Starting phenix.real_space_refine
on Thu Feb 13 01:11:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h5b_34490/02_2025/8h5b_34490.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h5b_34490/02_2025/8h5b_34490.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h5b_34490/02_2025/8h5b_34490.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h5b_34490/02_2025/8h5b_34490.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h5b_34490/02_2025/8h5b_34490.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h5b_34490/02_2025/8h5b_34490.cif"
  }
  resolution = 4.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.040
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    5514      2.51       5
     N    1389      2.21       5
     O    1630      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8570
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 902, 7213
          Classifications: {'peptide': 902}
          Link IDs: {'PTRANS': 25, 'TRANS': 876}
          Chain breaks: 7
    Chain: "B"
      Number of atoms: 1357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 173, 1357
          Classifications: {'peptide': 173}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 164}
  Time building chain proxies: 5.36, per 1000 atoms: 0.63
  Number of scatterers: 8570
  At special positions: 0
  Unit cell: (108.73, 113.71, 101.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1630      8.00
     N    1389      7.00
     C    5514      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: 2.28
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2094

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 1 sheets defined
      76.9% alpha, 3.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 11
    Processing helix  chain 'A' and resid 17 through 31
      removed outlier: 3.861A  pdb=" N   GLN A  24 " --> pdb=" O   VAL A  20 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LEU A  25 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   SER A  31 " --> pdb=" O   GLN A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 46
      removed outlier: 3.832A  pdb=" N   LYS A  38 " --> pdb=" O   SER A  34 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ALA A  44 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 69
      removed outlier: 4.168A  pdb=" N   LYS A  63 " --> pdb=" O   LEU A  59 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   MET A  67 " --> pdb=" O   LYS A  63 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   TYR A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 100
      removed outlier: 3.791A  pdb=" N   LYS A  96 " --> pdb=" O   GLU A  92 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 127
      removed outlier: 3.559A  pdb=" N   CYS A 114 " --> pdb=" O   GLY A 110 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL A 121 " --> pdb=" O   GLN A 117 " (cutoff:3.500A)
      Proline residue:  A 124  - end of helix
    Processing helix  chain 'A' and resid 129 through 141
    Processing helix  chain 'A' and resid 143 through 158
      removed outlier: 4.137A  pdb=" N   ASP A 155 " --> pdb=" O   ASN A 151 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   ASP A 156 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 165
    Processing helix  chain 'A' and resid 167 through 182
      removed outlier: 3.512A  pdb=" N   ALA A 171 " --> pdb=" O   GLY A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 207
      removed outlier: 3.630A  pdb=" N   ALA A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   GLN A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   MET A 204 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   SER A 206 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   HIS A 207 " --> pdb=" O   GLN A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 236
      removed outlier: 3.698A  pdb=" N   GLN A 228 " --> pdb=" O   ALA A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 264
    Processing helix  chain 'A' and resid 265 through 269
    Processing helix  chain 'A' and resid 270 through 291
    Processing helix  chain 'A' and resid 303 through 321
      removed outlier: 3.552A  pdb=" N   ILE A 312 " --> pdb=" O   HIS A 308 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   TYR A 313 " --> pdb=" O   ASP A 309 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ILE A 314 " --> pdb=" O   CYS A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 342
      removed outlier: 4.153A  pdb=" N   ILE A 340 " --> pdb=" O   THR A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 355
    Processing helix  chain 'A' and resid 355 through 364
      removed outlier: 4.326A  pdb=" N   PHE A 359 " --> pdb=" O   ASP A 355 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER A 361 " --> pdb=" O   ASN A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 382
      removed outlier: 3.977A  pdb=" N   ASN A 377 " --> pdb=" O   ARG A 373 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   GLU A 378 " --> pdb=" O   ASP A 374 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   THR A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   SER A 382 " --> pdb=" O   GLU A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 403
      removed outlier: 3.665A  pdb=" N   GLU A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 422
      removed outlier: 3.758A  pdb=" N   LEU A 409 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ASN A 422 " --> pdb=" O   CYS A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 448
      removed outlier: 4.318A  pdb=" N   GLN A 433 " --> pdb=" O   GLU A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 470
      Proline residue:  A 464  - end of helix
    Processing helix  chain 'A' and resid 476 through 494
      removed outlier: 3.617A  pdb=" N   SER A 482 " --> pdb=" O   LYS A 478 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LYS A 494 " --> pdb=" O   ASN A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 515
      removed outlier: 4.620A  pdb=" N   ILE A 506 " --> pdb=" O   SER A 502 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   TYR A 510 " --> pdb=" O   ILE A 506 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   PHE A 514 " --> pdb=" O   TYR A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 521
