REVERT: B  175 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.5909 (mp0)
REVERT: B  287 LYS cc_start: 0.7993 (tmtt) cc_final: 0.7550 (mtmt)
REVERT: B  353 ARG cc_start: 0.8201 (ptp-170) cc_final: 0.7539 (ptm-80)
REVERT: B  442 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8538 (tp40)
REVERT: B  481 LYS cc_start: 0.8565 (mttt) cc_final: 0.8008 (ptpt)
REVERT: C   47 MET cc_start: 0.8130 (tpp) cc_final: 0.7525 (tpt)
  outliers start: 36
  outliers final: 27
  residues processed: 184
  average time/residue: 0.1072
  time to fit residues: 27.4236
Evaluate side-chains
  182 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 153
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain A residue  315 TRP
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue   32 HIS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  175 GLU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  263 CYS
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  442 GLN
Chi-restraints excluded: chain B residue  597 ASN
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  133 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 77 optimal weight:    0.2980
   chunk 23 optimal weight:    7.9990
   chunk 101 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 105 optimal weight:    9.9990
   chunk 27 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
B 247 GLN
B 314 ASN
** C 242 GLN ** 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 = 0.3463 r_free = 0.3463 target = 0.129825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.106281 restraints weight = 16515.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.109259 restraints weight = 8586.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.111208 restraints weight = 5633.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.112470 restraints weight = 4286.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.113234 restraints weight = 3605.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10989  Z= 0.112
  Angle     :  0.486   7.617  14978  Z= 0.252
  Chirality :  0.039   0.144   1654
  Planarity :  0.003   0.039   1818
  Dihedral  : 11.986  75.965   1816
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 17.48 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.24), residues: 1243
  helix:  1.76 (0.23), residues: 541
  sheet:  0.05 (0.50), residues: 119
  loop : -1.46 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 260 
 TYR   0.011   0.001   TYR B 555 
 PHE   0.021   0.001   PHE A 352 
 TRP   0.008   0.001   TRP B 437 
 HIS   0.003   0.001   HIS B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (10989)
  covalent geometry    : angle       0.48600 (14978)
  hydrogen bonds       : bond        0.03580 (  465)
  hydrogen bonds       : angle       3.93814 ( 1290)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 156
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 SER cc_start: 0.9317 (m) cc_final: 0.9071 (t)
REVERT: A  414 ASN cc_start: 0.7995 (m-40) cc_final: 0.7755 (p0)
REVERT: A  568 ILE cc_start: 0.9007 (tp) cc_final: 0.8541 (pt)
REVERT: A  569 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8582 (mtpt)
REVERT: A  585 GLN cc_start: 0.8194 (tt0) cc_final: 0.7987 (tp40)
REVERT: A  598 LYS cc_start: 0.8636 (mmtt) cc_final: 0.7545 (tptm)
REVERT: B  118 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7474 (tpp80)
REVERT: B  157 LEU cc_start: 0.8467 (mt) cc_final: 0.7982 (mp)
REVERT: B  169 ASP cc_start: 0.7848 (m-30) cc_final: 0.7445 (m-30)
REVERT: B  175 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.5904 (mp0)
REVERT: B  256 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7909 (mm-30)
REVERT: B  287 LYS cc_start: 0.7980 (tmtt) cc_final: 0.7539 (mtmt)
REVERT: B  353 ARG cc_start: 0.7940 (ptp-170) cc_final: 0.7564 (ptm160)
REVERT: B  392 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.9025 (tt)
REVERT: B  442 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8448 (tp40)
REVERT: B  481 LYS cc_start: 0.8506 (mttt) cc_final: 0.7967 (ptpt)
REVERT: C   47 MET cc_start: 0.8087 (tpp) cc_final: 0.7442 (tpt)
  outliers start: 30
  outliers final: 24
  residues processed: 179
  average time/residue: 0.1068
  time to fit residues: 26.8066
Evaluate side-chains
  181 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 153
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain A residue  315 TRP
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  569 LYS
Chi-restraints excluded: chain B residue   32 HIS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  175 GLU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  263 CYS
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  442 GLN
Chi-restraints excluded: chain B residue  597 ASN
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  133 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 122 optimal weight:    7.9990
   chunk 85 optimal weight:    2.9990
   chunk 118 optimal weight:   10.0000
   chunk 84 optimal weight:    0.9990
   chunk 12 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   chunk 109 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 119 optimal weight:    2.9990
