Starting phenix.real_space_refine
on Fri Aug 22 23:20:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h5b_34490/08_2025/8h5b_34490.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h5b_34490/08_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_34490/08_2025/8h5b_34490.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h5b_34490/08_2025/8h5b_34490.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h5b_34490/08_2025/8h5b_34490.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h5b_34490/08_2025/8h5b_34490.cif"
  }
  resolution = 4.03
  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=   0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.16, per 1000 atoms: 0.25
  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: 0.91
  Conformation dependent library (CDL) restraints added in 315.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.30
  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: 1.38

  Time building geometry restraints manager: 1.15 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:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.680
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.380
-------------------------------------------------------------------------------
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= 0.203
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.67 (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
 ARG   0.019   0.002   ARG B 107 
 TYR   0.020   0.002   TYR A 614 
 PHE   0.028   0.002   PHE A 177 
 TRP   0.015   0.002   TRP A 813 
 HIS   0.005   0.001   HIS A 579 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 8709)
  covalent geometry    : angle       0.73560 (11786)
  hydrogen bonds       : bond        0.17208 (  542)
  hydrogen bonds       : angle       7.28170 ( 1611)

*********************** 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  : 0.344 
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: 0.7578 (t80)
REVERT: A  190 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8567 (mtmm)
REVERT: A  283 GLN cc_start: 0.8628 (tp-100) cc_final: 0.8397 (tp40)
REVERT: A  410 GLU cc_start: 0.6703 (tm-30) cc_final: 0.6332 (mt-10)
REVERT: A  719 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8330 (tm-30)
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: 0.9167 (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: 0.0885
  time to fit residues: 24.1545
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  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:   20.0000
   chunk 106 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.138442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.108402 restraints weight = 26201.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.108603 restraints weight = 15477.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.110038 restraints weight = 11752.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.110069 restraints weight = 9566.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.110211 restraints weight = 9481.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
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      :  0.004   0.043   8709  Z= 0.174
  Angle     :  0.707   9.746  11786  Z= 0.372
  Chirality :  0.046   0.204   1413
  Planarity :  0.005   0.066   1484
  Dihedral  :  4.951  20.071   1133
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  3.88 %
    Favored  : 95.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.25), residues: 1057
  helix:  0.40 (0.18), residues: 733
  sheet: -0.71 (0.85), residues: 37
  loop : -0.46 (0.36), residues: 287

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 8709)
  covalent geometry    : angle       0.70701 (11786)
  hydrogen bonds       : bond        0.05366 (  542)
  hydrogen bonds       : angle       5.31500 ( 1611)

