Starting phenix.real_space_refine
on Sat Aug 23 04:48:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wf9_37487/08_2025/8wf9_37487.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wf9_37487/08_2025/8wf9_37487.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wf9_37487/08_2025/8wf9_37487.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wf9_37487/08_2025/8wf9_37487.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wf9_37487/08_2025/8wf9_37487.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wf9_37487/08_2025/8wf9_37487.cif"
  }
  resolution = 3.13
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.038
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
     P      72      5.49       5
     Mg      1      5.21       5
     S      42      5.16       5
     C    5961      2.51       5
     N    1697      2.21       5
     O    2043      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9816
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8276
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1002, 8276
          Classifications: {'peptide': 1002}
          Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 969}
          Chain breaks: 10
    Chain: "B"
      Number of atoms: 1148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 1148
          Classifications: {'RNA': 54}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 23, 'rna3p_pyr': 25}
          Link IDs: {'rna2p': 6, 'rna3p': 47}
    Chain: "C"
      Number of atoms: 391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 391
          Classifications: {'RNA': 18}
          Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 6}
          Link IDs: {'rna3p': 17}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.86, per 1000 atoms: 0.19
  Number of scatterers: 9816
  At special positions: 0
  Unit cell: (101.26, 104.58, 127.82, 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)
     S      42     16.00
     P      72     15.00
     Mg      1     11.99
     O    2043      8.00
     N    1697      7.00
     C    5961      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 285.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1922

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 7 sheets defined
      65.5% alpha, 7.6% beta
      30 base pairs and 44 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 10
    Processing helix  chain 'A' and resid 10 through 36
    Processing helix  chain 'A' and resid 48 through 51
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 3.521A  pdb=" N   LYS A  62 " --> pdb=" O   LEU A  58 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ASN A  63 " --> pdb=" O   TYR A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 83
    Processing helix  chain 'A' and resid 84 through 97
      removed outlier: 4.488A  pdb=" N   ILE A  88 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 132
    Processing helix  chain 'A' and resid 138 through 142
    Processing helix  chain 'A' and resid 145 through 151
    Processing helix  chain 'A' and resid 151 through 175
      removed outlier: 3.637A  pdb=" N   VAL A 165 " --> pdb=" O   ASN A 161 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ASN A 171 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   GLU A 172 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 186
      removed outlier: 4.851A  pdb=" N   PHE A 183 " --> pdb=" O   GLU A 179 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   ILE A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 236
      removed outlier: 4.010A  pdb=" N   PHE A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 247
    Processing helix  chain 'A' and resid 259 through 271
    Processing helix  chain 'A' and resid 286 through 299
      removed outlier: 3.541A  pdb=" N   LYS A 299 " --> pdb=" O   LEU A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 307
    Processing helix  chain 'A' and resid 310 through 316
    Processing helix  chain 'A' and resid 335 through 348
    Processing helix  chain 'A' and resid 391 through 400
      removed outlier: 3.810A  pdb=" N   LYS A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 429
    Processing helix  chain 'A' and resid 482 through 494
    Processing helix  chain 'A' and resid 494 through 518
    Processing helix  chain 'A' and resid 525 through 530
    Processing helix  chain 'A' and resid 532 through 536
    Processing helix  chain 'A' and resid 537 through 546
    Processing helix  chain 'A' and resid 552 through 577
    Processing helix  chain 'A' and resid 605 through 613
    Processing helix  chain 'A' and resid 617 through 621
    Processing helix  chain 'A' and resid 625 through 635
    Processing helix  chain 'A' and resid 645 through 658
      removed outlier: 4.077A  pdb=" N   PHE A 655 " --> pdb=" O   PHE A 651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 676
      removed outlier: 3.805A  pdb=" N   VAL A 675 " --> pdb=" O   PHE A 671 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   PHE A 676 " --> pdb=" O   LEU A 672 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 671 through 676'
    Processing helix  chain 'A' and resid 683 through 708
    Processing helix  chain 'A' and resid 721 through 725
    Processing helix  chain 'A' and resid 728 through 739
    Processing helix  chain 'A' and resid 749 through 760
      removed outlier: 3.577A  pdb=" N   LEU A 760 " --> pdb=" O   HIS A 756 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 764
    Processing helix  chain 'A' and resid 767 through 771
      removed outlier: 4.026A  pdb=" N   ALA A 771 " --> pdb=" O   PHE A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 784
      removed outlier: 3.549A  pdb=" N   ALA A 778 " --> pdb=" O   THR A 774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 790 through 794
    Processing helix  chain 'A' and resid 799 through 807
    Processing helix  chain 'A' and resid 821 through 831
    Processing helix  chain 'A' and resid 831 through 849
    Processing helix  chain 'A' and resid 858 through 904
      removed outlier: 3.714A  pdb=" N   VAL A 888 " --> pdb=" O   ARG A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 913 through 917
    Processing helix  chain 'A' and resid 924 through 927
    Processing helix  chain 'A' and resid 953 through 955
      No H-bonds generated for 'chain 'A' and resid 953 through 955'
    Processing helix  chain 'A' and resid 956 through 963
      removed outlier: 3.537A  pdb=" N   VAL A 960 " --> pdb=" O   GLY A 956 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 975
    Processing helix  chain 'A' and resid 981 through 1013
      Proline residue:  A 996  - end of helix
    Processing helix  chain 'A' and resid 1014 through 1022
    Processing helix  chain 'A' and resid 1027 through 1038
    Processing helix  chain 'A' and resid 1042 through 1058
    Processing helix  chain 'A' and resid 1074 through 1087
    Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 190
    Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 213
    Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 283
      removed outlier: 5.713A  pdb=" N   MET A 930 " --> pdb=" O   GLY A 949 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   GLY A 949 " --> pdb=" O   MET A 930 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 318 through 320
    Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 389
      removed outlier: 4.256A  pdb=" N   GLY A 360 " --> pdb=" O   LEU A 386 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   GLY A 388 " --> pdb=" O   ASN A 358 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   ASN A 358 " --> pdb=" O   GLY A 388 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 413 through 414
      removed outlier: 4.093A  pdb=" N   LYS A 361 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   GLU A 447 " --> pdb=" O   HIS A 356 " (cutoff:3.500A)
      removed outlier: 11.316A  pdb=" N   ASN A 358 " --> pdb=" O   LYS A 445 " (cutoff:3.500A)
      removed outlier: 15.981A  pdb=" N   LYS A 445 " --> pdb=" O   ASN A 358 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 462 through 464
      removed outlier: 3.710A  pdb=" N   VAL A 462 " --> pdb=" O   VAL A 470 " (cutoff:3.500A)

    475 hydrogen bonds defined for protein.
