Starting phenix.real_space_refine
on Tue Feb 11 16:02:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cag_45390/02_2025/9cag_45390_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cag_45390/02_2025/9cag_45390.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cag_45390/02_2025/9cag_45390.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cag_45390/02_2025/9cag_45390.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cag_45390/02_2025/9cag_45390_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cag_45390/02_2025/9cag_45390_neut.cif"
  }
  resolution = 3.33
  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=   0.001 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Mn      2      7.51       5
     P       8      5.49       5
     S      39      5.16       5
     C    3906      2.51       5
     N    1077      2.21       5
     O    1199      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6231
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 612, 4840
          Classifications: {'peptide': 612}
          Link IDs: {'PTRANS': 30, 'TRANS': 581}
    Chain: "B"
      Number of atoms: 1219
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1219
          Classifications: {'peptide': 161}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 153}
    Chain: "E"
      Number of atoms: 170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 170
          Classifications: {'RNA': 8}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 1, 'rna3p': 6}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.68, per 1000 atoms: 0.75
  Number of scatterers: 6231
  At special positions: 0
  Unit cell: (73.04, 86.32, 133.63, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      2     24.99
     S      39     16.00
     P       8     15.00
     O    1199      8.00
     N    1077      7.00
     C    3906      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: 1.62
  Conformation dependent library (CDL) restraints added in 870.3 milliseconds
  

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1442

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 6 sheets defined
      44.1% alpha, 16.3% beta
      0 base pairs and 3 stacking pairs defined.
    Time for finding SS restraints: 1.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 23
    Processing helix  chain 'A' and resid 68 through 76
      removed outlier: 3.560A  pdb=" N   ASN A  71 " --> pdb=" O   GLY A  68 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   TRP A  73 " --> pdb=" O   TYR A  70 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ASP A  74 " --> pdb=" O   ASN A  71 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LYS A  75 " --> pdb=" O   LYS A  72 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL A  76 " --> pdb=" O   TRP A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 82
      removed outlier: 3.888A  pdb=" N   PHE A  82 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 106
    Processing helix  chain 'A' and resid 119 through 134
    Processing helix  chain 'A' and resid 135 through 137
      No H-bonds generated for 'chain 'A' and resid 135 through 137'
    Processing helix  chain 'A' and resid 156 through 166
    Processing helix  chain 'A' and resid 171 through 201
      removed outlier: 3.805A  pdb=" N   ALA A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 203
      No H-bonds generated for 'chain 'A' and resid 202 through 203'
    Processing helix  chain 'A' and resid 204 through 208
      removed outlier: 3.536A  pdb=" N   LEU A 207 " --> pdb=" O   TYR A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 234
      removed outlier: 3.629A  pdb=" N   CYS A 225 " --> pdb=" O   THR A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 278
    Processing helix  chain 'A' and resid 302 through 313
    Processing helix  chain 'A' and resid 317 through 331
    Processing helix  chain 'A' and resid 349 through 356
    Processing helix  chain 'A' and resid 363 through 374
    Processing helix  chain 'A' and resid 403 through 420
      removed outlier: 3.707A  pdb=" N   VAL A 420 " --> pdb=" O   PHE A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 455
    Processing helix  chain 'A' and resid 495 through 507
    Processing helix  chain 'A' and resid 513 through 524
    Processing helix  chain 'A' and resid 538 through 553
      removed outlier: 3.903A  pdb=" N   ALA A 553 " --> pdb=" O   TYR A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 557
      removed outlier: 4.049A  pdb=" N   LEU A 557 " --> pdb=" O   GLU A 554 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 554 through 557'
    Processing helix  chain 'A' and resid 558 through 573
      removed outlier: 3.915A  pdb=" N   SER A 562 " --> pdb=" O   PRO A 558 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ILE A 571 " --> pdb=" O   GLN A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 599
      removed outlier: 3.975A  pdb=" N   VAL A 588 " --> pdb=" O   HIS A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 608
    Processing helix  chain 'B' and resid 2 through 13
    Processing helix  chain 'B' and resid 17 through 24
