Starting phenix.real_space_refine
on Thu May  1 00:23:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jqh_36572/05_2025/8jqh_36572_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jqh_36572/05_2025/8jqh_36572.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jqh_36572/05_2025/8jqh_36572.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jqh_36572/05_2025/8jqh_36572.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jqh_36572/05_2025/8jqh_36572_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jqh_36572/05_2025/8jqh_36572_neut.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.070
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    6299      2.51       5
     N    1710      2.21       5
     O    1862      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9920
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9920
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1206, 9920
          Classifications: {'peptide': 1206}
          Link IDs: {'PTRANS': 53, 'TRANS': 1152}
          Chain breaks: 4
  Time building chain proxies: 6.18, per 1000 atoms: 0.62
  Number of scatterers: 9920
  At special positions: 0
  Unit cell: (96.8, 101.2, 118.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      49     16.00
     O    1862      8.00
     N    1710      7.00
     C    6299      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.84
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2314

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 17 sheets defined
      36.5% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 25
    Processing helix  chain 'A' and resid 79 through 83
      removed outlier: 3.686A  pdb=" N   GLU A  83 " --> pdb=" O   LYS A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 90
      removed outlier: 3.532A  pdb=" N   VAL A  88 " --> pdb=" O   ARG A  84 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ARG A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 93
      No H-bonds generated for 'chain 'A' and resid 91 through 93'
    Processing helix  chain 'A' and resid 115 through 136
    Processing helix  chain 'A' and resid 137 through 154
    Processing helix  chain 'A' and resid 163 through 173
      Proline residue:  A 171  - end of helix
    Processing helix  chain 'A' and resid 179 through 191
    Processing helix  chain 'A' and resid 199 through 214
    Processing helix  chain 'A' and resid 217 through 223
      removed outlier: 4.263A  pdb=" N   PHE A 221 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.690A  pdb=" N   ILE A 229 " --> pdb=" O   SER A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 253
    Processing helix  chain 'A' and resid 257 through 260
    Processing helix  chain 'A' and resid 261 through 274
      removed outlier: 3.641A  pdb=" N   VAL A 265 " --> pdb=" O   ASP A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 295
    Processing helix  chain 'A' and resid 296 through 300
    Processing helix  chain 'A' and resid 303 through 307
    Processing helix  chain 'A' and resid 310 through 314
    Processing helix  chain 'A' and resid 317 through 319
      No H-bonds generated for 'chain 'A' and resid 317 through 319'
    Processing helix  chain 'A' and resid 341 through 352
      removed outlier: 3.980A  pdb=" N   TYR A 345 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 393
    Processing helix  chain 'A' and resid 410 through 425
    Processing helix  chain 'A' and resid 426 through 429
    Processing helix  chain 'A' and resid 443 through 448
      removed outlier: 3.778A  pdb=" N   ARG A 448 " --> pdb=" O   SER A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 513
    Processing helix  chain 'A' and resid 539 through 550
    Processing helix  chain 'A' and resid 609 through 620
      removed outlier: 4.004A  pdb=" N   GLN A 615 " --> pdb=" O   TYR A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 644
    Processing helix  chain 'A' and resid 652 through 663
    Processing helix  chain 'A' and resid 712 through 721
    Processing helix  chain 'A' and resid 736 through 743
    Processing helix  chain 'A' and resid 830 through 843
    Processing helix  chain 'A' and resid 892 through 909
    Processing helix  chain 'A' and resid 927 through 932
    Processing helix  chain 'A' and resid 960 through 970
    Processing helix  chain 'A' and resid 970 through 981
      removed outlier: 3.798A  pdb=" N   LEU A 974 " --> pdb=" O   LYS A 970 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   LYS A 980 " --> pdb=" O   LYS A 976 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 999 through 1005
    Processing helix  chain 'A' and resid 1018 through 1034