    1335 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      76 hydrogen bonds
      140 hydrogen bond angles
      0 basepair planarities
      30 basepair parallelities
      44 stacking parallelities
  Total time for adding SS restraints: 1.85

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1581
        1.32 -     1.45: 3009
        1.45 -     1.57: 5333
        1.57 -     1.69: 146
        1.69 -     1.82: 78
  Bond restraints: 10147
  Sorted by residual:
  bond pdb=" CA  ALA A 485 "
       pdb=" CB  ALA A 485 "
    ideal  model  delta    sigma   weight residual
    1.528  1.475  0.053 1.59e-02 3.96e+03 1.11e+01
  bond pdb=" CA  PRO A 484 "
       pdb=" CB  PRO A 484 "
    ideal  model  delta    sigma   weight residual
    1.534  1.485  0.049 1.52e-02 4.33e+03 1.04e+01
  bond pdb=" C   ASP A 890 "
       pdb=" O   ASP A 890 "
    ideal  model  delta    sigma   weight residual
    1.237  1.200  0.037 1.17e-02 7.31e+03 9.77e+00
  bond pdb=" CA  SER A 475 "
       pdb=" CB  SER A 475 "
    ideal  model  delta    sigma   weight residual
    1.528  1.482  0.047 1.56e-02 4.11e+03 8.96e+00
  bond pdb=" CA  VAL A 714 "
       pdb=" CB  VAL A 714 "
    ideal  model  delta    sigma   weight residual
    1.539  1.555 -0.016 5.40e-03 3.43e+04 8.87e+00
  ... (remaining 10142 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.35: 13110
        3.35 -     6.70: 775
        6.70 -    10.04: 87
       10.04 -    13.39: 10
       13.39 -    16.74: 3
  Bond angle restraints: 13985
  Sorted by residual:
  angle pdb=" C3'   G B  10 "
        pdb=" C2'   G B  10 "
        pdb=" O2'   G B  10 "
      ideal   model   delta    sigma   weight residual
     110.70  125.05  -14.35 1.50e+00 4.44e-01 9.16e+01
  angle pdb=" CA  ARG A 835 "
        pdb=" CB  ARG A 835 "
        pdb=" CG  ARG A 835 "
      ideal   model   delta    sigma   weight residual
     114.10  129.74  -15.64 2.00e+00 2.50e-01 6.12e+01
  angle pdb=" O3'   A B  29 "
        pdb=" P     U B  30 "
        pdb=" O5'   U B  30 "
      ideal   model   delta    sigma   weight residual
     104.00   92.40   11.60 1.50e+00 4.44e-01 5.98e+01
  angle pdb=" CG  MET A 763 "
        pdb=" SD  MET A 763 "
        pdb=" CE  MET A 763 "
      ideal   model   delta    sigma   weight residual
     100.90  117.64  -16.74 2.20e+00 2.07e-01 5.79e+01
  angle pdb=" CA  PHE A 671 "
        pdb=" CB  PHE A 671 "
        pdb=" CG  PHE A 671 "
      ideal   model   delta    sigma   weight residual
     113.80  121.22   -7.42 1.00e+00 1.00e+00 5.50e+01
  ... (remaining 13980 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 5519
       17.43 -    34.85: 516
       34.85 -    52.28: 145
       52.28 -    69.71: 113
       69.71 -    87.13: 24
  Dihedral angle restraints: 6317
    sinusoidal: 3357
      harmonic: 2960
  Sorted by residual:
  dihedral pdb=" C5'   G B  21 "
           pdb=" C4'   G B  21 "
           pdb=" C3'   G B  21 "
           pdb=" O3'   G B  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  100.10   46.90     1      8.00e+00 1.56e-02 4.75e+01
  dihedral pdb=" C   LYS A 782 "
           pdb=" N   LYS A 782 "
           pdb=" CA  LYS A 782 "
           pdb=" CB  LYS A 782 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.70   17.10     0      2.50e+00 1.60e-01 4.68e+01
  dihedral pdb=" O4'   G B  21 "
           pdb=" C4'   G B  21 "
           pdb=" C3'   G B  21 "
           pdb=" C2'   G B  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -21.91   45.91     1      8.00e+00 1.56e-02 4.56e+01
  ... (remaining 6314 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.121: 1260
       0.121 -    0.242: 292
       0.242 -    0.362: 14
       0.362 -    0.483: 4
       0.483 -    0.604: 4
  Chirality restraints: 1574
  Sorted by residual:
  chirality pdb=" CA  LYS A 782 "
            pdb=" N   LYS A 782 "
            pdb=" C   LYS A 782 "
            pdb=" CB  LYS A 782 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.91    0.60 2.00e-01 2.50e+01 9.11e+00
  chirality pdb=" P     U C   1 "
            pdb=" OP1   U C   1 "
            pdb=" OP2   U C   1 "
            pdb=" O5'   U C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -3.00   -0.59 2.00e-01 2.50e+01 8.67e+00
  chirality pdb=" P     U B -17 "
            pdb=" OP1   U B -17 "
            pdb=" OP2   U B -17 "
            pdb=" O5'   U B -17 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.98   -0.57 2.00e-01 2.50e+01 8.11e+00
  ... (remaining 1571 not shown)

  Planarity restraints: 1530
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B  30 "   -0.063 2.00e-02 2.50e+03   3.34e-02 2.51e+01
        pdb=" N1    U B  30 "    0.062 2.00e-02 2.50e+03
        pdb=" C2    U B  30 "    0.014 2.00e-02 2.50e+03
        pdb=" O2    U B  30 "   -0.010 2.00e-02 2.50e+03
        pdb=" N3    U B  30 "    0.021 2.00e-02 2.50e+03
        pdb=" C4    U B  30 "   -0.007 2.00e-02 2.50e+03
        pdb=" O4    U B  30 "   -0.029 2.00e-02 2.50e+03
        pdb=" C5    U B  30 "   -0.010 2.00e-02 2.50e+03
        pdb=" C6    U B  30 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B  19 "   -0.054 2.00e-02 2.50e+03   3.20e-02 2.31e+01
        pdb=" N1    U B  19 "    0.067 2.00e-02 2.50e+03
        pdb=" C2    U B  19 "    0.009 2.00e-02 2.50e+03
        pdb=" O2    U B  19 "   -0.013 2.00e-02 2.50e+03
        pdb=" N3    U B  19 "    0.014 2.00e-02 2.50e+03
        pdb=" C4    U B  19 "    0.004 2.00e-02 2.50e+03