    Processing helix  chain 'A' and resid 522 through 542
    Processing helix  chain 'A' and resid 548 through 561
    Processing helix  chain 'A' and resid 570 through 588
      removed outlier: 3.766A  pdb=" N   GLU A 587 " --> pdb=" O   THR A 583 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ASP A 588 " --> pdb=" O   ILE A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 606
      removed outlier: 3.713A  pdb=" N   VAL A 595 " --> pdb=" O   ASN A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 634
      removed outlier: 4.753A  pdb=" N   ASN A 616 " --> pdb=" O   ASP A 612 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TYR A 617 " --> pdb=" O   ASN A 613 " (cutoff:3.500A)
      Proline residue:  A 623  - end of helix
      removed outlier: 3.875A  pdb=" N   ALA A 634 " --> pdb=" O   ASP A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 656
    Processing helix  chain 'A' and resid 664 through 682
      removed outlier: 3.780A  pdb=" N   ASN A 668 " --> pdb=" O   PRO A 664 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   GLU A 673 " --> pdb=" O   GLN A 669 " (cutoff:3.500A)
      Proline residue:  A 674  - end of helix
    Processing helix  chain 'A' and resid 684 through 702
      removed outlier: 3.988A  pdb=" N   ALA A 694 " --> pdb=" O   LEU A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 706
      removed outlier: 3.555A  pdb=" N   ALA A 706 " --> pdb=" O   ASP A 703 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 703 through 706'
    Processing helix  chain 'A' and resid 707 through 722
      removed outlier: 4.483A  pdb=" N   MET A 712 " --> pdb=" O   GLU A 708 " (cutoff:3.500A)
      removed outlier: 4.927A  pdb=" N   ASP A 713 " --> pdb=" O   PRO A 709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 732
    Processing helix  chain 'A' and resid 733 through 745
      removed outlier: 4.749A  pdb=" N   LEU A 737 " --> pdb=" O   ASN A 733 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   PHE A 745 " --> pdb=" O   ILE A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 767
      removed outlier: 4.192A  pdb=" N   LEU A 752 " --> pdb=" O   GLU A 748 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   GLY A 754 " --> pdb=" O   GLN A 750 " (cutoff:3.500A)
      removed outlier: 4.833A  pdb=" N   ARG A 755 " --> pdb=" O   PRO A 751 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LYS A 766 " --> pdb=" O   VAL A 762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 787
      removed outlier: 4.080A  pdb=" N   LEU A 780 " --> pdb=" O   LEU A 776 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   CYS A 781 " --> pdb=" O   LEU A 777 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   PHE A 782 " --> pdb=" O   SER A 778 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LEU A 783 " --> pdb=" O   VAL A 779 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASP A 787 " --> pdb=" O   LEU A 783 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 798
      removed outlier: 4.234A  pdb=" N   THR A 791 " --> pdb=" O   ASP A 787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 820
      removed outlier: 4.467A  pdb=" N   LEU A 808 " --> pdb=" O   ASP A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 838
      removed outlier: 3.577A  pdb=" N   ILE A 826 " --> pdb=" O   GLY A 822 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   GLU A 828 " --> pdb=" O   LYS A 824 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   PHE A 838 " --> pdb=" O   SER A 834 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 846
    Processing helix  chain 'A' and resid 878 through 896
      removed outlier: 4.002A  pdb=" N   ILE A 884 " --> pdb=" O   TYR A 880 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   LYS A 885 " --> pdb=" O   THR A 881 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LYS A 896 " --> pdb=" O   SER A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 934 through 941
      removed outlier: 4.124A  pdb=" N   GLU A 938 " --> pdb=" O   ASP A 934 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP A 941 " --> pdb=" O   LYS A 937 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 964 through 978
      removed outlier: 3.554A  pdb=" N   LEU A 968 " --> pdb=" O   SER A 964 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   SER A 978 " --> pdb=" O   LYS A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 990
      removed outlier: 3.846A  pdb=" N   ILE A 987 " --> pdb=" O   GLY A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 995 through 1000
      removed outlier: 3.946A  pdb=" N   SER A1000 " --> pdb=" O   ARG A 996 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 89
    Processing helix  chain 'B' and resid 128 through 146
    Processing helix  chain 'B' and resid 171 through 180
      removed outlier: 3.940A  pdb=" N   LEU B 175 " --> pdb=" O   ARG B 171 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   HIS B 179 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 235
      removed outlier: 3.588A  pdb=" N   ILE B 223 " --> pdb=" O   GLN B 219 " (cutoff:3.500A)
      Proline residue:  B 232  - end of helix
    Processing sheet with id=AA1, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.563A  pdb=" N   VAL B 122 " --> pdb=" O   LEU B 114 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   VAL B 161 " --> pdb=" O   GLN B  68 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   ILE B  70 " --> pdb=" O   ASN B 159 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   ASN B 159 " --> pdb=" O   ILE B  70 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ALA B  72 " --> pdb=" O   ILE B 157 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   ILE B 157 " --> pdb=" O   ALA B  72 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ILE B 202 " --> pdb=" O   MET B 197 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   MET B 197 " --> pdb=" O   ILE B 202 " (cutoff:3.500A)

    542 hydrogen bonds defined for protein.