*********************** 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
  210 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 208
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 LEU cc_start: 0.9201 (mt) cc_final: 0.8938 (pp)
REVERT: A  130 LEU cc_start: 0.9543 (tt) cc_final: 0.9210 (tt)
REVERT: A  135 TYR cc_start: 0.8504 (m-80) cc_final: 0.8194 (m-80)
REVERT: A  163 PHE cc_start: 0.7453 (t80) cc_final: 0.7142 (t80)
REVERT: A  200 CYS cc_start: 0.8318 (t) cc_final: 0.7948 (t)
REVERT: A  283 GLN cc_start: 0.8794 (tp-100) cc_final: 0.8576 (tp40)
REVERT: A  588 ASP cc_start: 0.6809 (t0) cc_final: 0.6248 (t0)
REVERT: A  601 CYS cc_start: 0.7232 (m) cc_final: 0.7008 (m)
REVERT: A  825 ARG cc_start: 0.8429 (mtt180) cc_final: 0.8198 (mtt180)
REVERT: A  886 LEU cc_start: 0.8579 (pp) cc_final: 0.8379 (pp)
REVERT: A  887 PHE cc_start: 0.6817 (m-80) cc_final: 0.6598 (m-80)
REVERT: B   98 ARG cc_start: 0.6293 (ptm160) cc_final: 0.5904 (ptm160)
REVERT: B  137 ARG cc_start: 0.8886 (mtp180) cc_final: 0.8028 (mtm-85)
  outliers start: 2
  outliers final: 0
  residues processed: 210
  average time/residue: 0.0995
  time to fit residues: 28.8110
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  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 54 optimal weight:    0.0050
   chunk 96 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 83 optimal weight:    9.9990
   chunk 94 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 343 GLN
** 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 = 0.4503 r_free = 0.4503 target = 0.139623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.109193 restraints weight = 26064.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.109842 restraints weight = 15265.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.111269 restraints weight = 11031.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.111369 restraints weight = 8938.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.111457 restraints weight = 8674.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.4048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8709  Z= 0.148
  Angle     :  0.645   8.814  11786  Z= 0.335
  Chirality :  0.043   0.176   1413
  Planarity :  0.004   0.053   1484
  Dihedral  :  4.687  23.291   1133
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  3.27 %
    Favored  : 96.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.25), residues: 1057
  helix:  0.71 (0.18), residues: 735
  sheet: -1.58 (0.62), residues: 58
  loop : -0.51 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 570 
 TYR   0.013   0.001   TYR A 154 
 PHE   0.025   0.002   PHE A 177 
 TRP   0.022   0.002   TRP A 127 
 HIS   0.002   0.001   HIS A 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8709)
  covalent geometry    : angle       0.64507 (11786)
  hydrogen bonds       : bond        0.04711 (  542)
  hydrogen bonds       : angle       5.00064 ( 1611)

*********************** 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
  210 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 208
  time to evaluate  : 0.337 
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   40 LEU cc_start: 0.9230 (mt) cc_final: 0.8972 (pp)
REVERT: A  131 LEU cc_start: 0.8830 (mt) cc_final: 0.8546 (mt)
REVERT: A  135 TYR cc_start: 0.8579 (m-80) cc_final: 0.8230 (m-80)
REVERT: A  255 GLU cc_start: 0.7921 (pp20) cc_final: 0.7597 (pp20)
REVERT: A  554 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7385 (tm-30)
REVERT: A  766 LYS cc_start: 0.6986 (mmmt) cc_final: 0.6600 (mmtm)
REVERT: A  887 PHE cc_start: 0.6940 (m-80) cc_final: 0.6642 (m-80)
REVERT: B  137 ARG cc_start: 0.8878 (mtp180) cc_final: 0.7912 (mtm-85)
  outliers start: 2
  outliers final: 0
  residues processed: 208
  average time/residue: 0.1034
  time to fit residues: 29.2184
Evaluate side-chains
  146 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 102 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 84 optimal weight:    8.9990
   chunk 72 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 43 optimal weight:    0.2980
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 490 ASN
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 967 GLN
B 225 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.139321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.109380 restraints weight = 26942.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.109927 restraints weight = 15743.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.110918 restraints weight = 11772.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.110925 restraints weight = 10054.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.111035 restraints weight = 9567.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.3253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8709  Z= 0.139
  Angle     :  0.622   9.037  11786  Z= 0.321
  Chirality :  0.043   0.160   1413
  Planarity :  0.004   0.054   1484
  Dihedral  :  4.601  20.420   1133
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  3.67 %
    Favored  : 96.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.25), residues: 1057
  helix:  0.80 (0.19), residues: 733
  sheet: -1.33 (0.64), residues: 55
  loop : -0.46 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  90 
 TYR   0.013   0.001   TYR A 154 
 PHE   0.023   0.002   PHE A 249 
 TRP   0.013   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8709)
  covalent geometry    : angle       0.62209 (11786)
  hydrogen bonds       : bond        0.04219 (  542)
  hydrogen bonds       : angle       4.84527 ( 1611)