    Processing helix  chain 'B' and resid 33 through 41
      removed outlier: 3.602A  pdb=" N   ILE B  37 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 49
    Processing helix  chain 'B' and resid 56 through 60
      removed outlier: 3.519A  pdb=" N   GLY B  60 " --> pdb=" O   ILE B  57 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30
      removed outlier: 5.951A  pdb=" N   SER A  37 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   SER A  56 " --> pdb=" O   SER A  37 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   LYS A   2 " --> pdb=" O   ARG A  51 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   LYS A  53 " --> pdb=" O   LYS A   2 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   VAL A   4 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 7.521A  pdb=" N   THR A  55 " --> pdb=" O   VAL A   4 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   MET A   6 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   THR A   3 " --> pdb=" O   TYR A 111 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   VAL A 113 " --> pdb=" O   THR A   3 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   LEU A   5 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   TRP A 115 " --> pdb=" O   LEU A   5 " (cutoff:3.500A)
      removed outlier: 5.793A  pdb=" N   VAL A   7 " --> pdb=" O   TRP A 115 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 66
    Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 476
      removed outlier: 5.700A  pdb=" N   VAL A 285 " --> pdb=" O   ARG A 434 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   ARG A 434 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ALA A 287 " --> pdb=" O   SER A 432 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   LYS A 425 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   SER A 443 " --> pdb=" O   LEU A 256 " (cutoff:3.500A)
      removed outlier: 8.665A  pdb=" N   LEU A 256 " --> pdb=" O   SER A 443 " (cutoff:3.500A)
      removed outlier: 13.679A  pdb=" N   LYS A 445 " --> pdb=" O   SER A 254 " (cutoff:3.500A)
      removed outlier: 15.883A  pdb=" N   SER A 254 " --> pdb=" O   LYS A 445 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA A 245 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   TRP A 259 " --> pdb=" O   LEU A 243 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   LEU A 243 " --> pdb=" O   TRP A 259 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU A 480 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ASN A 248 " --> pdb=" O   VAL A 478 " (cutoff:3.500A)
      removed outlier: 5.525A  pdb=" N   VAL A 478 " --> pdb=" O   ASN A 248 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 527 through 529
    Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 65
    Processing sheet with id=AA6, first strand: chain 'B' and resid 139 through 142
      removed outlier: 9.603A  pdb=" N   LEU B 140 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   THR B 107 " --> pdb=" O   LEU B 140 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   LEU B 142 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLU B 110 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   LEU B  95 " --> pdb=" O   GLU B 110 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ARG B  77 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LYS B  75 " --> pdb=" O   GLN B  98 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   THR B 100 " --> pdb=" O   ILE B  73 " (cutoff:3.500A)
      removed outlier: 5.582A  pdb=" N   ILE B  73 " --> pdb=" O   THR B 100 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   LYS B 126 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)

    278 hydrogen bonds defined for protein.
    792 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      3 stacking parallelities
  Total time for adding SS restraints: 1.81

  Time building geometry restraints manager: 1.83 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: 2015
        1.34 -     1.46: 918
        1.46 -     1.57: 3369
        1.57 -     1.69: 10
        1.69 -     1.81: 61
  Bond restraints: 6373
  Sorted by residual:
  bond pdb=" O3'   A E   3 "
       pdb=" P     U E   4 "
    ideal  model  delta    sigma   weight residual
    1.607  1.525  0.082 1.50e-02 4.44e+03 3.00e+01
  bond pdb=" O3'   U E  -1 "
       pdb=" P     A E   0 "
    ideal  model  delta    sigma   weight residual
    1.607  1.551  0.056 1.50e-02 4.44e+03 1.39e+01
  bond pdb=" O3'   A E   0 "
       pdb=" P     A E   1 "
    ideal  model  delta    sigma   weight residual
    1.607  1.552  0.055 1.50e-02 4.44e+03 1.32e+01
  bond pdb=" O3'   A E   1 "
       pdb=" P     A E   2 "
    ideal  model  delta    sigma   weight residual
    1.607  1.567  0.040 1.50e-02 4.44e+03 6.94e+00
  bond pdb=" O3'   A E   2 "
       pdb=" P     A E   3 "
    ideal  model  delta    sigma   weight residual
    1.607  1.568  0.039 1.50e-02 4.44e+03 6.84e+00
  ... (remaining 6368 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 8531
        2.27 -     4.53: 114
        4.53 -     6.80: 11
        6.80 -     9.06: 2