    1611 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.92

  Time building geometry restraints manager: 2.68 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2754
        1.34 -     1.46: 1393
        1.46 -     1.58: 4505
        1.58 -     1.69: 2
        1.69 -     1.81: 55
  Bond restraints: 8709
  Sorted by residual:
  bond pdb=" CG  PRO A 567 "
       pdb=" CD  PRO A 567 "
    ideal  model  delta    sigma   weight residual
    1.503  1.318  0.185 3.40e-02 8.65e+02 2.97e+01
  bond pdb=" CB  PRO A 567 "
       pdb=" CG  PRO A 567 "
    ideal  model  delta    sigma   weight residual
    1.492  1.644 -0.152 5.00e-02 4.00e+02 9.30e+00
  bond pdb=" CB  PRO B 169 "
       pdb=" CG  PRO B 169 "
    ideal  model  delta    sigma   weight residual
    1.492  1.602 -0.110 5.00e-02 4.00e+02 4.86e+00
  bond pdb=" N   PRO A 567 "
       pdb=" CA  PRO A 567 "
    ideal  model  delta    sigma   weight residual
    1.466  1.439  0.027 1.50e-02 4.44e+03 3.30e+00
  bond pdb=" C   VAL A 734 "
       pdb=" N   GLY A 735 "
    ideal  model  delta    sigma   weight residual
    1.330  1.356 -0.026 1.49e-02 4.50e+03 2.98e+00
  ... (remaining 8704 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.64: 11645
        2.64 -     5.28: 127
        5.28 -     7.91: 10
        7.91 -    10.55: 2
       10.55 -    13.19: 2
  Bond angle restraints: 11786
  Sorted by residual:
  angle pdb=" N   PRO A 567 "
        pdb=" CD  PRO A 567 "
        pdb=" CG  PRO A 567 "
      ideal   model   delta    sigma   weight residual
     103.20   90.01   13.19 1.50e+00 4.44e-01 7.73e+01
  angle pdb=" CA  PRO A 567 "
        pdb=" N   PRO A 567 "
        pdb=" CD  PRO A 567 "
      ideal   model   delta    sigma   weight residual
     112.00  100.64   11.36 1.40e+00 5.10e-01 6.59e+01
  angle pdb=" CA  PRO B 169 "
        pdb=" N   PRO B 169 "
        pdb=" CD  PRO B 169 "
      ideal   model   delta    sigma   weight residual
     112.00  105.15    6.85 1.40e+00 5.10e-01 2.39e+01
  angle pdb=" CA  PRO A 567 "
        pdb=" CB  PRO A 567 "
        pdb=" CG  PRO A 567 "
      ideal   model   delta    sigma   weight residual
     104.50   96.36    8.14 1.90e+00 2.77e-01 1.84e+01
  angle pdb=" C   ALA B  89 "
        pdb=" N   ARG B  90 "
        pdb=" CA  ARG B  90 "
      ideal   model   delta    sigma   weight residual
     121.54  128.43   -6.89 1.91e+00 2.74e-01 1.30e+01
  ... (remaining 11781 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.60: 4855
       17.60 -    35.19: 423
       35.19 -    52.79: 37
       52.79 -    70.38: 13
       70.38 -    87.98: 4
  Dihedral angle restraints: 5332
    sinusoidal: 2141
      harmonic: 3191
  Sorted by residual:
  dihedral pdb=" CA  TYR A 670 "
           pdb=" C   TYR A 670 "
           pdb=" N   LEU A 671 "
           pdb=" CA  LEU A 671 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.95  -19.05     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  PHE A 379 "
           pdb=" C   PHE A 379 "
           pdb=" N   PHE A 380 "
           pdb=" CA  PHE A 380 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.03  -18.97     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  THR B 111 "
           pdb=" C   THR B 111 "
           pdb=" N   THR B 112 "
           pdb=" CA  THR B 112 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.15   17.85     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 5329 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1199
       0.058 -    0.116: 188
       0.116 -    0.173: 25
       0.173 -    0.231: 0
       0.231 -    0.289: 1
  Chirality restraints: 1413
  Sorted by residual:
  chirality pdb=" CA  PRO A 567 "
            pdb=" N   PRO A 567 "
            pdb=" C   PRO A 567 "
            pdb=" CB  PRO A 567 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.43    0.29 2.00e-01 2.50e+01 2.09e+00
  chirality pdb=" CA  ILE B 202 "
            pdb=" N   ILE B 202 "
            pdb=" C   ILE B 202 "
            pdb=" CB  ILE B 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.76e-01
  chirality pdb=" CA  ILE B 160 "
            pdb=" N   ILE B 160 "
            pdb=" C   ILE B 160 "
            pdb=" CB  ILE B 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.57e-01
  ... (remaining 1410 not shown)

  Planarity restraints: 1484
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 168 "    0.069 5.00e-02 4.00e+02   1.01e-01 1.64e+01
        pdb=" N   PRO B 169 "   -0.175 5.00e-02 4.00e+02
        pdb=" CA  PRO B 169 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO B 169 "    0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 255 "   -0.010 2.00e-02 2.50e+03   1.99e-02 3.96e+00
        pdb=" C   GLU A 255 "    0.034 2.00e-02 2.50e+03
        pdb=" O   GLU A 255 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASN A 256 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 199 "   -0.032 5.00e-02 4.00e+02   4.93e-02 3.89e+00
        pdb=" N   PRO B 200 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B 200 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 200 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1481 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.49: 117
        2.49 -     3.09: 7677