*********************** 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  : 0.344 
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: symmetry clash
   revert: symmetry clash
REVERT: A   40 LEU cc_start: 0.9283 (mt) cc_final: 0.9057 (pp)
REVERT: A  131 LEU cc_start: 0.8834 (mt) cc_final: 0.8375 (pp)
REVERT: A  135 TYR cc_start: 0.8688 (m-80) cc_final: 0.8028 (m-80)
REVERT: A  262 ASN cc_start: 0.7558 (OUTLIER) cc_final: 0.7105 (m110)
REVERT: A  290 HIS cc_start: 0.8420 (m-70) cc_final: 0.8129 (m-70)
REVERT: A  554 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7506 (tm-30)
REVERT: A  766 LYS cc_start: 0.6927 (mmmt) cc_final: 0.6495 (mmmm)
REVERT: A  815 GLU cc_start: 0.8615 (mp0) cc_final: 0.8326 (mp0)
REVERT: A  825 ARG cc_start: 0.8544 (mtt180) cc_final: 0.7974 (mtt180)
REVERT: A  886 LEU cc_start: 0.8613 (pp) cc_final: 0.8391 (pp)
REVERT: A  887 PHE cc_start: 0.7004 (m-80) cc_final: 0.6733 (m-80)
REVERT: B  137 ARG cc_start: 0.8994 (mtp180) cc_final: 0.8048 (mtm-85)
REVERT: B  219 GLN cc_start: 0.8202 (mp10) cc_final: 0.7985 (mp10)
  outliers start: 3
  outliers final: 0
  residues processed: 203
  average time/residue: 0.0988
  time to fit residues: 27.6026
Evaluate side-chains
  154 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 71 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 80 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.4487 r_free = 0.4487 target = 0.138695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.108824 restraints weight = 26501.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.109614 restraints weight = 15830.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.110796 restraints weight = 12199.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.110498 restraints weight = 9535.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.110881 restraints weight = 9900.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.3453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8709  Z= 0.154
  Angle     :  0.619   8.751  11786  Z= 0.320
  Chirality :  0.042   0.158   1413
  Planarity :  0.004   0.067   1484
  Dihedral  :  4.612  20.445   1133
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.96 %
    Favored  : 96.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.25), residues: 1057
  helix:  0.80 (0.19), residues: 728
  sheet: -1.35 (0.61), residues: 56
  loop : -0.69 (0.37), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 107 
 TYR   0.012   0.001   TYR A 154 
 PHE   0.023   0.002   PHE A 249 
 TRP   0.009   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8709)
  covalent geometry    : angle       0.61891 (11786)
  hydrogen bonds       : bond        0.04087 (  542)
  hydrogen bonds       : angle       4.80670 ( 1611)

