Starting phenix.real_space_refine
on Sat Dec 28 13:07:57 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h5b_34490/12_2024/8h5b_34490.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h5b_34490/12_2024/8h5b_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_34490/12_2024/8h5b_34490.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h5b_34490/12_2024/8h5b_34490.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h5b_34490/12_2024/8h5b_34490.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h5b_34490/12_2024/8h5b_34490.cif"
  }
  resolution = 4.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

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

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 8570
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 902, 7213
          Classifications: {'peptide': 902}
          Link IDs: {'PTRANS': 25, 'TRANS': 876}
          Chain breaks: 7
    Chain: "B"
      Number of atoms: 1357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 173, 1357
          Classifications: {'peptide': 173}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 164}
  Time building chain proxies: 6.05, per 1000 atoms: 0.71
  Number of scatterers: 8570
  At special positions: 0
  Unit cell: (108.73, 113.71, 101.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1630      8.00
     N    1389      7.00
     C    5514      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.74
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 1 sheets defined
      76.9% alpha, 3.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 11
    Processing helix  chain 'A' and resid 17 through 31
      removed outlier: 3.861A  pdb=" N   GLN A  24 " --> pdb=" O   VAL A  20 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LEU A  25 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   SER A  31 " --> pdb=" O   GLN A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 46
      removed outlier: 3.832A  pdb=" N   LYS A  38 " --> pdb=" O   SER A  34 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ALA A  44 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 69
      removed outlier: 4.168A  pdb=" N   LYS A  63 " --> pdb=" O   LEU A  59 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   MET A  67 " --> pdb=" O   LYS A  63 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   TYR A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 100
      removed outlier: 3.791A  pdb=" N   LYS A  96 " --> pdb=" O   GLU A  92 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 127
      removed outlier: 3.559A  pdb=" N   CYS A 114 " --> pdb=" O   GLY A 110 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL A 121 " --> pdb=" O   GLN A 117 " (cutoff:3.500A)
      Proline residue:  A 124  - end of helix
    Processing helix  chain 'A' and resid 129 through 141
    Processing helix  chain 'A' and resid 143 through 158
      removed outlier: 4.137A  pdb=" N   ASP A 155 " --> pdb=" O   ASN A 151 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   ASP A 156 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 165
    Processing helix  chain 'A' and resid 167 through 182
      removed outlier: 3.512A  pdb=" N   ALA A 171 " --> pdb=" O   GLY A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 207
      removed outlier: 3.630A  pdb=" N   ALA A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   GLN A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   MET A 204 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   SER A 206 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   HIS A 207 " --> pdb=" O   GLN A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 236
      removed outlier: 3.698A  pdb=" N   GLN A 228 " --> pdb=" O   ALA A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 264
    Processing helix  chain 'A' and resid 265 through 269
    Processing helix  chain 'A' and resid 270 through 291
    Processing helix  chain 'A' and resid 303 through 321
      removed outlier: 3.552A  pdb=" N   ILE A 312 " --> pdb=" O   HIS A 308 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   TYR A 313 " --> pdb=" O   ASP A 309 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ILE A 314 " --> pdb=" O   CYS A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 342
      removed outlier: 4.153A  pdb=" N   ILE A 340 " --> pdb=" O   THR A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 355
    Processing helix  chain 'A' and resid 355 through 364
      removed outlier: 4.326A  pdb=" N   PHE A 359 " --> pdb=" O   ASP A 355 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER A 361 " --> pdb=" O   ASN A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 382
      removed outlier: 3.977A  pdb=" N   ASN A 377 " --> pdb=" O   ARG A 373 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   GLU A 378 " --> pdb=" O   ASP A 374 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   THR A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   SER A 382 " --> pdb=" O   GLU A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 403
      removed outlier: 3.665A  pdb=" N   GLU A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 422
      removed outlier: 3.758A  pdb=" N   LEU A 409 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ASN A 422 " --> pdb=" O   CYS A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 448
      removed outlier: 4.318A  pdb=" N   GLN A 433 " --> pdb=" O   GLU A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 470
      Proline residue:  A 464  - end of helix
    Processing helix  chain 'A' and resid 476 through 494
      removed outlier: 3.617A  pdb=" N   SER A 482 " --> pdb=" O   LYS A 478 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LYS A 494 " --> pdb=" O   ASN A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 515
      removed outlier: 4.620A  pdb=" N   ILE A 506 " --> pdb=" O   SER A 502 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   TYR A 510 " --> pdb=" O   ILE A 506 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   PHE A 514 " --> pdb=" O   TYR A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 521
