Starting phenix.real_space_refine
on Mon Jul 28 20:41:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uzb_42838/07_2025/8uzb_42838.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uzb_42838/07_2025/8uzb_42838.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uzb_42838/07_2025/8uzb_42838.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uzb_42838/07_2025/8uzb_42838.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uzb_42838/07_2025/8uzb_42838.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uzb_42838/07_2025/8uzb_42838.cif"
  }
  resolution = 2.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.047
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: 5
    Type Number    sf(0)   Gaussians
     P     162      5.49       5
     S      19      5.16       5
     C    6286      2.51       5
     N    1973      2.21       5
     O    2442      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10882
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7485
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 910, 7485
          Classifications: {'peptide': 910}
          Link IDs: {'PTRANS': 39, 'TRANS': 870}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 2267
          Classifications: {'RNA': 107}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 45, 'rna3p_pyr': 53}
          Link IDs: {'rna2p': 9, 'rna3p': 97}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 808
          Classifications: {'DNA': 39}
          Link IDs: {'rna3p': 38}
    Chain: "D"
      Number of atoms: 322
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 322
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
  Time building chain proxies: 6.98, per 1000 atoms: 0.64
  Number of scatterers: 10882
  At special positions: 0
  Unit cell: (97.65, 123.69, 132.99, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      19     16.00
     P     162     15.00
     O    2442      8.00
     N    1973      7.00
     C    6286      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: 2.93
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1728

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      45.1% alpha, 14.5% beta
      68 base pairs and 109 stacking pairs defined.
    Time for finding SS restraints: 5.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 78
    Processing helix  chain 'A' and resid 81 through 89
      removed outlier: 4.539A  pdb=" N   PHE A  89 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 104
    Processing helix  chain 'A' and resid 110 through 124
      removed outlier: 3.777A  pdb=" N   ARG A 124 " --> pdb=" O   HIS A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 155
      removed outlier: 3.699A  pdb=" N   SER A 155 " --> pdb=" O   ARG A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 167
    Processing helix  chain 'A' and resid 168 through 171
    Processing helix  chain 'A' and resid 186 through 205
    Processing helix  chain 'A' and resid 210 through 222
    Processing helix  chain 'A' and resid 233 through 237
    Processing helix  chain 'A' and resid 253 through 268
    Processing helix  chain 'A' and resid 280 through 294
    Processing helix  chain 'A' and resid 299 through 306
    Processing helix  chain 'A' and resid 324 through 329
    Processing helix  chain 'A' and resid 336 through 351
    Processing helix  chain 'A' and resid 353 through 358
      removed outlier: 4.184A  pdb=" N   SER A 356 " --> pdb=" O   GLY A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 373
      removed outlier: 3.534A  pdb=" N   PHE A 373 " --> pdb=" O   ALA A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 383
    Processing helix  chain 'A' and resid 403 through 411
    Processing helix  chain 'A' and resid 422 through 434
      Proline residue:  A 431  - end of helix
    Processing helix  chain 'A' and resid 438 through 447
    Processing helix  chain 'A' and resid 470 through 492
    Processing helix  chain 'A' and resid 503 through 506
      removed outlier: 4.097A  pdb=" N   SER A 506 " --> pdb=" O   ARG A 503 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 503 through 506'
    Processing helix  chain 'A' and resid 508 through 523
    Processing helix  chain 'A' and resid 667 through 679
    Processing helix  chain 'A' and resid 696 through 707
      removed outlier: 3.816A  pdb=" N   THR A 700 " --> pdb=" O   ASN A 696 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   HIS A 702 " --> pdb=" O   ARG A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 729
      removed outlier: 3.673A  pdb=" N   VAL A 722 " --> pdb=" O   LEU A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 748