        9.06 -    11.33: 1
  Bond angle restraints: 8659
  Sorted by residual:
  angle pdb=" C4'   A E   0 "
        pdb=" C3'   A E   0 "
        pdb=" O3'   A E   0 "
      ideal   model   delta    sigma   weight residual
     113.00  101.67   11.33 1.50e+00 4.44e-01 5.70e+01
  angle pdb=" C4'   A E   1 "
        pdb=" C3'   A E   1 "
        pdb=" O3'   A E   1 "
      ideal   model   delta    sigma   weight residual
     113.00  104.83    8.17 1.50e+00 4.44e-01 2.96e+01
  angle pdb=" C4'   A E   2 "
        pdb=" C3'   A E   2 "
        pdb=" O3'   A E   2 "
      ideal   model   delta    sigma   weight residual
     113.00  106.51    6.49 1.50e+00 4.44e-01 1.87e+01
  angle pdb=" C4'   C E  -2 "
        pdb=" C3'   C E  -2 "
        pdb=" O3'   C E  -2 "
      ideal   model   delta    sigma   weight residual
     113.00  106.84    6.16 1.50e+00 4.44e-01 1.69e+01
  angle pdb=" N   ILE A 125 "
        pdb=" CA  ILE A 125 "
        pdb=" C   ILE A 125 "
      ideal   model   delta    sigma   weight residual
     111.09  106.13    4.96 1.25e+00 6.40e-01 1.57e+01
  ... (remaining 8654 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.18: 3602
       24.18 -    48.36: 234
       48.36 -    72.55: 21
       72.55 -    96.73: 6
       96.73 -   120.91: 1
  Dihedral angle restraints: 3864
    sinusoidal: 1630
      harmonic: 2234
  Sorted by residual:
  dihedral pdb=" O4'   A E   1 "
           pdb=" C2'   A E   1 "
           pdb=" C1'   A E   1 "
           pdb=" C3'   A E   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00   -8.95   33.95     1      8.00e+00 1.56e-02 2.56e+01
  dihedral pdb=" C4'   A E   1 "
           pdb=" O4'   A E   1 "
           pdb=" C1'   A E   1 "
           pdb=" C2'   A E   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
       3.00  -30.89   33.89     1      8.00e+00 1.56e-02 2.55e+01
  dihedral pdb=" O4'   A E   0 "
           pdb=" C2'   A E   0 "
           pdb=" C1'   A E   0 "
           pdb=" C3'   A E   0 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00   -8.12   33.12     1      8.00e+00 1.56e-02 2.44e+01
  ... (remaining 3861 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 816
       0.057 -    0.115: 135
       0.115 -    0.172: 19
       0.172 -    0.229: 5
       0.229 -    0.286: 3
  Chirality restraints: 978
  Sorted by residual:
  chirality pdb=" C3'   A E   2 "
            pdb=" C4'   A E   2 "
            pdb=" O3'   A E   2 "
            pdb=" C2'   A E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.76    0.29 2.00e-01 2.50e+01 2.05e+00
  chirality pdb=" C3'   A E   1 "
            pdb=" C4'   A E   1 "
            pdb=" O3'   A E   1 "
            pdb=" C2'   A E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.73    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" C3'   A E   0 "
            pdb=" C4'   A E   0 "
            pdb=" O3'   A E   0 "
            pdb=" C2'   A E   0 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.73    0.25 2.00e-01 2.50e+01 1.57e+00
  ... (remaining 975 not shown)

  Planarity restraints: 1090
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  27 "   -0.055 5.00e-02 4.00e+02   8.31e-02 1.10e+01
        pdb=" N   PRO B  28 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO B  28 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO B  28 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A E   0 "    0.021 2.00e-02 2.50e+03   1.08e-02 3.20e+00
        pdb=" N9    A E   0 "   -0.026 2.00e-02 2.50e+03
        pdb=" C8    A E   0 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A E   0 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    A E   0 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    A E   0 "    0.003 2.00e-02 2.50e+03
        pdb=" N6    A E   0 "   -0.000 2.00e-02 2.50e+03
        pdb=" N1    A E   0 "    0.004 2.00e-02 2.50e+03
        pdb=" C2    A E   0 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    A E   0 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4    A E   0 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 172 "    0.013 2.00e-02 2.50e+03   1.41e-02 3.00e+00
        pdb=" CG  HIS A 172 "   -0.030 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 172 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 172 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 172 "    0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 172 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1087 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 69
        2.63 -     3.20: 5390
        3.20 -     3.76: 9386
        3.76 -     4.33: 12685
        4.33 -     4.90: 21354
  Nonbonded interactions: 48884
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 511 "
            pdb="MN    MN A 701 "
     model   vdw
     2.063 2.320
  nonbonded pdb=" OP1   A E   3 "
            pdb="MN    MN A 702 "
     model   vdw
     2.080 2.320
  nonbonded pdb=" OE1 GLU A 340 "
            pdb="MN    MN A 701 "
     model   vdw
     2.094 2.320
  nonbonded pdb=" OD2 ASP A 117 "
            pdb="MN    MN A 702 "
     model   vdw
     2.128 2.320