*********************** 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
  200 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 199
  time to evaluate  : 0.366 
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: symmetry clash
REVERT: A   40 LEU cc_start: 0.9305 (mt) cc_final: 0.9090 (pp)
REVERT: A  131 LEU cc_start: 0.8826 (mt) cc_final: 0.8571 (mt)
REVERT: A  135 TYR cc_start: 0.8656 (m-10) cc_final: 0.8334 (m-80)
REVERT: A  163 PHE cc_start: 0.7393 (t80) cc_final: 0.6821 (t80)
REVERT: A  200 CYS cc_start: 0.8445 (t) cc_final: 0.8242 (t)
REVERT: A  255 GLU cc_start: 0.7774 (pp20) cc_final: 0.7310 (pp20)
REVERT: A  290 HIS cc_start: 0.8336 (m-70) cc_final: 0.8115 (m-70)
REVERT: A  356 PHE cc_start: 0.7805 (p90) cc_final: 0.7560 (p90)
REVERT: A  554 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7595 (tm-30)
REVERT: A  766 LYS cc_start: 0.6996 (mmmt) cc_final: 0.6732 (mmmm)
REVERT: A  825 ARG cc_start: 0.8525 (mtt180) cc_final: 0.8247 (mtt-85)
REVERT: A  887 PHE cc_start: 0.6947 (m-80) cc_final: 0.6714 (m-80)
REVERT: B   84 THR cc_start: 0.9010 (p) cc_final: 0.8687 (t)
REVERT: B  137 ARG cc_start: 0.9006 (mtp180) cc_final: 0.8031 (mtm-85)
REVERT: B  219 GLN cc_start: 0.8121 (mp10) cc_final: 0.7862 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 199
  average time/residue: 0.1027
  time to fit residues: 28.2180
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  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   chunk 49 optimal weight:    8.9990
   chunk 9 optimal weight:    5.9990
   chunk 97 optimal weight:    0.6980
   chunk 63 optimal weight:    0.1980
   chunk 95 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 15 optimal weight:    0.3980
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 733 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.140658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.109773 restraints weight = 26267.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.110198 restraints weight = 14988.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.111676 restraints weight = 10593.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.111576 restraints weight = 10078.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.111804 restraints weight = 9251.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.4050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.3835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8709  Z= 0.131
  Angle     :  0.609   7.641  11786  Z= 0.313
  Chirality :  0.042   0.158   1413
  Planarity :  0.004   0.052   1484
  Dihedral  :  4.488  18.917   1133
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.63 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.26), residues: 1057
  helix:  0.96 (0.19), residues: 731
  sheet: -1.29 (0.63), residues: 55
  loop : -0.69 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 107 
 TYR   0.011   0.001   TYR B 185 
 PHE   0.024   0.002   PHE A 249 
 TRP   0.006   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 985 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8709)
  covalent geometry    : angle       0.60891 (11786)
  hydrogen bonds       : bond        0.03920 (  542)
  hydrogen bonds       : angle       4.66053 ( 1611)

*********************** 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
  208 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 207
  time to evaluate  : 0.414 
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: symmetry clash
REVERT: A   93 VAL cc_start: 0.8883 (t) cc_final: 0.8522 (m)
REVERT: A  131 LEU cc_start: 0.8830 (mt) cc_final: 0.8579 (mt)
REVERT: A  135 TYR cc_start: 0.8681 (m-10) cc_final: 0.8343 (m-80)
REVERT: A  163 PHE cc_start: 0.7306 (t80) cc_final: 0.6778 (t80)
REVERT: A  200 CYS cc_start: 0.8484 (t) cc_final: 0.8250 (t)
REVERT: A  255 GLU cc_start: 0.7684 (pp20) cc_final: 0.7359 (pp20)
REVERT: A  262 ASN cc_start: 0.7582 (OUTLIER) cc_final: 0.7129 (m110)
REVERT: A  290 HIS cc_start: 0.8426 (m-70) cc_final: 0.8205 (m-70)
REVERT: A  554 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7475 (tm-30)
REVERT: A  601 CYS cc_start: 0.7259 (m) cc_final: 0.6977 (m)
REVERT: A  719 GLU cc_start: 0.7988 (pp20) cc_final: 0.7684 (pp20)
REVERT: A  766 LYS cc_start: 0.6969 (mmmt) cc_final: 0.6715 (mmmm)
REVERT: A  825 ARG cc_start: 0.8533 (mtt180) cc_final: 0.7816 (mtt180)
REVERT: A  934 ASP cc_start: 0.8044 (p0) cc_final: 0.7793 (p0)
REVERT: B   84 THR cc_start: 0.8995 (p) cc_final: 0.8672 (t)
REVERT: B  219 GLN cc_start: 0.8139 (mp10) cc_final: 0.7850 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 208
  average time/residue: 0.0963
  time to fit residues: 27.9678
Evaluate side-chains
  156 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 29 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0020
   chunk 81 optimal weight:   20.0000
   chunk 8 optimal weight:   10.0000
   chunk 91 optimal weight:    3.9990
   chunk 100 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.7190