        pdb=" O4    U B  19 "   -0.022 2.00e-02 2.50e+03
        pdb=" C5    U B  19 "   -0.024 2.00e-02 2.50e+03
        pdb=" C6    U B  19 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B   8 "   -0.055 2.00e-02 2.50e+03   2.79e-02 2.14e+01
        pdb=" N9    A B   8 "    0.036 2.00e-02 2.50e+03
        pdb=" C8    A B   8 "    0.015 2.00e-02 2.50e+03
        pdb=" N7    A B   8 "    0.032 2.00e-02 2.50e+03
        pdb=" C5    A B   8 "   -0.020 2.00e-02 2.50e+03
        pdb=" C6    A B   8 "   -0.029 2.00e-02 2.50e+03
        pdb=" N6    A B   8 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1    A B   8 "   -0.013 2.00e-02 2.50e+03
        pdb=" C2    A B   8 "    0.030 2.00e-02 2.50e+03
        pdb=" N3    A B   8 "    0.023 2.00e-02 2.50e+03
        pdb=" C4    A B   8 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1527 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 232
        2.68 -     3.24: 8897
        3.24 -     3.79: 15710
        3.79 -     4.35: 21986
        4.35 -     4.90: 33177
  Nonbonded interactions: 80002
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 747 "
            pdb="MG    MG A1101 "
     model   vdw
     2.129 2.170
  nonbonded pdb=" OD2 ASP A 345 "
            pdb=" OH  TYR A 439 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" OG  SER A 259 "
            pdb=" OE1 GLU A 261 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OP1   G B  23 "
            pdb="MG    MG A1101 "
     model   vdw
     2.205 2.170
  nonbonded pdb=" O2'   U B  18 "
            pdb=" OP2   G B  21 "
     model   vdw
     2.290 3.040
  ... (remaining 79997 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:             1.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     9.720
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
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      :  0.010   0.069  10147  Z= 0.583
  Angle     :  1.784  16.739  13985  Z= 1.119
  Chirality :  0.098   0.604   1574
  Planarity :  0.007   0.071   1530
  Dihedral  : 17.420  87.133   4395
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.53 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  :  5.93 %
    Favored  : 91.00 %
  Cbeta Deviations :  0.83 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.03 (0.24), residues: 980
  helix: -1.10 (0.17), residues: 568
  sheet:  0.39 (0.82), residues: 44
  loop :  0.26 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.049   0.004   ARG A 835 
 TYR   0.051   0.007   TYR A 343 
 PHE   0.041   0.006   PHE A 355 
 TRP   0.029   0.006   TRP A 829 
 HIS   0.013   0.003   HIS A 756 

Details of bonding type rmsd
  covalent geometry    : bond        0.00966 (10147)
  covalent geometry    : angle       1.78424 (13985)
  hydrogen bonds       : bond        0.18634 (  551)
  hydrogen bonds       : angle       6.77911 ( 1475)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 193
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7281 (ttp) cc_final: 0.7028 (tmm)
REVERT: A   10 GLN cc_start: 0.7764 (mm110) cc_final: 0.7319 (mp10)
REVERT: A   96 TYR cc_start: 0.8132 (t80) cc_final: 0.7847 (t80)
REVERT: A  132 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7934 (m-40)
REVERT: A  139 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7041 (tm-30)
REVERT: A  171 ASN cc_start: 0.7025 (t0) cc_final: 0.6565 (m-40)
REVERT: A  176 TYR cc_start: 0.7238 (m-80) cc_final: 0.6939 (m-80)
REVERT: A  186 ASP cc_start: 0.7538 (m-30) cc_final: 0.7296 (t70)
REVERT: A  187 LYS cc_start: 0.7004 (mttt) cc_final: 0.6600 (mmtp)
REVERT: A  262 ARG cc_start: 0.6148 (ttt180) cc_final: 0.5873 (ttm170)
REVERT: A  365 LEU cc_start: 0.6662 (tt) cc_final: 0.6237 (tp)
REVERT: A  393 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6462 (tp30)
REVERT: A  453 LYS cc_start: 0.8076 (mttt) cc_final: 0.7762 (tptt)
REVERT: A  516 MET cc_start: 0.7109 (mtp) cc_final: 0.6742 (mtp)
REVERT: A  519 GLU cc_start: 0.6514 (mt-10) cc_final: 0.6234 (mp0)
REVERT: A  520 GLU cc_start: 0.6338 (mt-10) cc_final: 0.5235 (tm-30)
REVERT: A  534 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.7915 (p)
REVERT: A  547 ASN cc_start: 0.7860 (m-40) cc_final: 0.7502 (m110)
REVERT: A  730 LYS cc_start: 0.7441 (tttt) cc_final: 0.6593 (ptpt)
REVERT: A  738 GLU cc_start: 0.7600 (pt0) cc_final: 0.7206 (pt0)
REVERT: A  927 SER cc_start: 0.7705 (t) cc_final: 0.7275 (m)
REVERT: A  965 LYS cc_start: 0.8433 (mttt) cc_final: 0.8210 (tttt)
REVERT: A 1008 TRP cc_start: 0.7689 (t60) cc_final: 0.7371 (t60)
REVERT: A 1013 TYR cc_start: 0.8567 (m-80) cc_final: 0.7642 (m-10)
REVERT: A 1027 ASP cc_start: 0.8125 (t0) cc_final: 0.7847 (t0)
REVERT: A 1038 ASN cc_start: 0.8421 (m-40) cc_final: 0.7752 (t0)
REVERT: A 1047 ASP cc_start: 0.8068 (m-30) cc_final: 0.7739 (t0)
REVERT: A 1061 TYR cc_start: 0.8775 (m-80) cc_final: 0.8377 (m-80)
REVERT: A 1077 MET cc_start: 0.7705 (mmm) cc_final: 0.7296 (mmt)
  outliers start: 28
  outliers final: 12
  residues processed: 216
  average time/residue: 0.1049
  time to fit residues: 30.2726
Evaluate side-chains
  137 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 GLU
Chi-restraints excluded: chain A residue  132 ASN
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  393 GLU
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain A residue  671 PHE
Chi-restraints excluded: chain A residue  763 MET
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  907 PHE