      removed outlier: 3.919A  pdb=" N   LEU A1030 " --> pdb=" O   ALA A1026 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   ASN A1031 " --> pdb=" O   LEU A1027 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   GLY A1032 " --> pdb=" O   PHE A1028 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   THR A1034 " --> pdb=" O   LEU A1030 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1040 through 1045
      removed outlier: 3.670A  pdb=" N   ARG A1044 " --> pdb=" O   PRO A1040 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1156 through 1158
      No H-bonds generated for 'chain 'A' and resid 1156 through 1158'
    Processing helix  chain 'A' and resid 1190 through 1217
      removed outlier: 3.905A  pdb=" N   ARG A1204 " --> pdb=" O   CYS A1200 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   GLU A1209 " --> pdb=" O   ARG A1205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1230 through 1253
      removed outlier: 3.901A  pdb=" N   GLU A1234 " --> pdb=" O   ALA A1230 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63
      removed outlier: 4.289A  pdb=" N   SER A 110 " --> pdb=" O   PHE A  31 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU A  72 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 162
    Processing sheet with id=AA3, first strand: chain 'A' and resid 380 through 381
      removed outlier: 3.815A  pdb=" N   GLU A 357 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   VAL A1010 " --> pdb=" O   ILE A 323 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   SER A 325 " --> pdb=" O   VAL A1010 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU A 982 " --> pdb=" O   GLU A 954 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   LYS A 938 " --> pdb=" O   ILE A 955 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   SER A 957 " --> pdb=" O   LYS A 938 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 451 through 454
      removed outlier: 3.726A  pdb=" N   ILE A 356 " --> pdb=" O   ILE A 402 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLU A 357 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 849 through 854
      removed outlier: 6.123A  pdb=" N   PHE A 505 " --> pdb=" O   ARG A 850 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   ILE A 852 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LEU A 503 " --> pdb=" O   ILE A 852 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   TYR A 495 " --> pdb=" O   SER A 506 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ASP A 508 " --> pdb=" O   ARG A 493 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   ARG A 493 " --> pdb=" O   ASP A 508 " (cutoff:3.500A)
      removed outlier: 5.474A  pdb=" N   GLU A 887 " --> pdb=" O   TRP A 484 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   VAL A 873 " --> pdb=" O   ALA A 863 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 561 through 565
    Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 565
      removed outlier: 3.978A  pdb=" N   TYR A 573 " --> pdb=" O   ILE A 588 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 647 through 648
      removed outlier: 4.862A  pdb=" N   ALA A 668 " --> pdb=" O   ARG A 685 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 647 through 648
    Processing sheet with id=AB1, first strand: chain 'A' and resid 695 through 698
    Processing sheet with id=AB2, first strand: chain 'A' and resid 724 through 726
      removed outlier: 3.817A  pdb=" N   TYR A 726 " --> pdb=" O   MET A 729 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 774 through 776
    Processing sheet with id=AB4, first strand: chain 'A' and resid 797 through 801
      removed outlier: 3.960A  pdb=" N   VAL A 799 " --> pdb=" O   LYS A 808 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LYS A 808 " --> pdb=" O   VAL A 799 " (cutoff:3.500A)
      removed outlier: 5.216A  pdb=" N   GLY A 809 " --> pdb=" O   GLN A 816 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1061 through 1065
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1067 through 1071
      removed outlier: 6.602A  pdb=" N   VAL A1067 " --> pdb=" O   PHE A1183 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   PHE A1183 " --> pdb=" O   VAL A1067 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLY A1069 " --> pdb=" O   LEU A1181 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   ALA A1178 " --> pdb=" O   LEU A1167 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1097 through 1100
      removed outlier: 6.633A  pdb=" N   VAL A1136 " --> pdb=" O   LEU A1148 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1097 through 1100

    427 hydrogen bonds defined for protein.