    Processing helix  chain 'A' and resid 522 through 542
    Processing helix  chain 'A' and resid 548 through 561
    Processing helix  chain 'A' and resid 570 through 588
      removed outlier: 3.766A  pdb=" N   GLU A 587 " --> pdb=" O   THR A 583 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ASP A 588 " --> pdb=" O   ILE A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 606
      removed outlier: 3.713A  pdb=" N   VAL A 595 " --> pdb=" O   ASN A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 634
      removed outlier: 4.753A  pdb=" N   ASN A 616 " --> pdb=" O   ASP A 612 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TYR A 617 " --> pdb=" O   ASN A 613 " (cutoff:3.500A)
      Proline residue:  A 623  - end of helix
      removed outlier: 3.875A  pdb=" N   ALA A 634 " --> pdb=" O   ASP A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 656
    Processing helix  chain 'A' and resid 664 through 682
      removed outlier: 3.780A  pdb=" N   ASN A 668 " --> pdb=" O   PRO A 664 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   GLU A 673 " --> pdb=" O   GLN A 669 " (cutoff:3.500A)
      Proline residue:  A 674  - end of helix
    Processing helix  chain 'A' and resid 684 through 702
      removed outlier: 3.988A  pdb=" N   ALA A 694 " --> pdb=" O   LEU A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 706
      removed outlier: 3.555A  pdb=" N   ALA A 706 " --> pdb=" O   ASP A 703 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 703 through 706'
    Processing helix  chain 'A' and resid 707 through 722
      removed outlier: 4.483A  pdb=" N   MET A 712 " --> pdb=" O   GLU A 708 " (cutoff:3.500A)
      removed outlier: 4.927A  pdb=" N   ASP A 713 " --> pdb=" O   PRO A 709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 732
    Processing helix  chain 'A' and resid 733 through 745
      removed outlier: 4.749A  pdb=" N   LEU A 737 " --> pdb=" O   ASN A 733 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   PHE A 745 " --> pdb=" O   ILE A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 767
      removed outlier: 4.192A  pdb=" N   LEU A 752 " --> pdb=" O   GLU A 748 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   GLY A 754 " --> pdb=" O   GLN A 750 " (cutoff:3.500A)
      removed outlier: 4.833A  pdb=" N   ARG A 755 " --> pdb=" O   PRO A 751 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LYS A 766 " --> pdb=" O   VAL A 762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 787
      removed outlier: 4.080A  pdb=" N   LEU A 780 " --> pdb=" O   LEU A 776 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   CYS A 781 " --> pdb=" O   LEU A 777 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   PHE A 782 " --> pdb=" O   SER A 778 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LEU A 783 " --> pdb=" O   VAL A 779 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASP A 787 " --> pdb=" O   LEU A 783 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 798
      removed outlier: 4.234A  pdb=" N   THR A 791 " --> pdb=" O   ASP A 787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 820
      removed outlier: 4.467A  pdb=" N   LEU A 808 " --> pdb=" O   ASP A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 838
      removed outlier: 3.577A  pdb=" N   ILE A 826 " --> pdb=" O   GLY A 822 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   GLU A 828 " --> pdb=" O   LYS A 824 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   PHE A 838 " --> pdb=" O   SER A 834 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 846
    Processing helix  chain 'A' and resid 878 through 896
      removed outlier: 4.002A  pdb=" N   ILE A 884 " --> pdb=" O   TYR A 880 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   LYS A 885 " --> pdb=" O   THR A 881 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LYS A 896 " --> pdb=" O   SER A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 934 through 941
      removed outlier: 4.124A  pdb=" N   GLU A 938 " --> pdb=" O   ASP A 934 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP A 941 " --> pdb=" O   LYS A 937 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 964 through 978
      removed outlier: 3.554A  pdb=" N   LEU A 968 " --> pdb=" O   SER A 964 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   SER A 978 " --> pdb=" O   LYS A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 990
      removed outlier: 3.846A  pdb=" N   ILE A 987 " --> pdb=" O   GLY A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 995 through 1000
      removed outlier: 3.946A  pdb=" N   SER A1000 " --> pdb=" O   ARG A 996 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 89
    Processing helix  chain 'B' and resid 128 through 146
    Processing helix  chain 'B' and resid 171 through 180
      removed outlier: 3.940A  pdb=" N   LEU B 175 " --> pdb=" O   ARG B 171 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   HIS B 179 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 235
      removed outlier: 3.588A  pdb=" N   ILE B 223 " --> pdb=" O   GLN B 219 " (cutoff:3.500A)
      Proline residue:  B 232  - end of helix
    Processing sheet with id=AA1, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.563A  pdb=" N   VAL B 122 " --> pdb=" O   LEU B 114 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   VAL B 161 " --> pdb=" O   GLN B  68 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   ILE B  70 " --> pdb=" O   ASN B 159 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   ASN B 159 " --> pdb=" O   ILE B  70 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ALA B  72 " --> pdb=" O   ILE B 157 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   ILE B 157 " --> pdb=" O   ALA B  72 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ILE B 202 " --> pdb=" O   MET B 197 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   MET B 197 " --> pdb=" O   ILE B 202 " (cutoff:3.500A)