        3.09 -     3.69: 13951
        3.69 -     4.30: 20377
        4.30 -     4.90: 31324
  Nonbonded interactions: 73446
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 198 "
            pdb=" OE1 GLU A 255 "
     model   vdw
     1.882 3.120
  nonbonded pdb=" OG  SER A 495 "
            pdb=" O   LYS A 497 "
     model   vdw
     1.909 3.040
  nonbonded pdb=" O   THR A 583 "
            pdb=" OG  SER A 586 "
     model   vdw
     1.945 3.040
  nonbonded pdb=" O   ARG A 720 "
            pdb=" OG  SER A 723 "
     model   vdw
     2.012 3.040
  nonbonded pdb=" O   VAL A  20 "
            pdb=" OG1 THR A  23 "
     model   vdw
     2.067 3.040
  ... (remaining 73441 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:             1.500
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.060
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.185   8709  Z= 0.273
  Angle     :  0.736  13.190  11786  Z= 0.433
  Chirality :  0.041   0.289   1413
  Planarity :  0.005   0.101   1484
  Dihedral  : 12.981  87.977   3238
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 23.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.24), residues: 1057
  helix: -0.81 (0.18), residues: 702
  sheet: -1.38 (0.73), residues: 49
  loop : -1.36 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 813 
 HIS   0.005   0.001   HIS A 579 
 PHE   0.028   0.002   PHE A 177 
 TYR   0.020   0.002   TYR A 614 
 ARG   0.019   0.002   ARG B 107 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 TYR cc_start: 0.8496 (m-80) cc_final: 0.8224 (m-80)
REVERT: A  163 PHE cc_start: 0.7841 (t80) cc_final: 0.7580 (t80)
REVERT: A  190 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8568 (mtmm)
REVERT: A  283 GLN cc_start: 0.8628 (tp-100) cc_final: 0.8396 (tp40)
REVERT: A  410 GLU cc_start: 0.6703 (tm-30) cc_final: 0.6331 (mt-10)
REVERT: A  813 TRP cc_start: 0.7155 (t60) cc_final: 0.6646 (t60)
REVERT: B  153 THR cc_start: 0.9377 (p) cc_final: 0.9168 (p)
REVERT: B  219 GLN cc_start: 0.8100 (mp10) cc_final: 0.7898 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.2094
  time to fit residues: 56.4484
Evaluate side-chains
  140 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   chunk 45 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 54 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 232 GLN
A 375 GLN
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 876 GLN
** B 225 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 = 0.4479 r_free = 0.4479 target = 0.137405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.106605 restraints weight = 26438.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.106375 restraints weight = 15989.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.107627 restraints weight = 13033.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8709  Z= 0.278
  Angle     :  0.720   9.631  11786  Z= 0.379
  Chirality :  0.046   0.193   1413
  Planarity :  0.005   0.067   1484
  Dihedral  :  5.029  19.979   1133
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.39 %
    Favored  : 95.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.24), residues: 1057
  helix:  0.28 (0.18), residues: 730
  sheet: -1.23 (0.72), residues: 47
  loop : -0.59 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 813 
 HIS   0.003   0.001   HIS B 179 
 PHE   0.026   0.002   PHE A 249 
 TYR   0.021   0.002   TYR A 135 
 ARG   0.006   0.001   ARG A  62 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 200
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.9571 (tt) cc_final: 0.9226 (tt)
REVERT: A  135 TYR cc_start: 0.8574 (m-80) cc_final: 0.8272 (m-80)
REVERT: A  163 PHE cc_start: 0.7672 (t80) cc_final: 0.7450 (t80)
REVERT: A  200 CYS cc_start: 0.8355 (t) cc_final: 0.8011 (t)
REVERT: A  255 GLU cc_start: 0.8184 (pp20) cc_final: 0.7882 (pp20)
REVERT: A  283 GLN cc_start: 0.8778 (tp-100) cc_final: 0.8548 (tp40)
REVERT: A  601 CYS cc_start: 0.7234 (m) cc_final: 0.6889 (m)
REVERT: A  766 LYS cc_start: 0.6567 (mmtm) cc_final: 0.6309 (mmmt)
REVERT: A  825 ARG cc_start: 0.8461 (mtt180) cc_final: 0.8224 (mtt180)
REVERT: A  886 LEU cc_start: 0.8568 (pp) cc_final: 0.8346 (pp)
REVERT: A  887 PHE cc_start: 0.6910 (m-80) cc_final: 0.6699 (m-80)
REVERT: B  197 MET cc_start: 0.4403 (tmm) cc_final: 0.4077 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 201
  average time/residue: 0.2131
  time to fit residues: 58.8839
Evaluate side-chains
  140 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 103 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9990
   chunk 30 optimal weight:    8.9990
   chunk 95 optimal weight:    0.7980
   chunk 88 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   chunk 81 optimal weight:   10.0000
   chunk 45 optimal weight:   10.0000
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 343 GLN
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 967 GLN
B 225 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.138356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.108141 restraints weight = 26316.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.108370 restraints weight = 15238.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.109926 restraints weight = 11150.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.4030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8709  Z= 0.232