Chi-restraints excluded: chain A residue 1020 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.0770
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:   30.0000
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.3544

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A 153 GLN
A 169 ASN
A 171 ASN
A 219 GLN
A 358 ASN
A 387 ASN
A 514 GLN
A 756 HIS
A 794 GLN
A 852 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.200036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.148741 restraints weight = 11525.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 2.53
r_work: 0.3322 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10147  Z= 0.174
  Angle     :  0.581   6.300  13985  Z= 0.310
  Chirality :  0.040   0.212   1574
  Planarity :  0.004   0.044   1530
  Dihedral  : 16.705  79.285   2267
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  :  9.66 %
    Favored  : 87.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.26), residues: 980
  helix:  1.59 (0.20), residues: 576
  sheet:  0.20 (0.82), residues: 44
  loop :  0.18 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 363 
 TYR   0.018   0.002   TYR A 886 
 PHE   0.019   0.002   PHE A 792 
 TRP   0.013   0.002   TRP A 724 
 HIS   0.006   0.001   HIS A 489 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (10147)
  covalent geometry    : angle       0.58139 (13985)
  hydrogen bonds       : bond        0.05660 (  551)
  hydrogen bonds       : angle       4.22015 ( 1475)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 TYR cc_start: 0.8052 (t80) cc_final: 0.7800 (t80)
REVERT: A  126 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7726 (ttp)
REVERT: A  129 ASP cc_start: 0.8103 (m-30) cc_final: 0.7845 (m-30)
REVERT: A  170 MET cc_start: 0.7189 (mtp) cc_final: 0.6681 (mtp)
REVERT: A  186 ASP cc_start: 0.7738 (m-30) cc_final: 0.7490 (m-30)
REVERT: A  297 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7968 (tt0)
REVERT: A  365 LEU cc_start: 0.6927 (tt) cc_final: 0.6681 (tp)
REVERT: A  453 LYS cc_start: 0.8559 (mttt) cc_final: 0.8300 (mtmm)
REVERT: A  492 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8548 (mp)
REVERT: A  520 GLU cc_start: 0.6474 (mt-10) cc_final: 0.5611 (tm-30)
REVERT: A  549 HIS cc_start: 0.7898 (p-80) cc_final: 0.7611 (p-80)
REVERT: A  922 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7965 (mp0)
REVERT: A 1013 TYR cc_start: 0.8561 (m-80) cc_final: 0.8153 (m-10)
REVERT: A 1038 ASN cc_start: 0.8276 (m-40) cc_final: 0.7805 (t0)
  outliers start: 28
  outliers final: 12
  residues processed: 142
  average time/residue: 0.0920
  time to fit residues: 18.0586
Evaluate side-chains
  114 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 MET
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  393 GLU
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain A residue  456 SER
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain A residue  820 THR
Chi-restraints excluded: chain A residue  976 SER
Chi-restraints excluded: chain A residue  982 GLU
Chi-restraints excluded: chain A residue  984 ILE
Chi-restraints excluded: chain A residue  985 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 13 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A 153 GLN
A 219 GLN
A 517 GLN
A 722 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.198664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.145410 restraints weight = 11353.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 2.48
r_work: 0.3332 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10147  Z= 0.128
  Angle     :  0.480   5.963  13985  Z= 0.255
  Chirality :  0.037   0.163   1574
  Planarity :  0.004   0.038   1530
  Dihedral  : 16.463  74.042   2245
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 10.87 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.22 (0.27), residues: 980
  helix:  2.26 (0.21), residues: 578
  sheet:  0.51 (0.85), residues: 41
  loop :  0.37 (0.35), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 105 
 TYR   0.014   0.001   TYR A  17 
 PHE   0.017   0.001   PHE A 792 
 TRP   0.013   0.002   TRP A1008 
 HIS   0.003   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10147)
  covalent geometry    : angle       0.48024 (13985)
  hydrogen bonds       : bond        0.04636 (  551)
  hydrogen bonds       : angle       3.91471 ( 1475)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A   96 TYR cc_start: 0.8066 (t80) cc_final: 0.7859 (t80)
REVERT: A  129 ASP cc_start: 0.8148 (m-30) cc_final: 0.7929 (m-30)
REVERT: A  297 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8001 (tt0)
REVERT: A  365 LEU cc_start: 0.6808 (tt) cc_final: 0.6323 (tp)
REVERT: A  453 LYS cc_start: 0.8609 (mttt) cc_final: 0.8302 (mtmt)
REVERT: A  520 GLU cc_start: 0.6427 (mt-10) cc_final: 0.5616 (tm-30)
REVERT: A  781 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.7093 (ttt)
REVERT: A  982 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7307 (pm20)
REVERT: A 1013 TYR cc_start: 0.8483 (m-80) cc_final: 0.7928 (m-80)
REVERT: A 1038 ASN cc_start: 0.8116 (m-40) cc_final: 0.7760 (t0)
  outliers start: 21
  outliers final: 10
  residues processed: 129
  average time/residue: 0.0861
  time to fit residues: 15.3822
Evaluate side-chains
  111 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  393 GLU
Chi-restraints excluded: chain A residue  456 SER
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  917 ILE
Chi-restraints excluded: chain A residue  976 SER