  nonbonded pdb=" OE1 GLU A   9 "
            pdb="MN    MN A 702 "
     model   vdw
     2.128 2.320
  ... (remaining 48879 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:             2.130
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     19.770
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
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      :  0.004   0.082   6373  Z= 0.264
  Angle     :  0.627  11.328   8659  Z= 0.356
  Chirality :  0.048   0.286    978
  Planarity :  0.005   0.083   1090
  Dihedral  : 15.051 120.912   2422
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.68 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.15 %
    Favored  : 99.70 %
  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:  0.57 (0.31), residues: 769
  helix:  1.12 (0.30), residues: 302
  sheet:  0.67 (0.42), residues: 148
  loop : -0.39 (0.37), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 458 
 HIS   0.015   0.001   HIS A 172 
 PHE   0.026   0.002   PHE B 111 
 TYR   0.012   0.001   TYR A 411 
 ARG   0.007   0.001   ARG A 579 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 210
  time to evaluate  : 0.722 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7339 (tt0)
REVERT: A   65 ASP cc_start: 0.7595 (t0) cc_final: 0.7253 (t0)
REVERT: A  126 CYS cc_start: 0.7009 (m) cc_final: 0.6587 (m)
REVERT: A  231 LYS cc_start: 0.8240 (mmmm) cc_final: 0.7933 (ttmm)
REVERT: A  235 PHE cc_start: 0.8454 (t80) cc_final: 0.7908 (t80)
REVERT: A  424 CYS cc_start: 0.7402 (t) cc_final: 0.7111 (t)
REVERT: A  608 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7147 (tm-30)
REVERT: B  135 ILE cc_start: 0.8227 (tt) cc_final: 0.7966 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 210
  average time/residue: 0.2300
  time to fit residues: 61.3263
Evaluate side-chains
  196 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0270
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
A  33 ASN
A 284 GLN
A 347 ASN
A 382 HIS
B  74 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.108363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.097858 restraints weight = 9667.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 2.06
r_work: 0.3092 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.0932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6373  Z= 0.272
  Angle     :  0.549   6.541   8659  Z= 0.289
  Chirality :  0.044   0.253    978
  Planarity :  0.004   0.061   1090
  Dihedral  :  9.138 114.239    934
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.42 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 11.38 %
    Favored  : 86.68 %
  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 (0.31), residues: 769
  helix:  1.06 (0.30), residues: 306
  sheet:  0.81 (0.42), residues: 156
  loop : -0.50 (0.37), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 458 
 HIS   0.006   0.001   HIS A 382 
 PHE   0.023   0.002   PHE B 111 
 TYR   0.016   0.002   TYR A  41 
 ARG   0.005   0.001   ARG A 579 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 194
  time to evaluate  : 0.662 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7609 (tt0)
REVERT: A   63 THR cc_start: 0.8356 (t) cc_final: 0.7937 (p)
REVERT: A   65 ASP cc_start: 0.8067 (t0) cc_final: 0.7782 (t0)
REVERT: A  126 CYS cc_start: 0.7724 (m) cc_final: 0.7258 (m)
REVERT: A  176 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7980 (mp)
REVERT: A  210 SER cc_start: 0.8743 (p) cc_final: 0.8543 (p)
REVERT: A  231 LYS cc_start: 0.8579 (mmmm) cc_final: 0.8360 (ttmm)
REVERT: A  235 PHE cc_start: 0.8622 (t80) cc_final: 0.8177 (t80)
REVERT: A  347 ASN cc_start: 0.8030 (OUTLIER) cc_final: 0.7781 (p0)
REVERT: A  424 CYS cc_start: 0.8024 (t) cc_final: 0.7742 (t)
REVERT: A  480 GLU cc_start: 0.7646 (pm20) cc_final: 0.7202 (pm20)
REVERT: A  511 ASP cc_start: 0.6900 (p0) cc_final: 0.6691 (p0)
REVERT: A  608 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7328 (tm-30)
  outliers start: 13
  outliers final: 9
  residues processed: 196
  average time/residue: 0.2227
  time to fit residues: 54.6795
Evaluate side-chains
  201 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 190
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   33 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 21 optimal weight:    0.3980
   chunk 53 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 271 GLN
A 347 ASN
A 382 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.107649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.096964 restraints weight = 9700.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 2.07
r_work: 0.3082 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   6373  Z= 0.303
  Angle     :  0.547   7.798   8659  Z= 0.287
  Chirality :  0.044   0.255    978
  Planarity :  0.004   0.054   1090
  Dihedral  :  8.951 108.884    934
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.55 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.27 %
    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:  0.45 (0.31), residues: 769
  helix:  1.02 (0.30), residues: 305
  sheet:  0.72 (0.42), residues: 157