  Angle     :  0.653   8.683  11786  Z= 0.337
  Chirality :  0.044   0.179   1413
  Planarity :  0.004   0.055   1484
  Dihedral  :  4.737  19.040   1133
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  3.27 %
    Favored  : 96.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.25), residues: 1057
  helix:  0.62 (0.18), residues: 738
  sheet: -0.94 (0.71), residues: 47
  loop : -0.40 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 127 
 HIS   0.002   0.001   HIS A 308 
 PHE   0.022   0.002   PHE A 177 
 TYR   0.014   0.001   TYR A 154 
 ARG   0.005   0.001   ARG B 137 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 202
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 LEU cc_start: 0.8872 (mt) cc_final: 0.8535 (mt)
REVERT: A  135 TYR cc_start: 0.8566 (m-80) cc_final: 0.8218 (m-80)
REVERT: A  200 CYS cc_start: 0.8444 (t) cc_final: 0.8235 (t)
REVERT: A  255 GLU cc_start: 0.7984 (pp20) cc_final: 0.7674 (pp20)
REVERT: A  283 GLN cc_start: 0.8788 (tp-100) cc_final: 0.8562 (tp40)
REVERT: A  554 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7494 (tm-30)
REVERT: A  604 LYS cc_start: 0.8595 (mtpt) cc_final: 0.7968 (ttmm)
REVERT: A  886 LEU cc_start: 0.8632 (pp) cc_final: 0.8422 (pp)
REVERT: A  887 PHE cc_start: 0.6997 (m-80) cc_final: 0.6739 (m-80)
REVERT: B   84 THR cc_start: 0.9108 (p) cc_final: 0.8872 (t)
REVERT: B  137 ARG cc_start: 0.9005 (mtm-85) cc_final: 0.8111 (mtm-85)
  outliers start: 3
  outliers final: 0
  residues processed: 204
  average time/residue: 0.2170
  time to fit residues: 60.1848
Evaluate side-chains
  148 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 102 optimal weight:   30.0000
   chunk 11 optimal weight:    6.9990
   chunk 66 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0870
   overall best weight:    1.1362

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 ASN
A 490 ASN
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 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 = 0.4490 r_free = 0.4490 target = 0.138857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.109605 restraints weight = 26559.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.110818 restraints weight = 14403.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.111640 restraints weight = 11263.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.4059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8709  Z= 0.215
  Angle     :  0.636   9.472  11786  Z= 0.328
  Chirality :  0.043   0.174   1413
  Planarity :  0.004   0.055   1484
  Dihedral  :  4.627  20.088   1133
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  3.47 %
    Favored  : 96.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.25), residues: 1057
  helix:  0.73 (0.18), residues: 737
  sheet: -1.19 (0.64), residues: 53
  loop : -0.45 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 308 
 PHE   0.021   0.002   PHE A 249 
 TYR   0.013   0.001   TYR A 154 
 ARG   0.005   0.001   ARG A 465 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 201
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 LEU cc_start: 0.8849 (mt) cc_final: 0.8559 (mt)
REVERT: A  135 TYR cc_start: 0.8630 (m-80) cc_final: 0.8228 (m-80)
REVERT: A  163 PHE cc_start: 0.7634 (t80) cc_final: 0.7248 (t80)
REVERT: A  200 CYS cc_start: 0.8494 (t) cc_final: 0.8127 (t)
REVERT: A  255 GLU cc_start: 0.7943 (pp20) cc_final: 0.7554 (pp20)
REVERT: A  262 ASN cc_start: 0.7689 (OUTLIER) cc_final: 0.7216 (m110)
REVERT: A  290 HIS cc_start: 0.8345 (m-70) cc_final: 0.8030 (m-70)
REVERT: A  356 PHE cc_start: 0.7782 (p90) cc_final: 0.7551 (p90)
REVERT: A  554 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7538 (tm-30)
REVERT: A  604 LYS cc_start: 0.8623 (mtpt) cc_final: 0.8178 (mtpp)
REVERT: A  766 LYS cc_start: 0.7021 (mmmt) cc_final: 0.6645 (mmtm)
REVERT: A  825 ARG cc_start: 0.8536 (mtt180) cc_final: 0.7966 (mtt180)
REVERT: A  887 PHE cc_start: 0.6780 (m-80) cc_final: 0.6553 (m-80)
REVERT: B   84 THR cc_start: 0.9114 (p) cc_final: 0.8717 (t)
REVERT: B  137 ARG cc_start: 0.9019 (mtm-85) cc_final: 0.7833 (mtm-85)
  outliers start: 3
  outliers final: 0
  residues processed: 203
  average time/residue: 0.2512
  time to fit residues: 70.9870
Evaluate side-chains
  155 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 104 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 105 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 89 optimal weight:    7.9990
   chunk 29 optimal weight:    0.6980
   chunk 106 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0070
   chunk 25 optimal weight:    9.9990
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 568 HIS
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 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 = 0.4506 r_free = 0.4506 target = 0.140104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.109902 restraints weight = 26355.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.110140 restraints weight = 14516.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.111444 restraints weight = 10764.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.3454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8709  Z= 0.187