   chunk 104 optimal weight:    3.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
B 314 ASN
** C 242 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 = 0.3445 r_free = 0.3445 target = 0.128541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.105120 restraints weight = 16584.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.108027 restraints weight = 8538.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.109969 restraints weight = 5599.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.111206 restraints weight = 4276.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.112007 restraints weight = 3598.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10989  Z= 0.146
  Angle     :  0.511   9.349  14978  Z= 0.263
  Chirality :  0.040   0.152   1654
  Planarity :  0.003   0.038   1818
  Dihedral  : 11.991  78.913   1815
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 17.93 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.24), residues: 1243
  helix:  1.69 (0.23), residues: 541
  sheet:  0.08 (0.50), residues: 119
  loop : -1.47 (0.24), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 260 
 TYR   0.012   0.001   TYR A 475 
 PHE   0.023   0.001   PHE A 352 
 TRP   0.010   0.001   TRP B 438 
 HIS   0.003   0.001   HIS B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (10989)
  covalent geometry    : angle       0.51128 (14978)
  hydrogen bonds       : bond        0.03872 (  465)
  hydrogen bonds       : angle       4.01539 ( 1290)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 155
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 SER cc_start: 0.9324 (m) cc_final: 0.9070 (t)
REVERT: A  414 ASN cc_start: 0.8029 (m-40) cc_final: 0.7726 (p0)
REVERT: A  568 ILE cc_start: 0.9043 (tp) cc_final: 0.8528 (pt)
REVERT: A  569 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8567 (mtpt)
REVERT: A  585 GLN cc_start: 0.8198 (tt0) cc_final: 0.7992 (tp40)
REVERT: A  598 LYS cc_start: 0.8646 (mmtt) cc_final: 0.7566 (tptm)
REVERT: B  118 ARG cc_start: 0.7920 (mmm-85) cc_final: 0.7498 (tpp80)
REVERT: B  157 LEU cc_start: 0.8498 (mt) cc_final: 0.8022 (mp)
REVERT: B  169 ASP cc_start: 0.7875 (m-30) cc_final: 0.7471 (m-30)
REVERT: B  175 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.5930 (mp0)
REVERT: B  287 LYS cc_start: 0.7995 (tmtt) cc_final: 0.7554 (mtmt)
REVERT: B  353 ARG cc_start: 0.8135 (ptp-170) cc_final: 0.7503 (ptm-80)
REVERT: B  392 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.9024 (tt)
REVERT: B  442 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8499 (tp40)
REVERT: B  481 LYS cc_start: 0.8594 (mttt) cc_final: 0.8080 (ptpt)
REVERT: C   47 MET cc_start: 0.8130 (tpp) cc_final: 0.7515 (tpt)
  outliers start: 30
  outliers final: 26
  residues processed: 177
  average time/residue: 0.1086
  time to fit residues: 26.9991
Evaluate side-chains
  181 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 151
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain A residue  315 TRP
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  569 LYS
Chi-restraints excluded: chain B residue   32 HIS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  175 GLU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  263 CYS
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  290 MET
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  442 GLN
Chi-restraints excluded: chain B residue  597 ASN
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  133 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 99 optimal weight:    3.9990
   chunk 92 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
B 314 ASN
** C 242 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 = 0.3461 r_free = 0.3461 target = 0.129797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.106390 restraints weight = 16523.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.109379 restraints weight = 8449.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.111358 restraints weight = 5508.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.112629 restraints weight = 4174.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.113415 restraints weight = 3500.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.3086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10989  Z= 0.106
  Angle     :  0.483   9.367  14978  Z= 0.249
  Chirality :  0.039   0.143   1654
  Planarity :  0.003   0.037   1818
  Dihedral  : 11.929  78.566   1815
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 17.57 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.25), residues: 1243
  helix:  1.80 (0.23), residues: 542
  sheet:  0.11 (0.51), residues: 119
  loop : -1.41 (0.25), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 468 
 TYR   0.010   0.001   TYR B 555 
 PHE   0.021   0.001   PHE A 352 
 TRP   0.009   0.001   TRP B 437 
 HIS   0.006   0.001   HIS C 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (10989)
  covalent geometry    : angle       0.48315 (14978)
  hydrogen bonds       : bond        0.03499 (  465)
  hydrogen bonds       : angle       3.91060 ( 1290)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1717.39 seconds
wall clock time: 30 minutes 26.97 seconds (1826.97 seconds total)