-------------------------------------------------------------------------------
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 967 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.141034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.109425 restraints weight = 26613.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.110890 restraints weight = 14528.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.111921 restraints weight = 10290.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.112021 restraints weight = 8836.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.112115 restraints weight = 8492.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.4055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7323
moved from start:          0.4040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8709  Z= 0.137
  Angle     :  0.625   8.952  11786  Z= 0.321
  Chirality :  0.044   0.464   1413
  Planarity :  0.004   0.052   1484
  Dihedral  :  4.515  18.631   1133
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.26), residues: 1057
  helix:  0.94 (0.19), residues: 731
  sheet: -1.34 (0.61), residues: 62
  loop : -0.67 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 137 
 TYR   0.011   0.001   TYR A 697 
 PHE   0.024   0.001   PHE A 249 
 TRP   0.007   0.001   TRP A 813 
 HIS   0.002   0.000   HIS A 985 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8709)
  covalent geometry    : angle       0.62466 (11786)
  hydrogen bonds       : bond        0.03925 (  542)
  hydrogen bonds       : angle       4.69910 ( 1611)

*********************** 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
  194 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.353 
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: 0.8845 (mt) cc_final: 0.8588 (mt)
REVERT: A  135 TYR cc_start: 0.8747 (m-10) cc_final: 0.8420 (m-80)
REVERT: A  163 PHE cc_start: 0.7366 (t80) cc_final: 0.6859 (t80)
REVERT: A  200 CYS cc_start: 0.8537 (t) cc_final: 0.8309 (t)
REVERT: A  255 GLU cc_start: 0.7690 (pp20) cc_final: 0.7447 (pp20)
REVERT: A  554 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7429 (tm-30)
REVERT: A  601 CYS cc_start: 0.7385 (m) cc_final: 0.7181 (m)
REVERT: A  719 GLU cc_start: 0.8026 (pp20) cc_final: 0.7669 (pp20)
REVERT: A  766 LYS cc_start: 0.6950 (mmmt) cc_final: 0.6725 (mmmm)
REVERT: A  825 ARG cc_start: 0.8533 (mtt180) cc_final: 0.8145 (mtt180)
REVERT: A  934 ASP cc_start: 0.8057 (p0) cc_final: 0.7824 (p0)
REVERT: B   84 THR cc_start: 0.8963 (p) cc_final: 0.8710 (t)
REVERT: B  215 THR cc_start: 0.8372 (t) cc_final: 0.7957 (p)
REVERT: B  219 GLN cc_start: 0.8127 (mp10) cc_final: 0.7842 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.0990
  time to fit residues: 26.5780
Evaluate side-chains
  156 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 77 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 90 optimal weight:    0.5980
   chunk 105 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 101 optimal weight:   20.0000
   chunk 16 optimal weight:    8.9990
   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 262 ASN
A 357 ASN
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.140714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.109915 restraints weight = 26123.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.111280 restraints weight = 14554.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.112141 restraints weight = 11104.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.112188 restraints weight = 9243.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.112323 restraints weight = 8741.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.4212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8709  Z= 0.136
  Angle     :  0.620   7.628  11786  Z= 0.317
  Chirality :  0.044   0.532   1413
  Planarity :  0.004   0.052   1484
  Dihedral  :  4.481  18.725   1133
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.26), residues: 1057
  helix:  0.90 (0.19), residues: 731
  sheet: -1.26 (0.61), residues: 62
  loop : -0.71 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 755 
 TYR   0.016   0.001   TYR A 370 
 PHE   0.032   0.002   PHE A 177 
 TRP   0.007   0.001   TRP A 813 
 HIS   0.006   0.001   HIS A 290 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8709)
  covalent geometry    : angle       0.62009 (11786)
  hydrogen bonds       : bond        0.03836 (  542)
  hydrogen bonds       : angle       4.68525 ( 1611)