Chi-restraints excluded: chain A residue  982 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 58 optimal weight:    8.9990
   chunk 77 optimal weight:    9.9990
   chunk 95 optimal weight:    6.9990
   chunk 105 optimal weight:   20.0000
   chunk 44 optimal weight:    0.2980
   chunk 42 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 53 optimal weight:   20.0000
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
A 549 HIS
A 722 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.197651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.141733 restraints weight = 11497.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.57
r_work: 0.3307 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10147  Z= 0.147
  Angle     :  0.487   6.679  13985  Z= 0.256
  Chirality :  0.036   0.162   1574
  Planarity :  0.004   0.037   1530
  Dihedral  : 16.400  74.018   2244
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.73 %
    Favored  : 85.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.27), residues: 980
  helix:  2.33 (0.21), residues: 574
  sheet:  0.37 (0.87), residues: 41
  loop :  0.39 (0.35), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 128 
 TYR   0.014   0.001   TYR A  17 
 PHE   0.017   0.001   PHE A 792 
 TRP   0.011   0.002   TRP A1008 
 HIS   0.003   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (10147)
  covalent geometry    : angle       0.48672 (13985)
  hydrogen bonds       : bond        0.04554 (  551)
  hydrogen bonds       : angle       3.89960 ( 1475)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A  105 ARG cc_start: 0.6546 (ptp90) cc_final: 0.6124 (ptt-90)
REVERT: A  129 ASP cc_start: 0.8187 (m-30) cc_final: 0.7974 (m-30)
REVERT: A  297 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7963 (tt0)
REVERT: A  365 LEU cc_start: 0.6697 (tt) cc_final: 0.6192 (tp)
REVERT: A  398 MET cc_start: 0.8018 (tpp) cc_final: 0.7731 (mmm)
REVERT: A  453 LYS cc_start: 0.8662 (mttt) cc_final: 0.8183 (mtmt)
REVERT: A  520 GLU cc_start: 0.6444 (mt-10) cc_final: 0.5662 (tm-30)
REVERT: A  781 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.7106 (ttt)
REVERT: A  831 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6917 (mt-10)
REVERT: A 1013 TYR cc_start: 0.8424 (m-80) cc_final: 0.7983 (m-80)
REVERT: A 1038 ASN cc_start: 0.8076 (m-40) cc_final: 0.7682 (t0)
  outliers start: 19
  outliers final: 12
  residues processed: 119
  average time/residue: 0.0973
  time to fit residues: 16.0630
Evaluate side-chains
  111 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  403 ASN
Chi-restraints excluded: chain A residue  456 SER
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  841 LYS
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  917 ILE
Chi-restraints excluded: chain A residue  976 SER
Chi-restraints excluded: chain A residue  984 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0170
   chunk 0 optimal weight:    7.9990
   chunk 3 optimal weight:    7.9990
   chunk 32 optimal weight:    0.7980
   chunk 75 optimal weight:    6.9990
   chunk 10 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.8820

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
A 549 HIS
A 722 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.198871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.142878 restraints weight = 11428.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 2.49
r_work: 0.3336 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10147  Z= 0.118
  Angle     :  0.448   6.391  13985  Z= 0.236
  Chirality :  0.035   0.143   1574
  Planarity :  0.003   0.034   1530
  Dihedral  : 16.257  73.912   2241
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 12.73 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.46 (0.27), residues: 980
  helix:  2.48 (0.21), residues: 575
  sheet:  0.46 (0.89), residues: 41
  loop :  0.48 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 128 
 TYR   0.013   0.001   TYR A  17 
 PHE   0.016   0.001   PHE A 792 
 TRP   0.012   0.001   TRP A1008 
 HIS   0.002   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (10147)
  covalent geometry    : angle       0.44787 (13985)
  hydrogen bonds       : bond        0.04175 (  551)
  hydrogen bonds       : angle       3.79084 ( 1475)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A  105 ARG cc_start: 0.6478 (ptp90) cc_final: 0.5873 (ptt-90)
REVERT: A  129 ASP cc_start: 0.8185 (m-30) cc_final: 0.7959 (m-30)
REVERT: A  248 ARG cc_start: 0.8669 (mmt90) cc_final: 0.8457 (mmt-90)
REVERT: A  297 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7957 (tt0)
REVERT: A  365 LEU cc_start: 0.6694 (tt) cc_final: 0.6230 (tp)
REVERT: A  453 LYS cc_start: 0.8675 (mttt) cc_final: 0.8355 (mtmt)
REVERT: A  520 GLU cc_start: 0.6453 (mt-10) cc_final: 0.5653 (tm-30)
REVERT: A  781 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.7062 (ttt)
REVERT: A  831 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6940 (mt-10)
REVERT: A 1013 TYR cc_start: 0.8391 (m-80) cc_final: 0.8047 (m-10)
REVERT: A 1038 ASN cc_start: 0.8044 (m-40) cc_final: 0.7626 (t0)
  outliers start: 20
  outliers final: 11
  residues processed: 119
  average time/residue: 0.0911
  time to fit residues: 15.0232
Evaluate side-chains
  111 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  456 SER
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  841 LYS
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  917 ILE