  loop : -0.59 (0.37), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 458 
 HIS   0.006   0.001   HIS A 382 
 PHE   0.017   0.002   PHE B 111 
 TYR   0.017   0.002   TYR A  41 
 ARG   0.006   0.000   ARG A 579 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 191
  time to evaluate  : 0.882 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7626 (tt0)
REVERT: A   63 THR cc_start: 0.8460 (t) cc_final: 0.8118 (p)
REVERT: A   65 ASP cc_start: 0.8036 (t0) cc_final: 0.7802 (t0)
REVERT: A  100 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8173 (mtpp)
REVERT: A  126 CYS cc_start: 0.7778 (m) cc_final: 0.7302 (m)
REVERT: A  235 PHE cc_start: 0.8621 (t80) cc_final: 0.8160 (t80)
REVERT: A  347 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7891 (p0)
REVERT: A  424 CYS cc_start: 0.8065 (t) cc_final: 0.7747 (t)
REVERT: A  440 PHE cc_start: 0.8408 (m-80) cc_final: 0.7930 (m-80)
REVERT: A  480 GLU cc_start: 0.7690 (pm20) cc_final: 0.7337 (pm20)
REVERT: A  608 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7334 (tm-30)
  outliers start: 15
  outliers final: 12
  residues processed: 191
  average time/residue: 0.2250
  time to fit residues: 54.1540
Evaluate side-chains
  195 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 181
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  100 LYS
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue  135 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 49 optimal weight:    0.5980
   chunk 75 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0970
   chunk 66 optimal weight:    0.0570
   chunk 60 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0170
   chunk 74 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0040
   overall best weight:    0.1546

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

Flipped N/Q/H residues before XYZ refinement:
A 382 HIS
B  74 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.110240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.099402 restraints weight = 9752.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.11
r_work: 0.3110 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6373  Z= 0.144
  Angle     :  0.495   7.786   8659  Z= 0.257
  Chirality :  0.040   0.217    978
  Planarity :  0.004   0.049   1090
  Dihedral  :  8.961 106.410    934
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.90 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 16.32 %
    Favored  : 81.29 %
  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 (0.31), residues: 769
  helix:  1.32 (0.30), residues: 300
  sheet:  0.73 (0.41), residues: 157
  loop : -0.51 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 458 
 HIS   0.006   0.001   HIS A 382 
 PHE   0.013   0.001   PHE A 127 
 TYR   0.016   0.001   TYR A  41 
 ARG   0.005   0.000   ARG A 579 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 190
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7574 (tt0)
REVERT: A   63 THR cc_start: 0.8411 (t) cc_final: 0.8090 (p)
REVERT: A   65 ASP cc_start: 0.8046 (t0) cc_final: 0.7775 (t0)
REVERT: A  100 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8131 (mtpp)
REVERT: A  152 PHE cc_start: 0.8286 (p90) cc_final: 0.7975 (p90)
REVERT: A  176 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7892 (mp)
REVERT: A  235 PHE cc_start: 0.8603 (t80) cc_final: 0.8169 (t80)
REVERT: A  277 THR cc_start: 0.8786 (m) cc_final: 0.8579 (t)
REVERT: A  347 ASN cc_start: 0.8121 (p0) cc_final: 0.7811 (p0)
REVERT: A  424 CYS cc_start: 0.8062 (t) cc_final: 0.7771 (t)
REVERT: A  425 LYS cc_start: 0.8464 (mttp) cc_final: 0.8187 (mttm)
REVERT: A  440 PHE cc_start: 0.8389 (m-80) cc_final: 0.7936 (m-80)
REVERT: A  456 MET cc_start: 0.8705 (mtp) cc_final: 0.8481 (mtm)
REVERT: A  480 GLU cc_start: 0.7619 (pm20) cc_final: 0.7331 (pm20)
REVERT: A  608 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7250 (tm-30)
  outliers start: 16
  outliers final: 12
  residues processed: 194
  average time/residue: 0.2270
  time to fit residues: 55.2188
Evaluate side-chains
  203 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 189
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  100 LYS
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue  117 ILE
Chi-restraints excluded: chain B residue  135 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 37 optimal weight:    0.2980
   chunk 40 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0870
   chunk 11 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0670
   overall best weight:    0.3296

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

Flipped N/Q/H residues before XYZ refinement:
A 271 GLN
A 382 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.109828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.098983 restraints weight = 9738.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.10
r_work: 0.3108 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6373  Z= 0.181
  Angle     :  0.500   7.673   8659  Z= 0.258
  Chirality :  0.041   0.223    978
  Planarity :  0.004   0.046   1090
  Dihedral  :  8.899 103.143    934