*********************** 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
  189 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.383 
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: symmetry clash
REVERT: A   93 VAL cc_start: 0.8923 (t) cc_final: 0.8672 (m)
REVERT: A  131 LEU cc_start: 0.8826 (mt) cc_final: 0.8516 (mt)
REVERT: A  135 TYR cc_start: 0.8703 (m-10) cc_final: 0.8370 (m-80)
REVERT: A  163 PHE cc_start: 0.7217 (t80) cc_final: 0.6657 (t80)
REVERT: A  200 CYS cc_start: 0.8495 (t) cc_final: 0.8275 (t)
REVERT: A  290 HIS cc_start: 0.8291 (m-70) cc_final: 0.7994 (m90)
REVERT: A  554 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7422 (tm-30)
REVERT: A  719 GLU cc_start: 0.8039 (pp20) cc_final: 0.7747 (pp20)
REVERT: A  766 LYS cc_start: 0.6984 (mmmt) cc_final: 0.6740 (mmmm)
REVERT: A  825 ARG cc_start: 0.8483 (mtt180) cc_final: 0.8088 (mtt180)
REVERT: A  934 ASP cc_start: 0.8097 (p0) cc_final: 0.7821 (p0)
REVERT: B  215 THR cc_start: 0.8398 (t) cc_final: 0.7960 (p)
REVERT: B  219 GLN cc_start: 0.8127 (mp10) cc_final: 0.7855 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.0990
  time to fit residues: 26.0155
Evaluate side-chains
  149 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 104 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 89 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   chunk 97 optimal weight:    0.5980
   chunk 3 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.140148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.108598 restraints weight = 26529.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.109288 restraints weight = 15138.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.110897 restraints weight = 10959.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.110967 restraints weight = 8712.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.111155 restraints weight = 8868.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.4260

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= 0.146
  Angle     :  0.630   7.308  11786  Z= 0.327
  Chirality :  0.043   0.393   1413
  Planarity :  0.004   0.052   1484
  Dihedral  :  4.453  18.602   1133
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.26), residues: 1057
  helix:  0.91 (0.19), residues: 730
  sheet: -1.31 (0.62), residues: 62
  loop : -0.62 (0.38), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 755 
 TYR   0.009   0.001   TYR A 370 
 PHE   0.031   0.002   PHE A 177 
 TRP   0.008   0.001   TRP A 813 
 HIS   0.005   0.001   HIS A 290 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8709)
  covalent geometry    : angle       0.62957 (11786)
  hydrogen bonds       : bond        0.03878 (  542)
  hydrogen bonds       : angle       4.70919 ( 1611)

*********************** 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
  194 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.9012 (ptpt) cc_final: 0.8722 (ptmt)
REVERT: A  131 LEU cc_start: 0.8845 (mt) cc_final: 0.8500 (mt)
REVERT: A  135 TYR cc_start: 0.8732 (m-10) cc_final: 0.8399 (m-80)
REVERT: A  163 PHE cc_start: 0.7284 (t80) cc_final: 0.6768 (t80)
REVERT: A  190 LYS cc_start: 0.8635 (ptpt) cc_final: 0.8432 (ptpp)
REVERT: A  200 CYS cc_start: 0.8524 (t) cc_final: 0.8301 (t)
REVERT: A  255 GLU cc_start: 0.7724 (pp20) cc_final: 0.7252 (pp20)
REVERT: A  554 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7393 (tm-30)
REVERT: A  719 GLU cc_start: 0.8047 (pp20) cc_final: 0.7772 (pp20)
REVERT: A  766 LYS cc_start: 0.7045 (mmmt) cc_final: 0.6823 (mmmm)
REVERT: A  825 ARG cc_start: 0.8501 (mtt180) cc_final: 0.8100 (mtt180)
REVERT: A  886 LEU cc_start: 0.8432 (pp) cc_final: 0.8228 (pp)
REVERT: A  934 ASP cc_start: 0.8071 (p0) cc_final: 0.7810 (p0)
REVERT: B  215 THR cc_start: 0.8386 (t) cc_final: 0.7965 (p)
REVERT: B  219 GLN cc_start: 0.8117 (mp10) cc_final: 0.7848 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.1001
  time to fit residues: 27.0650
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  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 37 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 85 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 39 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 65 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 575 GLN ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.140201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.108323 restraints weight = 25929.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.109727 restraints weight = 14622.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.110963 restraints weight = 10081.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.110937 restraints weight = 8720.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.111073 restraints weight = 8581.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.4401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8709  Z= 0.144
  Angle     :  0.647   9.829  11786  Z= 0.332
  Chirality :  0.043   0.177   1413
  Planarity :  0.004   0.052   1484
  Dihedral  :  4.480  18.473   1133
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.26), residues: 1057
  helix:  0.90 (0.19), residues: 732
  sheet: -1.04 (0.69), residues: 52
  loop : -0.61 (0.37), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 755 
 TYR   0.010   0.001   TYR A 254 
 PHE   0.026   0.002   PHE A 177 
 TRP   0.006   0.001   TRP A 813 
 HIS   0.004   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8709)
  covalent geometry    : angle       0.64679 (11786)
  hydrogen bonds       : bond        0.03925 (  542)
  hydrogen bonds       : angle       4.69939 ( 1611)