  Angle     :  0.618  10.282  11786  Z= 0.317
  Chirality :  0.045   0.596   1413
  Planarity :  0.004   0.062   1484
  Dihedral  :  4.511  18.409   1133
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.25), residues: 1057
  helix:  0.83 (0.19), residues: 735
  sheet: -1.28 (0.63), residues: 58
  loop : -0.77 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 985 
 PHE   0.026   0.002   PHE A 177 
 TYR   0.011   0.001   TYR A 154 
 ARG   0.011   0.001   ARG B 107 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 LEU cc_start: 0.8833 (mt) cc_final: 0.8568 (mt)
REVERT: A  135 TYR cc_start: 0.8660 (m-10) cc_final: 0.8305 (m-80)
REVERT: A  163 PHE cc_start: 0.7582 (t80) cc_final: 0.7166 (t80)
REVERT: A  200 CYS cc_start: 0.8483 (t) cc_final: 0.8030 (t)
REVERT: A  255 GLU cc_start: 0.7792 (pp20) cc_final: 0.7559 (pp20)
REVERT: A  290 HIS cc_start: 0.8361 (m-70) cc_final: 0.8082 (m-70)
REVERT: A  379 PHE cc_start: 0.8633 (t80) cc_final: 0.8366 (t80)
REVERT: A  554 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7437 (tm-30)
REVERT: A  766 LYS cc_start: 0.6962 (mmmt) cc_final: 0.6499 (mmmm)
REVERT: A  815 GLU cc_start: 0.8565 (mp0) cc_final: 0.8215 (mp0)
REVERT: A  825 ARG cc_start: 0.8532 (mtt180) cc_final: 0.8235 (mtt180)
REVERT: A  886 LEU cc_start: 0.8563 (pp) cc_final: 0.8357 (pp)
REVERT: A  887 PHE cc_start: 0.6984 (m-80) cc_final: 0.6736 (m-80)
REVERT: B   84 THR cc_start: 0.9033 (p) cc_final: 0.8701 (t)
REVERT: B  137 ARG cc_start: 0.8894 (mtm-85) cc_final: 0.7914 (mtm-85)
REVERT: B  219 GLN cc_start: 0.8172 (mp10) cc_final: 0.7969 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.2193
  time to fit residues: 62.3201
Evaluate side-chains
  151 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 103 optimal weight:   10.0000
   chunk 54 optimal weight:    0.0370
   chunk 84 optimal weight:    4.9990
   chunk 80 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 12 optimal weight:   10.0000
   chunk 6 optimal weight:   20.0000
   chunk 5 optimal weight:    9.9990
   overall best weight:    3.8066

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 262 ASN
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 733 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.134478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.105947 restraints weight = 26576.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.105259 restraints weight = 16754.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.106189 restraints weight = 15816.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.3492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   8709  Z= 0.364
  Angle     :  0.726   8.664  11786  Z= 0.381
  Chirality :  0.047   0.455   1413
  Planarity :  0.005   0.074   1484
  Dihedral  :  4.897  20.878   1133
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 20.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.65 %
    Favored  : 97.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.25), residues: 1057
  helix:  0.40 (0.18), residues: 734
  sheet: -1.79 (0.58), residues: 60
  loop : -0.43 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 352 
 HIS   0.004   0.001   HIS A 308 
 PHE   0.024   0.003   PHE A 582 
 TYR   0.028   0.002   TYR B 139 
 ARG   0.005   0.001   ARG A 720 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 ILE cc_start: 0.8791 (mt) cc_final: 0.8562 (mt)
REVERT: A  135 TYR cc_start: 0.8581 (m-10) cc_final: 0.8222 (m-80)
REVERT: A  163 PHE cc_start: 0.7598 (t80) cc_final: 0.7183 (t80)
REVERT: A  200 CYS cc_start: 0.8424 (t) cc_final: 0.8082 (t)
REVERT: A  554 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7536 (tm-30)
REVERT: A  601 CYS cc_start: 0.7728 (m) cc_final: 0.7443 (m)
REVERT: A  719 GLU cc_start: 0.7991 (pp20) cc_final: 0.7721 (pp20)
REVERT: A  766 LYS cc_start: 0.7061 (mmmt) cc_final: 0.6799 (mmmm)
REVERT: A  825 ARG cc_start: 0.8438 (mtt180) cc_final: 0.8068 (mtt180)
REVERT: B  137 ARG cc_start: 0.9177 (mtm-85) cc_final: 0.8953 (mtm-85)
REVERT: B  219 GLN cc_start: 0.8161 (mp10) cc_final: 0.7893 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 176
  average time/residue: 0.2122
  time to fit residues: 51.3586
Evaluate side-chains
  140 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 101 optimal weight:   20.0000
   chunk 23 optimal weight:    6.9990
   chunk 73 optimal weight:    8.9990
   chunk 80 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 90 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 19 optimal weight:    8.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.137625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.106708 restraints weight = 26376.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.107637 restraints weight = 15558.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.108803 restraints weight = 11136.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.3752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8709  Z= 0.218
  Angle     :  0.642   8.398  11786  Z= 0.331
  Chirality :  0.045   0.468   1413
  Planarity :  0.004   0.053   1484
  Dihedral  :  4.652  20.634   1133