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.03 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 18.56 %
    Favored  : 79.34 %
  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:  0.68 (0.31), residues: 769
  helix:  1.32 (0.30), residues: 301
  sheet:  0.71 (0.41), residues: 157
  loop : -0.49 (0.37), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 458 
 HIS   0.006   0.001   HIS A 382 
 PHE   0.011   0.001   PHE A 127 
 TYR   0.014   0.001   TYR A  41 
 ARG   0.006   0.000   ARG A 579 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 190
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7595 (tt0)
REVERT: A   57 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7865 (p)
REVERT: A   63 THR cc_start: 0.8451 (t) cc_final: 0.8126 (p)
REVERT: A   65 ASP cc_start: 0.8030 (t0) cc_final: 0.7740 (t0)
REVERT: A  100 LYS cc_start: 0.8523 (ttmm) cc_final: 0.8163 (mtpp)
REVERT: A  126 CYS cc_start: 0.7644 (m) cc_final: 0.7274 (m)
REVERT: A  152 PHE cc_start: 0.8305 (p90) cc_final: 0.7975 (p90)
REVERT: A  235 PHE cc_start: 0.8615 (t80) cc_final: 0.8160 (t80)
REVERT: A  340 GLU cc_start: 0.8034 (tt0) cc_final: 0.7486 (mt-10)
REVERT: A  386 ASP cc_start: 0.7811 (t0) cc_final: 0.7568 (t0)
REVERT: A  424 CYS cc_start: 0.8082 (t) cc_final: 0.7770 (t)
REVERT: A  425 LYS cc_start: 0.8482 (mttp) cc_final: 0.8219 (mttm)
REVERT: A  554 GLU cc_start: 0.8009 (tt0) cc_final: 0.7796 (tt0)
REVERT: A  608 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7261 (tm-30)
REVERT: B   74 GLN cc_start: 0.8139 (mp10) cc_final: 0.7866 (mp10)
  outliers start: 14
  outliers final: 11
  residues processed: 193
  average time/residue: 0.2285
  time to fit residues: 55.1936
Evaluate side-chains
  198 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 186
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue  117 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0980
   chunk 41 optimal weight:    0.3980
   chunk 34 optimal weight:    0.3980
   chunk 9 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 27 optimal weight:    0.3980
   chunk 23 optimal weight:    0.0060
   overall best weight:    0.2596

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

Flipped N/Q/H residues before XYZ refinement:
A 382 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.110509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.099682 restraints weight = 9635.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.08
r_work: 0.3115 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6373  Z= 0.155
  Angle     :  0.491   7.975   8659  Z= 0.251
  Chirality :  0.040   0.214    978
  Planarity :  0.004   0.045   1090
  Dihedral  :  8.894 101.698    934
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.90 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.56 %
    Favored  : 78.89 %
  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 (0.31), residues: 769
  helix:  1.38 (0.30), residues: 301
  sheet:  0.62 (0.42), residues: 152
  loop : -0.50 (0.37), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 458 
 HIS   0.006   0.001   HIS A 382 
 PHE   0.011   0.001   PHE A 127 
 TYR   0.013   0.001   TYR A 411 
 ARG   0.006   0.000   ARG A 579 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 188
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7558 (tt0)
REVERT: A   57 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.7840 (p)
REVERT: A   63 THR cc_start: 0.8437 (t) cc_final: 0.8124 (p)
REVERT: A   65 ASP cc_start: 0.8058 (t0) cc_final: 0.7755 (t0)
REVERT: A  100 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8161 (mtpp)
REVERT: A  119 ASP cc_start: 0.7720 (p0) cc_final: 0.7460 (p0)
REVERT: A  126 CYS cc_start: 0.7658 (m) cc_final: 0.7255 (m)
REVERT: A  152 PHE cc_start: 0.8344 (p90) cc_final: 0.7997 (p90)
REVERT: A  176 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7873 (mp)
REVERT: A  235 PHE cc_start: 0.8601 (t80) cc_final: 0.8155 (t80)
REVERT: A  340 GLU cc_start: 0.7995 (tt0) cc_final: 0.7419 (mt-10)
REVERT: A  424 CYS cc_start: 0.8057 (t) cc_final: 0.7739 (t)
REVERT: A  425 LYS cc_start: 0.8473 (mttp) cc_final: 0.8215 (mttm)
REVERT: A  554 GLU cc_start: 0.8026 (tt0) cc_final: 0.7781 (tt0)
REVERT: A  608 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7228 (tm-30)
REVERT: B   79 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7435 (m)
  outliers start: 17
  outliers final: 11
  residues processed: 195
  average time/residue: 0.2254
  time to fit residues: 54.9044
Evaluate side-chains
  201 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 187
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  117 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0070
   chunk 12 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0970
   chunk 43 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A 284 GLN
A 382 HIS
B  74 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.109350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.098494 restraints weight = 9677.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.09
r_work: 0.3095 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6373  Z= 0.220