    1158 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.52

  Time building geometry restraints manager: 3.37 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1671
        1.31 -     1.44: 2764
        1.44 -     1.56: 5635
        1.56 -     1.69: 1
        1.69 -     1.81: 77
  Bond restraints: 10148
  Sorted by residual:
  bond pdb=" CA  ASN A1240 "
       pdb=" C   ASN A1240 "
    ideal  model  delta    sigma   weight residual
    1.524  1.435  0.089 1.26e-02 6.30e+03 5.01e+01
  bond pdb=" CA  LEU A1244 "
       pdb=" C   LEU A1244 "
    ideal  model  delta    sigma   weight residual
    1.524  1.440  0.084 1.24e-02 6.50e+03 4.60e+01
  bond pdb=" CA  GLU A 642 "
       pdb=" C   GLU A 642 "
    ideal  model  delta    sigma   weight residual
    1.523  1.450  0.073 1.34e-02 5.57e+03 3.00e+01
  bond pdb=" CA  TYR A 743 "
       pdb=" C   TYR A 743 "
    ideal  model  delta    sigma   weight residual
    1.524  1.445  0.079 1.48e-02 4.57e+03 2.86e+01
  bond pdb=" CA  LEU A1242 "
       pdb=" C   LEU A1242 "
    ideal  model  delta    sigma   weight residual
    1.525  1.458  0.067 1.29e-02 6.01e+03 2.73e+01
  ... (remaining 10143 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.69: 13542
        3.69 -     7.39: 130
        7.39 -    11.08: 18
       11.08 -    14.78: 3
       14.78 -    18.47: 1
  Bond angle restraints: 13694
  Sorted by residual:
  angle pdb=" N   ASN A 744 "
        pdb=" CA  ASN A 744 "
        pdb=" C   ASN A 744 "
      ideal   model   delta    sigma   weight residual
     111.71   99.80   11.91 1.15e+00 7.56e-01 1.07e+02
  angle pdb=" N   LYS A1233 "
        pdb=" CA  LYS A1233 "
        pdb=" C   LYS A1233 "
      ideal   model   delta    sigma   weight residual
     110.97  100.41   10.56 1.09e+00 8.42e-01 9.38e+01
  angle pdb=" N   GLU A1247 "
        pdb=" CA  GLU A1247 "
        pdb=" C   GLU A1247 "
      ideal   model   delta    sigma   weight residual
     113.20  101.57   11.63 1.21e+00 6.83e-01 9.24e+01
  angle pdb=" N   TYR A 743 "
        pdb=" CA  TYR A 743 "
        pdb=" C   TYR A 743 "
      ideal   model   delta    sigma   weight residual
     112.72  101.94   10.78 1.14e+00 7.69e-01 8.94e+01
  angle pdb=" N   HIS A 641 "
        pdb=" CA  HIS A 641 "
        pdb=" C   HIS A 641 "
      ideal   model   delta    sigma   weight residual
     111.75  102.04    9.71 1.28e+00 6.10e-01 5.75e+01
  ... (remaining 13689 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.60: 5520
       16.60 -    33.20: 511
       33.20 -    49.79: 117
       49.79 -    66.39: 16
       66.39 -    82.99: 11
  Dihedral angle restraints: 6175
    sinusoidal: 2610
      harmonic: 3565
  Sorted by residual:
  dihedral pdb=" CA  THR A 983 "
           pdb=" C   THR A 983 "
           pdb=" N   ARG A 984 "
           pdb=" CA  ARG A 984 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.17   19.83     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  ALA A1230 "
           pdb=" C   ALA A1230 "
           pdb=" N   LEU A1231 "
           pdb=" CA  LEU A1231 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.97   18.03     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  GLN A1213 "
           pdb=" C   GLN A1213 "
           pdb=" N   LEU A1214 "
           pdb=" CA  LEU A1214 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.23   17.77     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 6172 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1339
       0.082 -    0.163: 113
       0.163 -    0.245: 6
       0.245 -    0.326: 1
       0.326 -    0.408: 1
  Chirality restraints: 1460
  Sorted by residual:
  chirality pdb=" CA  LEU A1242 "
            pdb=" N   LEU A1242 "
            pdb=" C   LEU A1242 "
            pdb=" CB  LEU A1242 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.16e+00
  chirality pdb=" CB  VAL A1237 "
            pdb=" CA  VAL A1237 "
            pdb=" CG1 VAL A1237 "