      removed outlier: 3.610A  pdb=" N   ILE A 735 " --> pdb=" O   THR A 731 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ALA A 736 " --> pdb=" O   PRO A 732 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LYS A 737 " --> pdb=" O   SER A 733 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   VAL A 738 " --> pdb=" O   ASP A 734 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ARG A 744 " --> pdb=" O   ALA A 740 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLU A 746 " --> pdb=" O   TYR A 742 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   GLN A 747 " --> pdb=" O   GLN A 743 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 767 through 774
      removed outlier: 4.557A  pdb=" N   ARG A 771 " --> pdb=" O   ALA A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 777 through 785
      removed outlier: 3.502A  pdb=" N   LEU A 785 " --> pdb=" O   SER A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 796
    Processing helix  chain 'A' and resid 842 through 844
      No H-bonds generated for 'chain 'A' and resid 842 through 844'
    Processing helix  chain 'A' and resid 860 through 874
      removed outlier: 3.565A  pdb=" N   TYR A 864 " --> pdb=" O   ASP A 860 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 877 through 882
    Processing helix  chain 'A' and resid 945 through 951
    Processing helix  chain 'A' and resid 963 through 967
    Processing sheet with id=AA1, first strand: chain 'A' and resid 692 through 694
      removed outlier: 6.286A  pdb=" N   ILE A 497 " --> pdb=" O   TYR A 693 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   VAL A  14 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   VAL A  31 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   TRP A  16 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   LEU A  29 " --> pdb=" O   TRP A  16 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   VAL A  18 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 276 through 278
    Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 298
      removed outlier: 6.784A  pdb=" N   ILE A 297 " --> pdb=" O   PHE A 333 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 388
      removed outlier: 4.110A  pdb=" N   TYR A 387 " --> pdb=" O   MET A 394 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 822 through 826
      removed outlier: 5.818A  pdb=" N   TYR A 823 " --> pdb=" O   VAL A 836 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL A 836 " --> pdb=" O   TYR A 823 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 887 through 889
    Processing sheet with id=AA7, first strand: chain 'A' and resid 911 through 914
      removed outlier: 4.370A  pdb=" N   THR A 919 " --> pdb=" O   LEU A 914 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 937 through 944
      removed outlier: 6.394A  pdb=" N   VAL A 929 " --> pdb=" O   SER A 979 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   SER A 979 " --> pdb=" O   VAL A 929 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   VAL A 931 " --> pdb=" O   ARG A 977 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 956 through 957
      removed outlier: 3.843A  pdb=" N   LYS A 968 " --> pdb=" O   ALA A 957 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1033 through 1038
      removed outlier: 5.318A  pdb=" N   LEU A1023 " --> pdb=" O   GLY A1036 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   THR A1015 " --> pdb=" O   GLU A1024 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ILE A1026 " --> pdb=" O   TYR A1013 " (cutoff:3.500A)
      removed outlier: 5.705A  pdb=" N   TYR A1013 " --> pdb=" O   ILE A1026 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   ASP A1008 " --> pdb=" O   ARG A 992 " (cutoff:3.500A)
      removed outlier: 11.580A  pdb=" N   ARG A 992 " --> pdb=" O   ASP A1008 " (cutoff:3.500A)
      removed outlier: 11.729A  pdb=" N   PHE A1010 " --> pdb=" O   LEU A 990 " (cutoff:3.500A)
      removed outlier: 11.298A  pdb=" N   LEU A 990 " --> pdb=" O   PHE A1010 " (cutoff:3.500A)
      removed outlier: 9.940A  pdb=" N   TYR A1012 " --> pdb=" O   ILE A 988 " (cutoff:3.500A)
      removed outlier: 9.830A  pdb=" N   ILE A 988 " --> pdb=" O   TYR A1012 " (cutoff:3.500A)
      removed outlier: 9.883A  pdb=" N   LYS A1014 " --> pdb=" O   ILE A 986 " (cutoff:3.500A)
      removed outlier: 11.406A  pdb=" N   ILE A 986 " --> pdb=" O   LYS A1014 " (cutoff:3.500A)
      removed outlier: 11.110A  pdb=" N   ILE A1016 " --> pdb=" O   ASP A 984 " (cutoff:3.500A)
      removed outlier: 13.412A  pdb=" N   ASP A 984 " --> pdb=" O   ILE A1016 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU A 985 " --> pdb=" O   TYR A1048 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ARG A1044 " --> pdb=" O   GLU A 989 " (cutoff:3.500A)

    309 hydrogen bonds defined for protein.