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 16.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.26), residues: 1057
  helix:  0.67 (0.19), residues: 733
  sheet: -1.40 (0.65), residues: 49
  loop : -0.64 (0.38), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 127 
 HIS   0.005   0.001   HIS A 290 
 PHE   0.025   0.002   PHE A 249 
 TYR   0.015   0.001   TYR A 370 
 ARG   0.009   0.001   ARG B 107 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 TYR cc_start: 0.8648 (m-10) cc_final: 0.8271 (m-80)
REVERT: A  163 PHE cc_start: 0.7509 (t80) cc_final: 0.7057 (t80)
REVERT: A  200 CYS cc_start: 0.8459 (t) cc_final: 0.8064 (t)
REVERT: A  255 GLU cc_start: 0.7813 (pp20) cc_final: 0.7286 (pp20)
REVERT: A  290 HIS cc_start: 0.8364 (m-70) cc_final: 0.8052 (m90)
REVERT: A  378 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8513 (tm-30)
REVERT: A  379 PHE cc_start: 0.8608 (t80) cc_final: 0.8265 (t80)
REVERT: A  554 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7416 (tm-30)
REVERT: A  601 CYS cc_start: 0.7472 (m) cc_final: 0.7157 (m)
REVERT: A  719 GLU cc_start: 0.8007 (pp20) cc_final: 0.7727 (pp20)
REVERT: A  766 LYS cc_start: 0.7049 (mmmt) cc_final: 0.6806 (mmmm)
REVERT: A  825 ARG cc_start: 0.8465 (mtt180) cc_final: 0.8072 (mtt180)
REVERT: B   84 THR cc_start: 0.9032 (p) cc_final: 0.8583 (t)
REVERT: B  197 MET cc_start: 0.4165 (tmm) cc_final: 0.3892 (tmm)
REVERT: B  219 GLN cc_start: 0.8095 (mp10) cc_final: 0.7887 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.2201
  time to fit residues: 56.0281
Evaluate side-chains
  150 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    7.9990
   chunk 69 optimal weight:    1.9990
   chunk 102 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   chunk 105 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 181 ASN
** A 575 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 = 0.4497 r_free = 0.4497 target = 0.139464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.107228 restraints weight = 26864.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.107536 restraints weight = 16887.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.108727 restraints weight = 11680.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.4045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8709  Z= 0.200
  Angle     :  0.629   8.147  11786  Z= 0.325
  Chirality :  0.044   0.417   1413
  Planarity :  0.004   0.053   1484
  Dihedral  :  4.527  20.740   1133
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.25), residues: 1057
  helix:  0.77 (0.19), residues: 736
  sheet: -1.17 (0.66), residues: 52
  loop : -0.85 (0.37), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 127 
 HIS   0.004   0.001   HIS A 290 
 PHE   0.025   0.002   PHE A 249 
 TYR   0.010   0.001   TYR A 370 
 ARG   0.009   0.001   ARG A 755 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.9041 (ptpt) cc_final: 0.8755 (ptmt)
REVERT: A  135 TYR cc_start: 0.8770 (m-10) cc_final: 0.8440 (m-80)
REVERT: A  255 GLU cc_start: 0.7807 (pp20) cc_final: 0.7363 (pp20)
REVERT: A  290 HIS cc_start: 0.8445 (m-70) cc_final: 0.8106 (m90)
REVERT: A  378 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8475 (tm-30)
REVERT: A  379 PHE cc_start: 0.8596 (t80) cc_final: 0.8323 (t80)
REVERT: A  554 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7464 (tm-30)
REVERT: A  601 CYS cc_start: 0.7391 (m) cc_final: 0.7185 (m)
REVERT: A  719 GLU cc_start: 0.8126 (pp20) cc_final: 0.7784 (pp20)
REVERT: A  766 LYS cc_start: 0.7035 (mmmt) cc_final: 0.6816 (mmmm)
REVERT: A  825 ARG cc_start: 0.8544 (mtt180) cc_final: 0.7844 (mtt180)
REVERT: A  934 ASP cc_start: 0.8030 (p0) cc_final: 0.7813 (p0)
REVERT: B   84 THR cc_start: 0.9032 (p) cc_final: 0.8651 (t)
REVERT: B  137 ARG cc_start: 0.8826 (mtm-85) cc_final: 0.7563 (mtm-85)
REVERT: B  197 MET cc_start: 0.3946 (tmm) cc_final: 0.3674 (tmm)
REVERT: B  219 GLN cc_start: 0.8075 (mp10) cc_final: 0.7779 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 197
  average time/residue: 0.2065
  time to fit residues: 56.0545
Evaluate side-chains
  153 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 65 optimal weight:    7.9990
   chunk 30 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 75 optimal weight:    4.9990
   chunk 88 optimal weight:   10.0000
   chunk 55 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0970
   chunk 6 optimal weight:   10.0000
   chunk 102 optimal weight:    6.9990
   overall best weight:    3.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 290 HIS
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 632 ASN
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.135005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.106496 restraints weight = 26726.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.105832 restraints weight = 16991.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.106493 restraints weight = 16142.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   8709  Z= 0.347
  Angle     :  0.724   7.965  11786  Z= 0.379
  Chirality :  0.047   0.399   1413
  Planarity :  0.005   0.070   1484
  Dihedral  :  4.818  21.259   1133