    542 hydrogen bonds defined for protein.
    1611 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.87

  Time building geometry restraints manager: 3.12 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:             4.120
  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:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     25.010
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.0000

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

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

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

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

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

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 TYR cc_start: 0.8496 (m-80) cc_final: 0.8224 (m-80)
REVERT: A  163 PHE cc_start: 0.7841 (t80) cc_final: 0.7580 (t80)
REVERT: A  190 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8568 (mtmm)
REVERT: A  283 GLN cc_start: 0.8628 (tp-100) cc_final: 0.8396 (tp40)
REVERT: A  410 GLU cc_start: 0.6703 (tm-30) cc_final: 0.6331 (mt-10)
REVERT: A  813 TRP cc_start: 0.7155 (t60) cc_final: 0.6646 (t60)
REVERT: B  153 THR cc_start: 0.9377 (p) cc_final: 0.9168 (p)
REVERT: B  219 GLN cc_start: 0.8100 (mp10) cc_final: 0.7898 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.2151
  time to fit residues: 57.9449
Evaluate side-chains
  140 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   chunk 45 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 54 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 232 GLN
A 375 GLN
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 876 GLN
** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.1876

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

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

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

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

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

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 200
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.9619 (tt) cc_final: 0.9297 (tt)
REVERT: A  135 TYR cc_start: 0.8593 (m-80) cc_final: 0.8303 (m-80)
REVERT: A  163 PHE cc_start: 0.7637 (t80) cc_final: 0.7400 (t80)
REVERT: A  200 CYS cc_start: 0.8386 (t) cc_final: 0.8044 (t)
REVERT: A  255 GLU cc_start: 0.8153 (pp20) cc_final: 0.7865 (pp20)
REVERT: A  601 CYS cc_start: 0.7485 (m) cc_final: 0.7224 (m)
REVERT: A  766 LYS cc_start: 0.6576 (mmtm) cc_final: 0.6286 (mmmt)
REVERT: A  825 ARG cc_start: 0.8440 (mtt180) cc_final: 0.8201 (mtt180)
REVERT: A  886 LEU cc_start: 0.8583 (pp) cc_final: 0.8371 (pp)
REVERT: B  197 MET cc_start: 0.4534 (tmm) cc_final: 0.4233 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 201
  average time/residue: 0.2135
  time to fit residues: 58.4694
Evaluate side-chains
  139 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 80 optimal weight:    6.9990
   chunk 66 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 97 optimal weight:    0.5980
   chunk 105 optimal weight:    5.9990
   chunk 86 optimal weight:    5.9990
   chunk 96 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   overall best weight:    2.9186

-------------------------------------------------------------------------------
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**
A 632 ASN
A 967 GLN
B 225 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8709  Z= 0.323
  Angle     :  0.706   7.892  11786  Z= 0.370
  Chirality :  0.045   0.175   1413
  Planarity :  0.005   0.054   1484
  Dihedral  :  4.972  21.044   1133
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 17.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  4.08 %
    Favored  : 95.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.25), residues: 1057
  helix:  0.35 (0.18), residues: 739
  sheet: -1.39 (0.71), residues: 47
  loop : -0.49 (0.38), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 127 
 HIS   0.003   0.001   HIS A 568 
 PHE   0.023   0.002   PHE A 582 
 TYR   0.020   0.002   TYR B 139 
 ARG   0.006   0.001   ARG B 137 