    888 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      171 hydrogen bonds
      326 hydrogen bond angles
      0 basepair planarities
      68 basepair parallelities
      109 stacking parallelities
  Total time for adding SS restraints: 5.68

  Time building geometry restraints manager: 3.47 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: 2908
        1.34 -     1.46: 2984
        1.46 -     1.58: 5187
        1.58 -     1.70: 319
        1.70 -     1.82: 33
  Bond restraints: 11431
  Sorted by residual:
  bond pdb=" CB  PRO A 778 "
       pdb=" CG  PRO A 778 "
    ideal  model  delta    sigma   weight residual
    1.492  1.567 -0.075 5.00e-02 4.00e+02 2.24e+00
  bond pdb=" C3'  DG C  16 "
       pdb=" O3'  DG C  16 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.69e+00
  bond pdb=" C3'   C B  77 "
       pdb=" O3'   C B  77 "
    ideal  model  delta    sigma   weight residual
    1.427  1.442 -0.015 1.50e-02 4.44e+03 1.03e+00
  bond pdb=" CG  PRO A 778 "
       pdb=" CD  PRO A 778 "
    ideal  model  delta    sigma   weight residual
    1.503  1.470  0.033 3.40e-02 8.65e+02 9.58e-01
  bond pdb=" CA  THR A 416 "
       pdb=" CB  THR A 416 "
    ideal  model  delta    sigma   weight residual
    1.521  1.535 -0.014 1.48e-02 4.57e+03 9.16e-01
  ... (remaining 11426 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 15774
        1.46 -     2.92: 314
        2.92 -     4.39: 49
        4.39 -     5.85: 8
        5.85 -     7.31: 5
  Bond angle restraints: 16150
  Sorted by residual:
  angle pdb=" C   THR A 416 "
        pdb=" N   LYS A 417 "
        pdb=" CA  LYS A 417 "
      ideal   model   delta    sigma   weight residual
     121.91  128.69   -6.78 2.03e+00 2.43e-01 1.11e+01
  angle pdb=" C3'   C B  77 "
        pdb=" O3'   C B  77 "
        pdb=" P     A B  78 "
      ideal   model   delta    sigma   weight residual
     120.20  124.88   -4.68 1.50e+00 4.44e-01 9.75e+00
  angle pdb=" N   THR A 416 "
        pdb=" CA  THR A 416 "
        pdb=" C   THR A 416 "
      ideal   model   delta    sigma   weight residual
     107.20  111.47   -4.27 1.70e+00 3.46e-01 6.32e+00
  angle pdb=" CB  MET A 207 "
        pdb=" CG  MET A 207 "
        pdb=" SD  MET A 207 "
      ideal   model   delta    sigma   weight residual
     112.70  120.01   -7.31 3.00e+00 1.11e-01 5.94e+00
  angle pdb=" N   PRO A 778 "
        pdb=" CD  PRO A 778 "
        pdb=" CG  PRO A 778 "
      ideal   model   delta    sigma   weight residual
     103.20   99.67    3.53 1.50e+00 4.44e-01 5.53e+00
  ... (remaining 16145 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.01: 6437
       33.01 -    66.02: 539
       66.02 -    99.03: 41
       99.03 -   132.04: 0
      132.04 -   165.05: 3
  Dihedral angle restraints: 7020
    sinusoidal: 4348
      harmonic: 2672
  Sorted by residual:
  dihedral pdb=" C4'  DT C   6 "
           pdb=" C3'  DT C   6 "
           pdb=" O3'  DT C   6 "
           pdb=" P    DG C   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   54.95  165.05     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'   C B  77 "
           pdb=" C3'   C B  77 "
           pdb=" O3'   C B  77 "
           pdb=" P     A B  78 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -110.00   55.03 -165.03     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'  DG C  16 "
           pdb=" C3'  DG C  16 "
           pdb=" O3'  DG C  16 "
           pdb=" P    DG C  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   61.09  158.91     1      3.50e+01 8.16e-04 1.51e+01
  ... (remaining 7017 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1417
       0.038 -    0.075: 329
       0.075 -    0.113: 85
       0.113 -    0.150: 20
       0.150 -    0.188: 3
  Chirality restraints: 1854
  Sorted by residual:
  chirality pdb=" C3'   C B  77 "
            pdb=" C4'   C B  77 "
            pdb=" O3'   C B  77 "
            pdb=" C2'   C B  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.56   -0.19 2.00e-01 2.50e+01 8.83e-01
  chirality pdb=" CB  THR A 416 "
            pdb=" CA  THR A 416 "
            pdb=" OG1 THR A 416 "
            pdb=" CG2 THR A 416 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.19 2.00e-01 2.50e+01 8.69e-01
  chirality pdb=" CA  TRP A 763 "
            pdb=" N   TRP A 763 "
            pdb=" C   TRP A 763 "
            pdb=" CB  TRP A 763 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.99e-01
  ... (remaining 1851 not shown)

  Planarity restraints: 1494
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 777 "   -0.041 5.00e-02 4.00e+02   6.19e-02 6.12e+00
        pdb=" N   PRO A 778 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A 778 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 778 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT C  13 "    0.024 2.00e-02 2.50e+03   1.18e-02 3.50e+00
        pdb=" N1   DT C  13 "   -0.027 2.00e-02 2.50e+03
        pdb=" C2   DT C  13 "   -0.003 2.00e-02 2.50e+03
        pdb=" O2   DT C  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DT C  13 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DT C  13 "    0.003 2.00e-02 2.50e+03
        pdb=" O4   DT C  13 "    0.008 2.00e-02 2.50e+03
        pdb=" C5   DT C  13 "    0.000 2.00e-02 2.50e+03
        pdb=" C7   DT C  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DT C  13 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  93 "   -0.020 2.00e-02 2.50e+03   8.95e-03 2.40e+00