  Angle     :  0.510   8.063   8659  Z= 0.262
  Chirality :  0.041   0.226    978
  Planarity :  0.004   0.044   1090
  Dihedral  :  8.814  99.324    934
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.77 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.01 %
    Favored  : 78.44 %
  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 (0.31), residues: 769
  helix:  1.33 (0.30), residues: 301
  sheet:  0.64 (0.41), residues: 158
  loop : -0.48 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 458 
 HIS   0.006   0.001   HIS A 382 
 PHE   0.010   0.001   PHE A 127 
 TYR   0.012   0.001   TYR A  41 
 ARG   0.006   0.000   ARG A 579 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 186
  time to evaluate  : 0.686 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7599 (tt0)
REVERT: A   57 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7844 (p)
REVERT: A   63 THR cc_start: 0.8487 (t) cc_final: 0.8169 (p)
REVERT: A   65 ASP cc_start: 0.8013 (t0) cc_final: 0.7735 (t0)
REVERT: A  126 CYS cc_start: 0.7701 (m) cc_final: 0.7296 (m)
REVERT: A  235 PHE cc_start: 0.8604 (t80) cc_final: 0.8125 (t80)
REVERT: A  322 MET cc_start: 0.8390 (tpp) cc_final: 0.8144 (mmt)
REVERT: A  340 GLU cc_start: 0.8067 (tt0) cc_final: 0.7516 (mt-10)
REVERT: A  424 CYS cc_start: 0.8079 (t) cc_final: 0.7764 (t)
REVERT: A  425 LYS cc_start: 0.8486 (mttp) cc_final: 0.8218 (mttm)
REVERT: A  554 GLU cc_start: 0.8036 (tt0) cc_final: 0.7834 (tt0)
REVERT: A  608 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7202 (tm-30)
  outliers start: 17
  outliers final: 13
  residues processed: 191
  average time/residue: 0.2310
  time to fit residues: 55.7463
Evaluate side-chains
  199 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 185
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  117 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 3 optimal weight:    0.0370
   chunk 28 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 7 optimal weight:    0.2980
   chunk 75 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
A 382 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.109224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.098354 restraints weight = 9708.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 2.08
r_work: 0.3097 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6373  Z= 0.225
  Angle     :  0.514   8.272   8659  Z= 0.265
  Chirality :  0.042   0.235    978
  Planarity :  0.004   0.045   1090
  Dihedral  :  8.812  97.874    934
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.90 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 19.31 %
    Favored  : 78.29 %
  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:  0.65 (0.31), residues: 769
  helix:  1.31 (0.30), residues: 301
  sheet:  0.60 (0.41), residues: 158
  loop : -0.47 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 458 
 HIS   0.006   0.001   HIS A 382 
 PHE   0.013   0.001   PHE A 152 
 TYR   0.019   0.002   TYR A  41 
 ARG   0.007   0.001   ARG A 472 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 188
  time to evaluate  : 0.687 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7626 (tt0)
REVERT: A   62 MET cc_start: 0.8066 (mtt) cc_final: 0.7847 (mtt)
REVERT: A   63 THR cc_start: 0.8435 (t) cc_final: 0.8138 (p)
REVERT: A   65 ASP cc_start: 0.8005 (t0) cc_final: 0.7740 (t0)
REVERT: A  119 ASP cc_start: 0.7806 (p0) cc_final: 0.7526 (p0)
REVERT: A  126 CYS cc_start: 0.7704 (m) cc_final: 0.7303 (m)
REVERT: A  128 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6982 (mm-30)
REVERT: A  235 PHE cc_start: 0.8608 (t80) cc_final: 0.8150 (t80)
REVERT: A  322 MET cc_start: 0.8406 (tpp) cc_final: 0.8167 (mmt)
REVERT: A  334 ILE cc_start: 0.8279 (mm) cc_final: 0.7626 (pt)
REVERT: A  340 GLU cc_start: 0.8113 (tt0) cc_final: 0.7610 (mt-10)
REVERT: A  424 CYS cc_start: 0.8091 (t) cc_final: 0.7780 (t)
REVERT: A  425 LYS cc_start: 0.8501 (mttp) cc_final: 0.8228 (mttm)
REVERT: A  554 GLU cc_start: 0.8062 (tt0) cc_final: 0.7842 (tt0)
REVERT: A  608 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7210 (tm-30)
  outliers start: 16
  outliers final: 14
  residues processed: 191
  average time/residue: 0.2227
  time to fit residues: 53.2124
Evaluate side-chains
  200 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 186
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  117 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0870
   chunk 17 optimal weight:    0.3980
   chunk 15 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 54 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
A 382 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.109269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.098428 restraints weight = 9739.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 2.09
r_work: 0.3096 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6373  Z= 0.221
  Angle     :  0.517   8.246   8659  Z= 0.267
  Chirality :  0.042   0.236    978
  Planarity :  0.004   0.045   1090
  Dihedral  :  8.795  96.356    934
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.16 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 19.01 %