Chi-restraints excluded: chain A residue  976 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 97 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 103 optimal weight:    3.9990
   chunk 104 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 549 HIS
A 722 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.198637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.142339 restraints weight = 11565.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 2.64
r_work: 0.3324 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.3706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10147  Z= 0.121
  Angle     :  0.451   6.649  13985  Z= 0.236
  Chirality :  0.035   0.141   1574
  Planarity :  0.003   0.033   1530
  Dihedral  : 16.213  73.864   2241
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.62 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.27), residues: 980
  helix:  2.48 (0.21), residues: 576
  sheet:  0.25 (0.83), residues: 43
  loop :  0.54 (0.35), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 119 
 TYR   0.013   0.001   TYR A  17 
 PHE   0.017   0.001   PHE A 792 
 TRP   0.014   0.002   TRP A1008 
 HIS   0.002   0.001   HIS A 489 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10147)
  covalent geometry    : angle       0.45052 (13985)
  hydrogen bonds       : bond        0.04101 (  551)
  hydrogen bonds       : angle       3.76973 ( 1475)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A   94 ARG cc_start: 0.7967 (ttp80) cc_final: 0.7612 (ttp80)
REVERT: A  105 ARG cc_start: 0.6516 (ptp90) cc_final: 0.5915 (ptt-90)
REVERT: A  129 ASP cc_start: 0.8226 (m-30) cc_final: 0.7980 (m-30)
REVERT: A  297 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7975 (tt0)
REVERT: A  365 LEU cc_start: 0.6667 (tt) cc_final: 0.6200 (tp)
REVERT: A  453 LYS cc_start: 0.8713 (mttt) cc_final: 0.8230 (mtmm)
REVERT: A  520 GLU cc_start: 0.6510 (mt-10) cc_final: 0.5707 (tm-30)
REVERT: A  564 MET cc_start: 0.5955 (mtp) cc_final: 0.5693 (mmm)
REVERT: A  781 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.7082 (ttt)
REVERT: A  831 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6985 (mt-10)
REVERT: A  937 GLU cc_start: 0.7618 (tt0) cc_final: 0.7392 (mt-10)
REVERT: A 1013 TYR cc_start: 0.8373 (m-80) cc_final: 0.8150 (m-10)
REVERT: A 1038 ASN cc_start: 0.8017 (m-40) cc_final: 0.7706 (t0)
  outliers start: 19
  outliers final: 13
  residues processed: 119
  average time/residue: 0.0989
  time to fit residues: 16.1931
Evaluate side-chains
  112 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  456 SER
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain A residue  616 SER
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  841 LYS
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  917 ILE
Chi-restraints excluded: chain A residue  976 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 57 optimal weight:    4.9990
   chunk 44 optimal weight:    0.5980
   chunk 89 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 77 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
A 549 HIS
A 722 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.197934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.145275 restraints weight = 11423.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 2.37
r_work: 0.3325 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.3823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10147  Z= 0.130
  Angle     :  0.465   8.656  13985  Z= 0.241
  Chirality :  0.035   0.145   1574
  Planarity :  0.004   0.034   1530
  Dihedral  : 16.195  73.902   2241
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 12.62 %
    Favored  : 85.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.47 (0.27), residues: 980
  helix:  2.48 (0.21), residues: 575
  sheet:  0.25 (0.83), residues: 43
  loop :  0.51 (0.35), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 718 
 TYR   0.013   0.001   TYR A  17 
 PHE   0.017   0.001   PHE A 792 
 TRP   0.015   0.002   TRP A1008 
 HIS   0.003   0.001   HIS A 489 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (10147)
  covalent geometry    : angle       0.46456 (13985)
  hydrogen bonds       : bond        0.04110 (  551)
  hydrogen bonds       : angle       3.75347 ( 1475)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A   87 LYS cc_start: 0.7518 (mttt) cc_final: 0.7068 (mtpp)
REVERT: A   94 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7595 (ttp80)
REVERT: A  105 ARG cc_start: 0.6578 (ptp90) cc_final: 0.5981 (ptt-90)
REVERT: A  129 ASP cc_start: 0.8215 (m-30) cc_final: 0.7981 (m-30)
REVERT: A  297 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7968 (tt0)
REVERT: A  365 LEU cc_start: 0.6697 (tt) cc_final: 0.6275 (tp)
REVERT: A  453 LYS cc_start: 0.8733 (mttt) cc_final: 0.8236 (mtmm)
REVERT: A  520 GLU cc_start: 0.6527 (mt-10) cc_final: 0.5723 (tm-30)
REVERT: A  564 MET cc_start: 0.6007 (mtp) cc_final: 0.5730 (mmm)
REVERT: A  781 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7136 (ttt)
REVERT: A  831 GLU cc_start: 0.7217 (mt-10) cc_final: 0.7002 (mt-10)
REVERT: A  930 MET cc_start: 0.7911 (ptm) cc_final: 0.7609 (ptp)
REVERT: A  937 GLU cc_start: 0.7639 (tt0) cc_final: 0.7417 (mt-10)
REVERT: A  948 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7276 (tm-30)
REVERT: A 1077 MET cc_start: 0.8169 (mmt) cc_final: 0.7737 (mmt)
  outliers start: 20
  outliers final: 14
  residues processed: 119