        pdb=" N9    G B  93 "    0.023 2.00e-02 2.50e+03
        pdb=" C8    G B  93 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    G B  93 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G B  93 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G B  93 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6    G B  93 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    G B  93 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    G B  93 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G B  93 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    G B  93 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    G B  93 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1491 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 396
        2.70 -     3.25: 9681
        3.25 -     3.80: 19056
        3.80 -     4.35: 25439
        4.35 -     4.90: 37296
  Nonbonded interactions: 91868
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 381 "
            pdb=" O   GLU A 386 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" OG1 THR A  12 "
            pdb=" O   PHE A  34 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OD1 ASP A 768 "
            pdb=" NH2 ARG A 771 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" OD1 ASP A 337 "
            pdb=" NE2 GLN A 341 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" OD2 ASP A  28 "
            pdb=" OH  TYR A 491 "
     model   vdw
     2.254 3.040
  ... (remaining 91863 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     33.760
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
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      :  0.003   0.075  11431  Z= 0.139
  Angle     :  0.528   7.309  16150  Z= 0.284
  Chirality :  0.037   0.188   1854
  Planarity :  0.004   0.062   1494
  Dihedral  : 20.256 165.051   5292
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.28), residues: 902
  helix:  1.28 (0.27), residues: 375
  sheet: -0.76 (0.47), residues: 120
  loop : -0.12 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 763 
 HIS   0.002   0.001   HIS A1028 
 PHE   0.009   0.001   PHE A 759 
 TYR   0.020   0.001   TYR A 864 
 ARG   0.007   0.000   ARG A 503 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15725 (  480)
  hydrogen bonds       : angle       5.45626 ( 1214)
  covalent geometry    : bond        0.00314 (11431)
  covalent geometry    : angle       0.52798 (16150)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 1.033 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 1.6043
  time to fit residues: 182.4447
Evaluate side-chains
  80 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 79 optimal weight:    0.3980
   chunk 44 optimal weight:    2.9990
   chunk 27 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 82 optimal weight:    2.9990
   chunk 31 optimal weight:    9.9990
   chunk 50 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 95 optimal weight:    8.9990
   overall best weight:    1.4384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.166339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.114974 restraints weight = 11064.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 1.59
r_work: 0.3191 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.1006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11431  Z= 0.168
  Angle     :  0.555   6.830  16150  Z= 0.299
  Chirality :  0.039   0.176   1854
  Planarity :  0.004   0.035   1494
  Dihedral  : 22.135 165.805   3337
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  9.74 %
    Favored  : 88.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.28), residues: 902
  helix:  1.52 (0.27), residues: 386
  sheet: -0.86 (0.45), residues: 121
  loop : -0.02 (0.32), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 763 
 HIS   0.003   0.001   HIS A 720 
 PHE   0.010   0.001   PHE A 932 
 TYR   0.016   0.001   TYR A 491 
 ARG   0.006   0.000   ARG A 908 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04847 (  480)
  hydrogen bonds       : angle       3.98357 ( 1214)
  covalent geometry    : bond        0.00378 (11431)
  covalent geometry    : angle       0.55524 (16150)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.997 
Fit side-chains
REVERT: A   28 ASP cc_start: 0.8363 (m-30) cc_final: 0.7748 (m-30)
REVERT: A  335 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7558 (mt-10)
REVERT: A 1060 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7725 (ttp80)
  outliers start: 14
  outliers final: 3
  residues processed: 97
  average time/residue: 1.6698
  time to fit residues: 172.3153
Evaluate side-chains
  89 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  335 GLU
Chi-restraints excluded: chain A residue  795 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 77 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0980
   chunk 16 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0270
   chunk 42 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 97 optimal weight:    7.9990
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1028 HIS ** 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 = 0.3965 r_free = 0.3965 target = 0.171094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.129053 restraints weight = 11217.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 1.95
r_work: 0.3221 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11431  Z= 0.115
  Angle     :  0.501   6.880  16150  Z= 0.269
  Chirality :  0.036   0.175   1854