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 20.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.25), residues: 1057
  helix:  0.42 (0.19), residues: 734
  sheet: -1.92 (0.58), residues: 59
  loop : -0.86 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 127 
 HIS   0.003   0.001   HIS A 308 
 PHE   0.025   0.003   PHE A 177 
 TYR   0.024   0.002   TYR B 139 
 ARG   0.005   0.001   ARG B 105 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 TYR cc_start: 0.8560 (m-10) cc_final: 0.8188 (m-80)
REVERT: A  163 PHE cc_start: 0.7423 (t80) cc_final: 0.6895 (t80)
REVERT: A  255 GLU cc_start: 0.8116 (pp20) cc_final: 0.7527 (pp20)
REVERT: A  290 HIS cc_start: 0.8203 (m90) cc_final: 0.7993 (m-70)
REVERT: A  370 TYR cc_start: 0.7969 (t80) cc_final: 0.7627 (t80)
REVERT: A  554 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7471 (tm-30)
REVERT: A  601 CYS cc_start: 0.7664 (m) cc_final: 0.7315 (m)
REVERT: A  766 LYS cc_start: 0.7075 (mmmt) cc_final: 0.6862 (mmmm)
REVERT: A  825 ARG cc_start: 0.8440 (mtt180) cc_final: 0.8064 (mtt180)
REVERT: B   84 THR cc_start: 0.9098 (p) cc_final: 0.8884 (p)
REVERT: B  197 MET cc_start: 0.4045 (tmm) cc_final: 0.3710 (tmm)
REVERT: B  219 GLN cc_start: 0.8118 (mp10) cc_final: 0.7887 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.2118
  time to fit residues: 50.7255
Evaluate side-chains
  137 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 79 optimal weight:   10.0000
   chunk 93 optimal weight:    0.4980
   chunk 78 optimal weight:    8.9990
   chunk 23 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 829 ASN
** B 225 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 = 0.4485 r_free = 0.4485 target = 0.138636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.107930 restraints weight = 25866.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.108758 restraints weight = 14129.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.109543 restraints weight = 11112.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.4011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.4238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8709  Z= 0.214
  Angle     :  0.673   9.429  11786  Z= 0.350
  Chirality :  0.044   0.188   1413
  Planarity :  0.004   0.052   1484
  Dihedral  :  4.646  20.551   1133
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 18.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.26), residues: 1057
  helix:  0.66 (0.19), residues: 732
  sheet: -1.55 (0.62), residues: 57
  loop : -0.83 (0.38), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 127 
 HIS   0.003   0.001   HIS A 579 
 PHE   0.033   0.002   PHE A 177 
 TYR   0.018   0.002   TYR A 370 
 ARG   0.010   0.001   ARG A 755 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 TYR cc_start: 0.8654 (m-10) cc_final: 0.8309 (m-80)
REVERT: A  163 PHE cc_start: 0.7443 (t80) cc_final: 0.7000 (t80)
REVERT: A  200 CYS cc_start: 0.8520 (t) cc_final: 0.8272 (t)
REVERT: A  290 HIS cc_start: 0.8283 (m90) cc_final: 0.8043 (m90)
REVERT: A  554 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7429 (tm-30)
REVERT: A  601 CYS cc_start: 0.7557 (m) cc_final: 0.7216 (m)
REVERT: A  719 GLU cc_start: 0.8070 (pp20) cc_final: 0.7763 (pp20)
REVERT: A  766 LYS cc_start: 0.7113 (mmmt) cc_final: 0.6884 (mmmm)
REVERT: A  825 ARG cc_start: 0.8533 (mtt180) cc_final: 0.8173 (mtt180)
REVERT: B  197 MET cc_start: 0.3933 (tmm) cc_final: 0.3650 (tmm)
REVERT: B  219 GLN cc_start: 0.8090 (mp10) cc_final: 0.7827 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.2191
  time to fit residues: 54.1467
Evaluate side-chains
  147 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 93 optimal weight:    0.4980
   chunk 40 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0980
   chunk 87 optimal weight:    5.9990
   chunk 98 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9980
   chunk 86 optimal weight:    8.9990
   chunk 96 optimal weight:    0.9980
   chunk 102 optimal weight:    2.9990
   chunk 99 optimal weight:    0.5980
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 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 = 0.4501 r_free = 0.4501 target = 0.140340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.108641 restraints weight = 25986.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.109403 restraints weight = 14589.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.110305 restraints weight = 11853.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.4511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8709  Z= 0.199
  Angle     :  0.656   9.889  11786  Z= 0.337
  Chirality :  0.044   0.355   1413
  Planarity :  0.004   0.052   1484
  Dihedral  :  4.473  20.096   1133
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 15.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.26), residues: 1057
  helix:  0.78 (0.19), residues: 733
  sheet: -0.83 (0.70), residues: 44
  loop : -0.78 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 127 
 HIS   0.005   0.001   HIS A 207 
 PHE   0.033   0.002   PHE A 177 
 TYR   0.012   0.001   TYR A 697 
 ARG   0.010   0.001   ARG A 755 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3010.43 seconds
wall clock time: 54 minutes 52.98 seconds (3292.98 seconds total)