  average time/residue: 0.0945
  time to fit residues: 15.6027
Evaluate side-chains
  111 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  456 SER
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain A residue  616 SER
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  841 LYS
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  917 ILE
Chi-restraints excluded: chain A residue  948 GLU
Chi-restraints excluded: chain A residue  976 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 75 optimal weight:    6.9990
   chunk 42 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 105 optimal weight:   20.0000
   chunk 82 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 549 HIS
A 722 ASN
A1040 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.198450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.145050 restraints weight = 11431.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 2.38
r_work: 0.3339 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.3939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10147  Z= 0.119
  Angle     :  0.451   6.525  13985  Z= 0.237
  Chirality :  0.035   0.138   1574
  Planarity :  0.004   0.035   1530
  Dihedral  : 16.147  73.849   2241
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 12.51 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.62 (0.27), residues: 980
  helix:  2.62 (0.21), residues: 569
  sheet:  0.22 (0.84), residues: 43
  loop :  0.60 (0.35), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 718 
 TYR   0.023   0.001   TYR A1013 
 PHE   0.016   0.001   PHE A 792 
 TRP   0.017   0.002   TRP A1008 
 HIS   0.003   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (10147)
  covalent geometry    : angle       0.45085 (13985)
  hydrogen bonds       : bond        0.04008 (  551)
  hydrogen bonds       : angle       3.76839 ( 1475)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A   87 LYS cc_start: 0.7497 (mttt) cc_final: 0.7043 (mtpp)
REVERT: A   94 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7741 (ttp-170)
REVERT: A  105 ARG cc_start: 0.6532 (ptp90) cc_final: 0.5926 (ptt-90)
REVERT: A  129 ASP cc_start: 0.8214 (m-30) cc_final: 0.7962 (m-30)
REVERT: A  297 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7941 (tt0)
REVERT: A  365 LEU cc_start: 0.6678 (tt) cc_final: 0.6251 (tp)
REVERT: A  453 LYS cc_start: 0.8742 (mttt) cc_final: 0.8247 (mtmm)
REVERT: A  520 GLU cc_start: 0.6498 (mt-10) cc_final: 0.5768 (tm-30)
REVERT: A  564 MET cc_start: 0.6103 (mtp) cc_final: 0.5803 (mmm)
REVERT: A  831 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6971 (mt-10)
REVERT: A  930 MET cc_start: 0.8013 (ptm) cc_final: 0.7583 (ptp)
REVERT: A  937 GLU cc_start: 0.7601 (tt0) cc_final: 0.7381 (mt-10)
REVERT: A  948 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7284 (tm-30)
  outliers start: 20
  outliers final: 16
  residues processed: 117
  average time/residue: 0.0910
  time to fit residues: 14.6972
Evaluate side-chains
  115 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  403 ASN
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  456 SER
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain A residue  616 SER
Chi-restraints excluded: chain A residue  748 MET
Chi-restraints excluded: chain A residue  841 LYS
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  917 ILE
Chi-restraints excluded: chain A residue  948 GLU
Chi-restraints excluded: chain A residue  976 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 57 optimal weight:   10.0000
   chunk 95 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 70 optimal weight:    0.5980
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
A 549 HIS
A 722 ASN
A1038 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.197019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.143217 restraints weight = 11355.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 2.47
r_work: 0.3318 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.3999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10147  Z= 0.134
  Angle     :  0.466   7.322  13985  Z= 0.243
  Chirality :  0.035   0.145   1574
  Planarity :  0.004   0.049   1530
  Dihedral  : 16.150  73.925   2241
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 12.73 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.58 (0.27), residues: 980
  helix:  2.58 (0.21), residues: 569
  sheet:  0.12 (0.85), residues: 43
  loop :  0.60 (0.35), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 718 
 TYR   0.014   0.001   TYR A  17 
 PHE   0.017   0.001   PHE A 792 
 TRP   0.018   0.002   TRP A1008 
 HIS   0.003   0.001   HIS A 489 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10147)
  covalent geometry    : angle       0.46626 (13985)
  hydrogen bonds       : bond        0.04093 (  551)
  hydrogen bonds       : angle       3.78901 ( 1475)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A   20 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8637 (ttt)
REVERT: A   87 LYS cc_start: 0.7516 (mttt) cc_final: 0.7066 (mtpp)
REVERT: A   94 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7743 (ttp-170)
REVERT: A  105 ARG cc_start: 0.6539 (ptp90) cc_final: 0.5876 (ptt-90)
REVERT: A  129 ASP cc_start: 0.8222 (m-30) cc_final: 0.7989 (m-30)
REVERT: A  297 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7956 (tt0)
REVERT: A  365 LEU cc_start: 0.6672 (tt) cc_final: 0.6249 (tp)
REVERT: A  453 LYS cc_start: 0.8751 (mttt) cc_final: 0.8245 (mtmm)