  Planarity :  0.004   0.032   1494
  Dihedral  : 22.034 165.700   3337
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.34 %
    Favored  : 87.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.29), residues: 902
  helix:  1.80 (0.27), residues: 386
  sheet: -0.59 (0.46), residues: 116
  loop : -0.01 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 763 
 HIS   0.004   0.001   HIS A 300 
 PHE   0.008   0.001   PHE A 759 
 TYR   0.011   0.001   TYR A 864 
 ARG   0.006   0.000   ARG A 698 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04000 (  480)
  hydrogen bonds       : angle       3.66469 ( 1214)
  covalent geometry    : bond        0.00252 (11431)
  covalent geometry    : angle       0.50093 (16150)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 1.086 
Fit side-chains
REVERT: A   28 ASP cc_start: 0.8405 (m-30) cc_final: 0.8167 (m-30)
REVERT: A  162 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7353 (tp30)
REVERT: A  306 LEU cc_start: 0.7175 (mp) cc_final: 0.6799 (mt)
REVERT: A  337 ASP cc_start: 0.8196 (t70) cc_final: 0.7839 (t0)
REVERT: A  500 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7927 (tt0)
REVERT: A  817 ARG cc_start: 0.8937 (mmp-170) cc_final: 0.8713 (mmm160)
REVERT: A 1031 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7568 (ttm-80)
  outliers start: 13
  outliers final: 4
  residues processed: 101
  average time/residue: 1.9882
  time to fit residues: 214.8043
Evaluate side-chains
  90 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 2.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  500 GLU
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue 1046 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 91 optimal weight:    8.9990
   chunk 82 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 27 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 86 optimal weight:    3.9990
   chunk 63 optimal weight:   10.0000
   chunk 71 optimal weight:    4.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 290 GLN
A1005 ASN
** A1028 HIS ** 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 = 0.3894 r_free = 0.3894 target = 0.164273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.121756 restraints weight = 11063.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 2.13
r_work: 0.3104 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  11431  Z= 0.232
  Angle     :  0.597   7.059  16150  Z= 0.320
  Chirality :  0.041   0.175   1854
  Planarity :  0.005   0.040   1494
  Dihedral  : 22.175 167.320   3337
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 11.22 %
    Favored  : 85.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.28), residues: 902
  helix:  1.62 (0.27), residues: 381
  sheet: -0.79 (0.44), residues: 120
  loop : -0.14 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 763 
 HIS   0.003   0.001   HIS A  93 
 PHE   0.017   0.002   PHE A 932 
 TYR   0.012   0.001   TYR A 864 
 ARG   0.005   0.001   ARG A  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05297 (  480)
  hydrogen bonds       : angle       3.82717 ( 1214)
  covalent geometry    : bond        0.00527 (11431)
  covalent geometry    : angle       0.59686 (16150)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 1.306 
Fit side-chains
REVERT: A   28 ASP cc_start: 0.8513 (m-30) cc_final: 0.8240 (m-30)
REVERT: A  335 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7675 (mt-10)
REVERT: A  337 ASP cc_start: 0.8207 (t70) cc_final: 0.7806 (t0)
REVERT: A  500 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8048 (tt0)
REVERT: A  706 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6801 (mmt90)
REVERT: A  858 GLU cc_start: 0.7904 (pm20) cc_final: 0.7689 (pm20)
REVERT: A  869 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7556 (mm-40)
REVERT: A  948 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8439 (mt)
REVERT: A 1044 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7687 (ttm-80)
  outliers start: 23
  outliers final: 6
  residues processed: 104
  average time/residue: 2.1674
  time to fit residues: 238.6423
Evaluate side-chains
  88 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  335 GLU
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  500 GLU
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  706 ARG
Chi-restraints excluded: chain A residue  795 LEU
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue 1044 ARG
Chi-restraints excluded: chain A residue 1046 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 19 optimal weight:    6.9990
   chunk 47 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 793 GLN
** A1028 HIS ** 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 = 0.3934 r_free = 0.3934 target = 0.168052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.126326 restraints weight = 11188.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.05
r_work: 0.3172 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11431  Z= 0.124
  Angle     :  0.514   6.932  16150  Z= 0.277
  Chirality :  0.037   0.200   1854
  Planarity :  0.004   0.034   1494
  Dihedral  : 22.012 166.406   3337
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.44 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.29), residues: 902
  helix:  1.82 (0.27), residues: 388
  sheet: -1.05 (0.44), residues: 122
  loop : -0.00 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 763 
 HIS   0.002   0.001   HIS A1028 
 PHE   0.007   0.001   PHE A 932 