********************** 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
  187 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.9043 (ptpt) cc_final: 0.8745 (ptmt)
REVERT: A  135 TYR cc_start: 0.8767 (m-10) cc_final: 0.8434 (m-80)
REVERT: A  163 PHE cc_start: 0.7363 (t80) cc_final: 0.7040 (t80)
REVERT: A  190 LYS cc_start: 0.8653 (ptpt) cc_final: 0.8428 (ptpp)
REVERT: A  255 GLU cc_start: 0.7806 (pp20) cc_final: 0.7330 (pp20)
REVERT: A  554 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7543 (tm-30)
REVERT: A  719 GLU cc_start: 0.8113 (pp20) cc_final: 0.7833 (pp20)
REVERT: A  766 LYS cc_start: 0.7041 (mmmt) cc_final: 0.6804 (mmmm)
REVERT: A  825 ARG cc_start: 0.8523 (mtt180) cc_final: 0.8133 (mtt180)
REVERT: A  934 ASP cc_start: 0.8062 (p0) cc_final: 0.7753 (p0)
REVERT: B  137 ARG cc_start: 0.9017 (mtm-85) cc_final: 0.8016 (mtm-85)
REVERT: B  215 THR cc_start: 0.8343 (t) cc_final: 0.7955 (p)
REVERT: B  219 GLN cc_start: 0.8139 (mp10) cc_final: 0.7852 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.0976
  time to fit residues: 25.3223
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  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 41 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 76 optimal weight:    7.9990
   chunk 100 optimal weight:    8.9990
   chunk 45 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.140891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.108460 restraints weight = 26463.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.109221 restraints weight = 15475.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.110471 restraints weight = 11257.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.110741 restraints weight = 9458.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.110813 restraints weight = 9186.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.4586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8709  Z= 0.137
  Angle     :  0.626   9.546  11786  Z= 0.323
  Chirality :  0.043   0.364   1413
  Planarity :  0.004   0.051   1484
  Dihedral  :  4.402  17.660   1133
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 15.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.51 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.26), residues: 1057
  helix:  0.94 (0.19), residues: 730
  sheet: -0.92 (0.70), residues: 50
  loop : -0.81 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  62 
 TYR   0.008   0.001   TYR A 154 
 PHE   0.032   0.002   PHE A 794 
 TRP   0.007   0.001   TRP A 813 
 HIS   0.004   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8709)
  covalent geometry    : angle       0.62606 (11786)
  hydrogen bonds       : bond        0.03775 (  542)
  hydrogen bonds       : angle       4.66058 ( 1611)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1852.22 seconds
wall clock time: 32 minutes 48.45 seconds (1968.45 seconds total)