REVERT: A  520 GLU cc_start: 0.6544 (mt-10) cc_final: 0.5739 (tm-30)
REVERT: A  564 MET cc_start: 0.6103 (mtp) cc_final: 0.5768 (mmm)
REVERT: A  831 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6986 (mt-10)
REVERT: A  948 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7343 (tm-30)
REVERT: A 1077 MET cc_start: 0.8196 (mmt) cc_final: 0.7844 (mmt)
  outliers start: 22
  outliers final: 17
  residues processed: 114
  average time/residue: 0.0857
  time to fit residues: 13.7599
Evaluate side-chains
  115 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 MET
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  403 ASN
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  456 SER
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain A residue  616 SER
Chi-restraints excluded: chain A residue  841 LYS
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  917 ILE
Chi-restraints excluded: chain A residue  948 GLU
Chi-restraints excluded: chain A residue  976 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 44 optimal weight:    0.6980
   chunk 66 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 94 optimal weight:    7.9990
   chunk 50 optimal weight:    0.0370
   chunk 10 optimal weight:    0.5980
   chunk 19 optimal weight:   10.0000
   chunk 81 optimal weight:    0.0980
   chunk 1 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   overall best weight:    0.4258

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
A 282 HIS
A 722 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.199900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.146818 restraints weight = 11176.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3710 rms_B_bonded: 2.20
r_work: 0.3386 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.4160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10147  Z= 0.096
  Angle     :  0.437  10.653  13985  Z= 0.228
  Chirality :  0.034   0.134   1574
  Planarity :  0.003   0.032   1530
  Dihedral  : 16.083  73.835   2241
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 13.61 %
    Favored  : 84.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.84 (0.27), residues: 980
  helix:  2.79 (0.21), residues: 569
  sheet:  0.33 (0.84), residues: 43
  loop :  0.71 (0.35), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 718 
 TYR   0.012   0.001   TYR A  17 
 PHE   0.014   0.001   PHE A 792 
 TRP   0.018   0.002   TRP A1008 
 HIS   0.004   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 (10147)
  covalent geometry    : angle       0.43690 (13985)
  hydrogen bonds       : bond        0.03689 (  551)
  hydrogen bonds       : angle       3.68024 ( 1475)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   94 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7468 (tmm160)
REVERT: A  105 ARG cc_start: 0.6571 (ptp90) cc_final: 0.5995 (ptt-90)
REVERT: A  129 ASP cc_start: 0.8213 (m-30) cc_final: 0.7997 (m-30)
REVERT: A  297 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7919 (tt0)
REVERT: A  365 LEU cc_start: 0.6556 (tt) cc_final: 0.6173 (tp)
REVERT: A  453 LYS cc_start: 0.8750 (mttt) cc_final: 0.8260 (mtmm)
REVERT: A  520 GLU cc_start: 0.6507 (mt-10) cc_final: 0.5757 (tm-30)
REVERT: A  564 MET cc_start: 0.6153 (mtp) cc_final: 0.5771 (mmm)
REVERT: A  948 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7251 (tm-30)
REVERT: A 1077 MET cc_start: 0.8152 (mmt) cc_final: 0.7803 (mmt)
  outliers start: 15
  outliers final: 11
  residues processed: 111
  average time/residue: 0.0994
  time to fit residues: 15.3304
Evaluate side-chains
  109 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  403 ASN
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain A residue  748 MET
Chi-restraints excluded: chain A residue  841 LYS
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  917 ILE
Chi-restraints excluded: chain A residue  948 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 104 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 75 optimal weight:    5.9990
   chunk 61 optimal weight:   10.0000
   chunk 0 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  80 GLN
A 219 GLN
A 356 HIS
A 722 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.193996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.139769 restraints weight = 11418.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 2.44
r_work: 0.3276 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.4086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072  10147  Z= 0.223
  Angle     :  0.558   7.878  13985  Z= 0.289
  Chirality :  0.039   0.170   1574
  Planarity :  0.005   0.048   1530
  Dihedral  : 16.228  74.275   2241
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.17 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.36 (0.27), residues: 980
  helix:  2.37 (0.21), residues: 566
  sheet:  0.09 (0.84), residues: 43
  loop :  0.60 (0.35), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 718 
 TYR   0.017   0.002   TYR A  17 
 PHE   0.020   0.002   PHE A 792 
 TRP   0.016   0.002   TRP A1008 
 HIS   0.005   0.001   HIS A 489 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 (10147)
  covalent geometry    : angle       0.55822 (13985)
  hydrogen bonds       : bond        0.04680 (  551)
  hydrogen bonds       : angle       3.97657 ( 1475)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2229.02 seconds
wall clock time: 38 minutes 50.57 seconds (2330.57 seconds total)