 TYR   0.010   0.001   TYR A 864 
 ARG   0.006   0.000   ARG A1060 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04089 (  480)
  hydrogen bonds       : angle       3.59254 ( 1214)
  covalent geometry    : bond        0.00271 (11431)
  covalent geometry    : angle       0.51379 (16150)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 1.085 
Fit side-chains
REVERT: A   28 ASP cc_start: 0.8442 (m-30) cc_final: 0.8118 (m-30)
REVERT: A   38 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7772 (pm20)
REVERT: A  337 ASP cc_start: 0.8088 (t70) cc_final: 0.7725 (t0)
REVERT: A  706 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6895 (mmt90)
REVERT: A  798 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.7023 (mp)
REVERT: A  858 GLU cc_start: 0.7793 (pm20) cc_final: 0.7592 (pm20)
REVERT: A  869 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7480 (mm-40)
REVERT: A  948 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8190 (mt)
  outliers start: 19
  outliers final: 6
  residues processed: 110
  average time/residue: 1.6759
  time to fit residues: 195.9578
Evaluate side-chains
  95 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   38 GLU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  706 ARG
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue 1046 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 104 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 7 optimal weight:    0.4980
   chunk 59 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 94 optimal weight:    8.9990
   chunk 50 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1028 HIS ** 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 = 0.3908 r_free = 0.3908 target = 0.165478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.113993 restraints weight = 11268.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.59
r_work: 0.3174 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11431  Z= 0.166
  Angle     :  0.545   6.989  16150  Z= 0.293
  Chirality :  0.038   0.174   1854
  Planarity :  0.004   0.037   1494
  Dihedral  : 22.044 167.352   3337
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 13.32 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.28), residues: 902
  helix:  1.75 (0.27), residues: 388
  sheet: -0.87 (0.46), residues: 115
  loop : -0.05 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 763 
 HIS   0.002   0.001   HIS A 380 
 PHE   0.011   0.001   PHE A 932 
 TYR   0.013   0.001   TYR A 864 
 ARG   0.008   0.000   ARG A1060 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04555 (  480)
  hydrogen bonds       : angle       3.65342 ( 1214)
  covalent geometry    : bond        0.00372 (11431)
  covalent geometry    : angle       0.54491 (16150)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.938 
Fit side-chains
REVERT: A   38 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7697 (pm20)
REVERT: A  154 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6576 (tp)
REVERT: A  290 GLN cc_start: 0.6419 (mt0) cc_final: 0.5907 (mm-40)
REVERT: A  337 ASP cc_start: 0.8044 (t70) cc_final: 0.7685 (t0)
REVERT: A  500 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8043 (tt0)
REVERT: A  706 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6811 (mmt90)
REVERT: A  798 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7019 (mp)
REVERT: A  858 GLU cc_start: 0.7807 (pm20) cc_final: 0.7602 (pm20)
REVERT: A  869 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7509 (mm-40)
REVERT: A  948 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8289 (mt)
REVERT: A  966 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7547 (mt-10)
REVERT: A 1044 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7580 (ttm-80)
  outliers start: 22
  outliers final: 7
  residues processed: 100
  average time/residue: 1.7338
  time to fit residues: 183.8112
Evaluate side-chains
  99 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 GLU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  500 GLU
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  705 SER
Chi-restraints excluded: chain A residue  706 ARG
Chi-restraints excluded: chain A residue  795 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue  966 GLU
Chi-restraints excluded: chain A residue 1044 ARG
Chi-restraints excluded: chain A residue 1046 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 92 optimal weight:    4.9990
   chunk 82 optimal weight:    0.1980
   chunk 61 optimal weight:    1.9990
   chunk 27 optimal weight:    9.9990
   chunk 102 optimal weight:    3.9990
   chunk 51 optimal weight:    9.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    2.2388

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

Flipped N/Q/H residues before XYZ refinement:
** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 793 GLN
** A1028 HIS ** 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 = 0.3890 r_free = 0.3890 target = 0.163812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.121356 restraints weight = 11332.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 2.15
r_work: 0.3089 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  11431  Z= 0.222
  Angle     :  0.601   7.731  16150  Z= 0.320
  Chirality :  0.041   0.174   1854
  Planarity :  0.005   0.039   1494
  Dihedral  : 22.155 168.738   3337
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 14.43 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.28), residues: 902
  helix:  1.54 (0.27), residues: 389