    Favored  : 78.29 %
  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:  0.65 (0.31), residues: 769
  helix:  1.33 (0.30), residues: 301
  sheet:  0.60 (0.42), residues: 159
  loop : -0.49 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 458 
 HIS   0.006   0.001   HIS A 382 
 PHE   0.022   0.001   PHE A 152 
 TYR   0.018   0.001   TYR A  41 
 ARG   0.007   0.000   ARG A 472 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 192
  time to evaluate  : 0.671 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7622 (tt0)
REVERT: A   63 THR cc_start: 0.8446 (t) cc_final: 0.8138 (p)
REVERT: A   65 ASP cc_start: 0.8014 (t0) cc_final: 0.7750 (t0)
REVERT: A  126 CYS cc_start: 0.7750 (m) cc_final: 0.7345 (m)
REVERT: A  235 PHE cc_start: 0.8611 (t80) cc_final: 0.8149 (t80)
REVERT: A  322 MET cc_start: 0.8409 (tpp) cc_final: 0.8165 (mmt)
REVERT: A  340 GLU cc_start: 0.8093 (tt0) cc_final: 0.7742 (mt-10)
REVERT: A  424 CYS cc_start: 0.8099 (t) cc_final: 0.7752 (t)
REVERT: A  544 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7782 (mp)
REVERT: A  608 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7196 (tm-30)
  outliers start: 18
  outliers final: 15
  residues processed: 196
  average time/residue: 0.2415
  time to fit residues: 59.3118
Evaluate side-chains
  205 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 189
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  117 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 47 optimal weight:    0.0670
   chunk 63 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0270
   chunk 8 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.5176

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

Flipped N/Q/H residues before XYZ refinement:
A 275 ASN
A 382 HIS
A 387 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.108937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.098072 restraints weight = 9711.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 2.09
r_work: 0.3093 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6373  Z= 0.244
  Angle     :  0.533   7.324   8659  Z= 0.276
  Chirality :  0.042   0.240    978
  Planarity :  0.004   0.045   1090
  Dihedral  :  8.771  94.587    934
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.16 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 19.61 %
    Favored  : 78.14 %
  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:  0.62 (0.31), residues: 769
  helix:  1.32 (0.30), residues: 300
  sheet:  0.61 (0.43), residues: 153
  loop : -0.52 (0.37), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 458 
 HIS   0.007   0.001   HIS A 387 
 PHE   0.023   0.002   PHE A 152 
 TYR   0.018   0.002   TYR A  41 
 ARG   0.008   0.001   ARG A 369 

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 189
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7619 (tt0)
REVERT: A   63 THR cc_start: 0.8459 (t) cc_final: 0.8165 (p)
REVERT: A   65 ASP cc_start: 0.7993 (t0) cc_final: 0.7740 (t0)
REVERT: A  126 CYS cc_start: 0.7798 (m) cc_final: 0.7350 (m)
REVERT: A  235 PHE cc_start: 0.8624 (t80) cc_final: 0.8152 (t80)
REVERT: A  322 MET cc_start: 0.8411 (tpp) cc_final: 0.8174 (mmt)
REVERT: A  340 GLU cc_start: 0.8113 (tt0) cc_final: 0.7757 (mt-10)
REVERT: A  424 CYS cc_start: 0.8107 (t) cc_final: 0.7759 (t)
REVERT: A  603 MET cc_start: 0.7652 (mtt) cc_final: 0.7295 (mtt)
REVERT: A  608 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7199 (tm-30)
  outliers start: 15
  outliers final: 15
  residues processed: 192
  average time/residue: 0.2203
  time to fit residues: 52.7436
Evaluate side-chains
  204 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 189
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  117 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 20 optimal weight:    0.2980
   chunk 76 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 36 optimal weight:    0.2980
   chunk 18 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 271 GLN
A 275 ASN
A 382 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.108886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.098032 restraints weight = 9842.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 2.10
r_work: 0.3084 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6373  Z= 0.245
  Angle     :  0.535   8.211   8659  Z= 0.278
  Chirality :  0.042   0.241    978
  Planarity :  0.004   0.045   1090
  Dihedral  :  8.755  92.724    934
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.03 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 19.31 %
    Favored  : 77.99 %
  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:  0.58 (0.31), residues: 769
  helix:  1.29 (0.30), residues: 300
  sheet:  0.57 (0.43), residues: 153
  loop : -0.53 (0.37), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 458 
 HIS   0.006   0.001   HIS A 382 
 PHE   0.023   0.002   PHE A 152 
 TYR   0.018   0.002   TYR A  41 
 ARG   0.009   0.001   ARG A 369 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3347.26 seconds
wall clock time: 60 minutes 8.40 seconds (3608.40 seconds total)