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

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 186
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 TYR cc_start: 0.8619 (m-80) cc_final: 0.8244 (m-80)
REVERT: A  255 GLU cc_start: 0.8002 (pp20) cc_final: 0.7618 (pp20)
REVERT: A  720 ARG cc_start: 0.7515 (ptm-80) cc_final: 0.7041 (ptm-80)
REVERT: A  766 LYS cc_start: 0.6624 (mmtm) cc_final: 0.6238 (mmmm)
REVERT: B   84 THR cc_start: 0.9112 (p) cc_final: 0.8628 (t)
REVERT: B  197 MET cc_start: 0.4558 (tmm) cc_final: 0.4256 (tmm)
  outliers start: 3
  outliers final: 0
  residues processed: 188
  average time/residue: 0.2490
  time to fit residues: 64.0359
Evaluate side-chains
  136 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 1.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 10 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 65 optimal weight:    0.4980
   chunk 97 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0370
   chunk 51 optimal weight:    0.9990
   chunk 92 optimal weight:    6.9990
   chunk 27 optimal weight:    8.9990
   overall best weight:    0.7060

-------------------------------------------------------------------------------
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 568 HIS
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.3132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8709  Z= 0.204
  Angle     :  0.634   9.838  11786  Z= 0.327
  Chirality :  0.043   0.165   1413
  Planarity :  0.004   0.052   1484
  Dihedral  :  4.702  19.374   1133
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  3.57 %
    Favored  : 96.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.25), residues: 1057
  helix:  0.70 (0.19), residues: 736
  sheet: -1.37 (0.64), residues: 53
  loop : -0.46 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 985 
 PHE   0.022   0.002   PHE A 249 
 TYR   0.013   0.001   TYR A 154 
 ARG   0.004   0.001   ARG A 744 

*********************** 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
  209 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 206
  time to evaluate  : 0.986 
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: 0.9308 (mt) cc_final: 0.9057 (pp)
REVERT: A  131 LEU cc_start: 0.8845 (mt) cc_final: 0.8505 (mt)
REVERT: A  135 TYR cc_start: 0.8651 (m-80) cc_final: 0.8325 (m-80)
REVERT: A  163 PHE cc_start: 0.7512 (t80) cc_final: 0.7198 (t80)
REVERT: A  200 CYS cc_start: 0.8397 (t) cc_final: 0.8184 (t)
REVERT: A  255 GLU cc_start: 0.7888 (pp20) cc_final: 0.7643 (pp20)
REVERT: A  262 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7460 (m110)
REVERT: A  554 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7445 (tm-30)
REVERT: A  611 MET cc_start: 0.6958 (mmt) cc_final: 0.6358 (mmm)
REVERT: A  766 LYS cc_start: 0.6556 (mmtm) cc_final: 0.6236 (mmmt)
REVERT: A  815 GLU cc_start: 0.8612 (mp0) cc_final: 0.8289 (mp0)
REVERT: A  825 ARG cc_start: 0.8449 (mtt-85) cc_final: 0.7964 (mtt180)
REVERT: B   84 THR cc_start: 0.8881 (p) cc_final: 0.8524 (t)
  outliers start: 3
  outliers final: 0
  residues processed: 208
  average time/residue: 0.2141
  time to fit residues: 60.8652
Evaluate side-chains
  148 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 147
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 77 optimal weight:    7.9990
   chunk 42 optimal weight:    0.0270
   chunk 88 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 52 optimal weight:    0.8980
   chunk 92 optimal weight:    0.8980
   chunk 26 optimal weight:    6.9990
   overall best weight:    1.3642

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.3416

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= 0.215
  Angle     :  0.616   8.125  11786  Z= 0.320
  Chirality :  0.042   0.169   1413
  Planarity :  0.005   0.070   1484
  Dihedral  :  4.649  19.139   1133
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.35 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.25), residues: 1057
  helix:  0.74 (0.19), residues: 732
  sheet: -1.45 (0.62), residues: 56
  loop : -0.68 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 579 
 PHE   0.022   0.002   PHE A 249 
 TYR   0.012   0.001   TYR A 154 
 ARG   0.014   0.001   ARG B 107 