  sheet: -0.86 (0.45), residues: 120
  loop : -0.14 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 763 
 HIS   0.003   0.001   HIS A  93 
 PHE   0.014   0.002   PHE A 932 
 TYR   0.016   0.001   TYR A 864 
 ARG   0.007   0.001   ARG A1031 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05143 (  480)
  hydrogen bonds       : angle       3.78270 ( 1214)
  covalent geometry    : bond        0.00503 (11431)
  covalent geometry    : angle       0.60068 (16150)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.927 
Fit side-chains
REVERT: A  337 ASP cc_start: 0.8107 (t70) cc_final: 0.7729 (t0)
REVERT: A  500 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8169 (tt0)
REVERT: A  706 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6777 (mmt90)
REVERT: A  858 GLU cc_start: 0.7874 (pm20) cc_final: 0.7603 (pm20)
REVERT: A  869 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7463 (mm-40)
REVERT: A  948 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8379 (mt)
REVERT: A  966 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7642 (mt-10)
REVERT: A 1044 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7554 (ttm-80)
  outliers start: 19
  outliers final: 6
  residues processed: 97
  average time/residue: 1.8129
  time to fit residues: 187.3792
Evaluate side-chains
  92 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  500 GLU
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  705 SER
Chi-restraints excluded: chain A residue  706 ARG
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue  966 GLU
Chi-restraints excluded: chain A residue 1044 ARG
Chi-restraints excluded: chain A residue 1046 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 69 optimal weight:    0.5980
   chunk 68 optimal weight:    0.7980
   chunk 100 optimal weight:    5.9990
   chunk 59 optimal weight:    9.9990
   chunk 2 optimal weight:    2.9990
   chunk 84 optimal weight:    9.9990
   chunk 90 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1028 HIS ** 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 = 0.3913 r_free = 0.3913 target = 0.166022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.114381 restraints weight = 11114.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 1.59
r_work: 0.3181 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11431  Z= 0.149
  Angle     :  0.541   7.826  16150  Z= 0.290
  Chirality :  0.038   0.174   1854
  Planarity :  0.004   0.035   1494
  Dihedral  : 22.035 167.789   3337
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.29 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.28), residues: 902
  helix:  1.72 (0.27), residues: 389
  sheet: -0.75 (0.45), residues: 120
  loop : -0.06 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 763 
 HIS   0.002   0.001   HIS A 380 
 PHE   0.010   0.001   PHE A 932 
 TYR   0.013   0.001   TYR A 864 
 ARG   0.008   0.000   ARG A1060 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04355 (  480)
  hydrogen bonds       : angle       3.63302 ( 1214)
  covalent geometry    : bond        0.00335 (11431)
  covalent geometry    : angle       0.54128 (16150)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.921 
Fit side-chains
REVERT: A  290 GLN cc_start: 0.6332 (mt0) cc_final: 0.5710 (mp10)
REVERT: A  337 ASP cc_start: 0.8009 (t70) cc_final: 0.7618 (t0)
REVERT: A  706 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6682 (mmt90)
REVERT: A  798 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.7012 (mp)
REVERT: A  858 GLU cc_start: 0.7802 (pm20) cc_final: 0.7546 (pm20)
REVERT: A  869 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7407 (mm-40)
REVERT: A  966 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7534 (mt-10)
  outliers start: 18
  outliers final: 8
  residues processed: 100
  average time/residue: 1.7555
  time to fit residues: 186.3699
Evaluate side-chains
  91 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  705 SER
Chi-restraints excluded: chain A residue  706 ARG
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  966 GLU
Chi-restraints excluded: chain A residue 1046 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 51 optimal weight:    9.9990
   chunk 44 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 102 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 95 optimal weight:    8.9990
   chunk 8 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1028 HIS ** 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 = 0.3898 r_free = 0.3898 target = 0.164587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.122482 restraints weight = 11190.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 2.26
r_work: 0.3095 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.1738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  11431  Z= 0.198
  Angle     :  0.587   7.962  16150  Z= 0.313
  Chirality :  0.040   0.174   1854
  Planarity :  0.005   0.038   1494
  Dihedral  : 22.094 168.598   3337
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.29 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.28), residues: 902
  helix:  1.61 (0.27), residues: 387
  sheet: -0.86 (0.45), residues: 120
  loop : -0.11 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 763 
 HIS   0.002   0.001   HIS A 300 
 PHE   0.014   0.001   PHE A 932 
 TYR   0.018   0.001   TYR A 864 
 ARG   0.008   0.000   ARG A1060 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04879 (  480)