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

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 198
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 LEU cc_start: 0.9344 (mt) cc_final: 0.9109 (pp)
REVERT: A  131 LEU cc_start: 0.8824 (mt) cc_final: 0.8469 (mt)
REVERT: A  135 TYR cc_start: 0.8656 (m-10) cc_final: 0.8326 (m-80)
REVERT: A  163 PHE cc_start: 0.7543 (t80) cc_final: 0.7197 (t80)
REVERT: A  200 CYS cc_start: 0.8354 (t) cc_final: 0.7956 (t)
REVERT: A  255 GLU cc_start: 0.7762 (pp20) cc_final: 0.7326 (pp20)
REVERT: A  290 HIS cc_start: 0.8271 (m-70) cc_final: 0.8022 (m-70)
REVERT: A  554 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7556 (tm-30)
REVERT: A  766 LYS cc_start: 0.6544 (mmtm) cc_final: 0.6255 (mmmt)
REVERT: B   84 THR cc_start: 0.8894 (p) cc_final: 0.8443 (t)
REVERT: B  137 ARG cc_start: 0.8879 (mtm-85) cc_final: 0.7711 (mtm-85)
  outliers start: 1
  outliers final: 0
  residues processed: 198
  average time/residue: 0.2184
  time to fit residues: 59.1321
Evaluate side-chains
  144 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 93 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 103 optimal weight:    0.0980
   chunk 85 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 262 ASN
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.3741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8709  Z= 0.198
  Angle     :  0.622   7.402  11786  Z= 0.322
  Chirality :  0.043   0.158   1413
  Planarity :  0.004   0.053   1484
  Dihedral  :  4.570  18.745   1133
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.25), residues: 1057
  helix:  0.79 (0.19), residues: 737
  sheet: -1.15 (0.64), residues: 53
  loop : -0.59 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 813 
 HIS   0.002   0.001   HIS A 985 
 PHE   0.023   0.002   PHE A 249 
 TYR   0.011   0.001   TYR A 154 
 ARG   0.007   0.001   ARG B 107 

*********************** 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
  200 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 LEU cc_start: 0.9352 (mt) cc_final: 0.9122 (pp)
REVERT: A  131 LEU cc_start: 0.8845 (mt) cc_final: 0.8414 (mt)
REVERT: A  135 TYR cc_start: 0.8629 (m-10) cc_final: 0.8291 (m-80)
REVERT: A  163 PHE cc_start: 0.7408 (t80) cc_final: 0.7004 (t80)
REVERT: A  255 GLU cc_start: 0.7686 (pp20) cc_final: 0.7378 (pp20)
REVERT: A  554 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7609 (tm-30)
REVERT: A  693 GLU cc_start: 0.6467 (pm20) cc_final: 0.6209 (tm-30)
REVERT: A  719 GLU cc_start: 0.7917 (pp20) cc_final: 0.7634 (pp20)
REVERT: A  766 LYS cc_start: 0.6542 (mmtm) cc_final: 0.6336 (mmmt)
REVERT: A  825 ARG cc_start: 0.8435 (mtt180) cc_final: 0.8127 (mtt180)
REVERT: B   84 THR cc_start: 0.8853 (p) cc_final: 0.8433 (t)
REVERT: B  137 ARG cc_start: 0.8815 (mtm-85) cc_final: 0.7671 (mtm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 200
  average time/residue: 0.2194
  time to fit residues: 60.3497
Evaluate side-chains
  152 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 11 optimal weight:    0.0870
   chunk 58 optimal weight:    5.9990
   chunk 75 optimal weight:    0.1980
   chunk 87 optimal weight:    8.9990
   chunk 57 optimal weight:    0.9990
   chunk 103 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   overall best weight:    0.6562

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.4020

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= 0.188
  Angle     :  0.611   7.382  11786  Z= 0.317
  Chirality :  0.042   0.164   1413
  Planarity :  0.004   0.051   1484
  Dihedral  :  4.479  18.884   1133
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.26), residues: 1057
  helix:  0.82 (0.19), residues: 736
  sheet: -0.92 (0.66), residues: 50
  loop : -0.77 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 813 
 HIS   0.005   0.001   HIS A 290 
 PHE   0.026   0.002   PHE A 177 
 TYR   0.010   0.001   TYR A 154 
 ARG   0.009   0.001   ARG A 755 

*********************** 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
  195 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.108 
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  135 TYR cc_start: 0.8631 (m-10) cc_final: 0.8288 (m-80)
REVERT: A  200 CYS cc_start: 0.8312 (t) cc_final: 0.8063 (t)
REVERT: A  255 GLU cc_start: 0.7733 (pp20) cc_final: 0.7494 (pp20)
REVERT: A  290 HIS cc_start: 0.8240 (m-70) cc_final: 0.7991 (m90)
REVERT: A  554 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7425 (tm-30)
REVERT: A  693 GLU cc_start: 0.6394 (pm20) cc_final: 0.5935 (tm-30)
REVERT: A  719 GLU cc_start: 0.7940 (pp20) cc_final: 0.7679 (pp20)
REVERT: A  766 LYS cc_start: 0.6553 (mmtm) cc_final: 0.6345 (mmmt)
REVERT: B   84 THR cc_start: 0.8819 (p) cc_final: 0.8402 (t)
REVERT: B  137 ARG cc_start: 0.8818 (mtm-85) cc_final: 0.7710 (mtm-85)
REVERT: B  219 GLN cc_start: 0.8052 (mp10) cc_final: 0.7818 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.2109
  time to fit residues: 56.9296
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  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 31 optimal weight:    0.1980
   chunk 20 optimal weight:    0.9980
   chunk 19 optimal weight:    8.9990
   chunk 65 optimal weight:    6.9990
   chunk 70 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 81 optimal weight:    8.9990
   chunk 93 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 181 ASN
A 262 ASN
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.4139

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= 0.205
  Angle     :  0.636  10.880  11786  Z= 0.324
  Chirality :  0.042   0.160   1413
  Planarity :  0.004   0.052   1484
  Dihedral  :  4.437  19.453   1133
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.26), residues: 1057
  helix:  0.89 (0.19), residues: 730
  sheet: -1.20 (0.62), residues: 60
  loop : -0.61 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 813 
 HIS   0.004   0.001   HIS A 290 
 PHE   0.032   0.002   PHE A 177 
 TYR   0.011   0.001   TYR A 154 
 ARG   0.008   0.001   ARG B 220 

*********************** 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
  193 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 VAL cc_start: 0.9028 (t) cc_final: 0.8785 (m)
REVERT: A  106 LYS cc_start: 0.9006 (ptpt) cc_final: 0.8728 (ptmt)
REVERT: A  135 TYR cc_start: 0.8649 (m-10) cc_final: 0.8326 (m-80)
REVERT: A  163 PHE cc_start: 0.7148 (t80) cc_final: 0.6682 (t80)
REVERT: A  290 HIS cc_start: 0.8284 (m-70) cc_final: 0.8021 (m90)
REVERT: A  554 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7488 (tm-30)
REVERT: A  693 GLU cc_start: 0.6459 (pm20) cc_final: 0.5926 (tm-30)
REVERT: A  719 GLU cc_start: 0.7982 (pp20) cc_final: 0.7666 (pp20)
REVERT: A  766 LYS cc_start: 0.6575 (mmtm) cc_final: 0.6359 (mmmt)
REVERT: A  815 GLU cc_start: 0.8519 (mp0) cc_final: 0.8302 (mp0)
REVERT: B  137 ARG cc_start: 0.8849 (mtm-85) cc_final: 0.7705 (mtm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.2193
  time to fit residues: 57.6377
Evaluate side-chains
  145 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    0.4980
   chunk 96 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 86 optimal weight:    9.9990
   chunk 95 optimal weight:    0.8980
   chunk 63 optimal weight:    0.2980
   chunk 101 optimal weight:   20.0000
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.4354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8709  Z= 0.196
  Angle     :  0.642   8.850  11786  Z= 0.324
  Chirality :  0.043   0.223   1413
  Planarity :  0.004   0.051   1484
  Dihedral  :  4.386  19.792   1133
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.26), residues: 1057
  helix:  0.87 (0.19), residues: 734
  sheet: -1.12 (0.63), residues: 62
  loop : -0.76 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 813 
 HIS   0.003   0.001   HIS A 290 
 PHE   0.024   0.002   PHE A 249 
 TYR   0.012   0.001   TYR A 370 
 ARG   0.009   0.001   ARG A 720 