  hydrogen bonds       : angle       3.74638 ( 1214)
  covalent geometry    : bond        0.00449 (11431)
  covalent geometry    : angle       0.58659 (16150)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 1.227 
Fit side-chains
REVERT: A   38 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8165 (pt0)
REVERT: A  290 GLN cc_start: 0.6332 (mt0) cc_final: 0.5514 (mm110)
REVERT: A  337 ASP cc_start: 0.8078 (t70) cc_final: 0.7681 (t0)
REVERT: A  706 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6714 (mmt90)
REVERT: A  798 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7037 (mp)
REVERT: A  858 GLU cc_start: 0.7879 (pm20) cc_final: 0.7609 (pm20)
REVERT: A  869 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7468 (mm-40)
REVERT: A  966 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7635 (mt-10)
REVERT: A 1044 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7573 (ttm-80)
  outliers start: 20
  outliers final: 9
  residues processed: 97
  average time/residue: 1.8817
  time to fit residues: 193.6780
Evaluate side-chains
  93 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 GLU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  705 SER
Chi-restraints excluded: chain A residue  706 ARG
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  966 GLU
Chi-restraints excluded: chain A residue 1003 GLU
Chi-restraints excluded: chain A residue 1044 ARG
Chi-restraints excluded: chain A residue 1046 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 32 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 98 optimal weight:   10.0000
   chunk 85 optimal weight:    4.9990
   chunk 88 optimal weight:    0.7980
   chunk 95 optimal weight:    8.9990
   chunk 100 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    2.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 793 GLN
** A1028 HIS ** 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 = 0.3919 r_free = 0.3919 target = 0.165804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.124114 restraints weight = 11103.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.19
r_work: 0.3115 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  11431  Z= 0.226
  Angle     :  0.619   9.134  16150  Z= 0.329
  Chirality :  0.042   0.329   1854
  Planarity :  0.005   0.041   1494
  Dihedral  : 22.176 169.791   3337
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.28 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.28), residues: 902
  helix:  1.48 (0.27), residues: 388
  sheet: -1.00 (0.46), residues: 114
  loop : -0.21 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 763 
 HIS   0.002   0.001   HIS A 120 
 PHE   0.015   0.002   PHE A 932 
 TYR   0.020   0.001   TYR A 864 
 ARG   0.008   0.001   ARG A1031 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05154 (  480)
  hydrogen bonds       : angle       3.83506 ( 1214)
  covalent geometry    : bond        0.00514 (11431)
  covalent geometry    : angle       0.61914 (16150)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.985 
Fit side-chains
REVERT: A   38 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8193 (pt0)
REVERT: A  182 ILE cc_start: 0.7889 (mt) cc_final: 0.7541 (mm)
REVERT: A  337 ASP cc_start: 0.8186 (t70) cc_final: 0.7846 (t0)
REVERT: A  706 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6997 (mmt90)
REVERT: A  869 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7624 (mm-40)
REVERT: A  966 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7682 (mt-10)
REVERT: A 1044 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7761 (ttm-80)
  outliers start: 16
  outliers final: 9
  residues processed: 90
  average time/residue: 1.8062
  time to fit residues: 171.9229
Evaluate side-chains
  92 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 GLU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  705 SER
Chi-restraints excluded: chain A residue  706 ARG
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  966 GLU
Chi-restraints excluded: chain A residue 1003 GLU
Chi-restraints excluded: chain A residue 1044 ARG
Chi-restraints excluded: chain A residue 1046 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 91 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1028 HIS ** 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 = 0.3914 r_free = 0.3914 target = 0.165399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.124738 restraints weight = 11033.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.12
r_work: 0.3112 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  11431  Z= 0.242
  Angle     :  0.634  10.099  16150  Z= 0.337
  Chirality :  0.043   0.311   1854
  Planarity :  0.005   0.043   1494
  Dihedral  : 22.230 170.990   3337
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 16.52 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.28), residues: 902
  helix:  1.46 (0.27), residues: 381
  sheet: -1.10 (0.46), residues: 114
  loop : -0.24 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 763 
 HIS   0.003   0.001   HIS A 120 
 PHE   0.017   0.002   PHE A 932 
 TYR   0.021   0.002   TYR A 864 
 ARG   0.008   0.001   ARG A1031 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05272 (  480)
  hydrogen bonds       : angle       3.84525 ( 1214)
  covalent geometry    : bond        0.00553 (11431)
  covalent geometry    : angle       0.63375 (16150)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10004.09 seconds
wall clock time: 178 minutes 37.26 seconds (10717.26 seconds total)