*********************** 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
  191 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.9029 (ptpt) cc_final: 0.8740 (ptmt)
REVERT: A  135 TYR cc_start: 0.8633 (m-10) cc_final: 0.8313 (m-80)
REVERT: A  163 PHE cc_start: 0.7066 (t80) cc_final: 0.6606 (t80)
REVERT: A  255 GLU cc_start: 0.7544 (pp20) cc_final: 0.7112 (pp20)
REVERT: A  290 HIS cc_start: 0.8266 (m-70) cc_final: 0.8013 (m90)
REVERT: A  554 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7476 (tm-30)
REVERT: A  693 GLU cc_start: 0.6422 (pm20) cc_final: 0.5860 (tm-30)
REVERT: A  719 GLU cc_start: 0.7963 (pp20) cc_final: 0.7704 (pp20)
REVERT: A  766 LYS cc_start: 0.6555 (mmtm) cc_final: 0.6344 (mmmt)
REVERT: A  825 ARG cc_start: 0.8511 (mtt-85) cc_final: 0.8231 (mtt180)
REVERT: B   84 THR cc_start: 0.8752 (p) cc_final: 0.8351 (t)
REVERT: B  137 ARG cc_start: 0.8773 (mtm-85) cc_final: 0.7699 (mtm-85)
REVERT: B  219 GLN cc_start: 0.8056 (mp10) cc_final: 0.7809 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.2133
  time to fit residues: 55.8653
Evaluate side-chains
  141 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 106 optimal weight:    7.9990
   chunk 98 optimal weight:    5.9990
   chunk 84 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 90 optimal weight:    0.5980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 262 ASN
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 ASN
** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.4475

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= 0.204
  Angle     :  0.643   9.316  11786  Z= 0.333
  Chirality :  0.043   0.234   1413
  Planarity :  0.004   0.052   1484
  Dihedral  :  4.361  19.941   1133
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.25), residues: 1057
  helix:  0.86 (0.19), residues: 733
  sheet: -0.82 (0.67), residues: 56
  loop : -0.75 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 813 
 HIS   0.003   0.001   HIS A 290 
 PHE   0.027   0.002   PHE A 794 
 TYR   0.015   0.001   TYR A 254 
 ARG   0.009   0.001   ARG A 720 

********************** 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
  183 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.9037 (ptpt) cc_final: 0.8753 (ptmt)
REVERT: A  135 TYR cc_start: 0.8644 (m-10) cc_final: 0.8319 (m-80)
REVERT: A  554 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7508 (tm-30)
REVERT: A  719 GLU cc_start: 0.8007 (pp20) cc_final: 0.7717 (pp20)
REVERT: A  766 LYS cc_start: 0.6579 (mmtm) cc_final: 0.6359 (mmmt)
REVERT: A  825 ARG cc_start: 0.8527 (mtt-85) cc_final: 0.8206 (mtt180)
REVERT: B   84 THR cc_start: 0.8698 (p) cc_final: 0.8435 (t)
REVERT: B  137 ARG cc_start: 0.8832 (mtm-85) cc_final: 0.7703 (mtm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.2203
  time to fit residues: 55.4986
Evaluate side-chains
  145 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 78 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 74 optimal weight:    8.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    2.1988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.137931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.110009 restraints weight = 26394.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.109885 restraints weight = 15637.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.110271 restraints weight = 13829.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.4402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8709  Z= 0.262
  Angle     :  0.656   8.443  11786  Z= 0.339
  Chirality :  0.043   0.166   1413
  Planarity :  0.005   0.053   1484
  Dihedral  :  4.460  20.266   1133
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 17.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.26), residues: 1057
  helix:  0.80 (0.19), residues: 736
  sheet: -1.10 (0.65), residues: 56
  loop : -0.64 (0.38), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 813 
 HIS   0.003   0.001   HIS A 308 
 PHE   0.025   0.002   PHE A 794 
 TYR   0.013   0.002   TYR B 139 
 ARG   0.010   0.001   ARG A 755 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2128.80 seconds
wall clock time: 40 minutes 3.10 seconds (2403.10 seconds total)