            pdb=" CG2 VAL A1237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CA  VAL A1232 "
            pdb=" N   VAL A1232 "
            pdb=" C   VAL A1232 "
            pdb=" CB  VAL A1232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 1457 not shown)

  Planarity restraints: 1770
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 882 "   -0.017 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   GLY A 882 "    0.058 2.00e-02 2.50e+03
        pdb=" O   GLY A 882 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ASP A 883 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 734 "    0.015 2.00e-02 2.50e+03   2.88e-02 8.27e+00
        pdb=" C   PRO A 734 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   PRO A 734 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL A 735 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A1243 "    0.014 2.00e-02 2.50e+03   2.75e-02 7.54e+00
        pdb=" C   GLN A1243 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   GLN A1243 "    0.018 2.00e-02 2.50e+03
        pdb=" N   LEU A1244 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1767 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1089
        2.74 -     3.28: 11074
        3.28 -     3.82: 17583
        3.82 -     4.36: 21611
        4.36 -     4.90: 33641
  Nonbonded interactions: 84998
  Sorted by model distance:
  nonbonded pdb=" N   CYS A 624 "
            pdb=" O   PHE A 627 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" OD1 ASP A 572 "
            pdb=" OG  SER A 590 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OE1 GLN A1022 "
            pdb=" NH2 ARG A1133 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" NE2 HIS A1150 "
            pdb=" O   ASN A1169 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" O   ARG A 164 "
            pdb=" N   LYS A 167 "
     model   vdw
     2.245 3.120
  ... (remaining 84993 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=0.02 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     28.690
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
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      :  0.006   0.140  10148  Z= 0.375
  Angle     :  0.982  18.470  13694  Z= 0.626
  Chirality :  0.048   0.408   1460
  Planarity :  0.006   0.082   1770
  Dihedral  : 13.855  82.988   3861
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 31.35
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.43 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.64 %
    Favored  : 98.27 %
  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: -1.95 (0.24), residues: 1196
  helix: -0.77 (0.26), residues: 375
  sheet: -1.99 (0.30), residues: 240
  loop : -1.21 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 322 
 HIS   0.007   0.001   HIS A1072 
 PHE   0.026   0.002   PHE A 399 
 TYR   0.028   0.002   TYR A1036 
 ARG   0.012   0.001   ARG A 968 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17395 (  410)
  hydrogen bonds       : angle       8.29228 ( 1158)
  covalent geometry    : bond        0.00567 (10148)
  covalent geometry    : angle       0.98152 (13694)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 263
  time to evaluate  : 1.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.8170 (tpt) cc_final: 0.7859 (tpp)
REVERT: A   49 THR cc_start: 0.9376 (p) cc_final: 0.9137 (t)
REVERT: A  306 TYR cc_start: 0.8068 (m-10) cc_final: 0.7792 (m-10)
REVERT: A  313 ASP cc_start: 0.8318 (m-30) cc_final: 0.7840 (m-30)
REVERT: A  348 CYS cc_start: 0.9046 (m) cc_final: 0.8595 (m)
REVERT: A  391 ASP cc_start: 0.8946 (t0) cc_final: 0.8143 (t0)
REVERT: A  481 LEU cc_start: 0.8674 (mt) cc_final: 0.7684 (mt)
REVERT: A  483 MET cc_start: 0.7530 (tmm) cc_final: 0.7299 (tmm)
REVERT: A  496 CYS cc_start: 0.9191 (m) cc_final: 0.8566 (m)
REVERT: A  507 ASP cc_start: 0.8252 (t0) cc_final: 0.7643 (t0)
REVERT: A  710 PHE cc_start: 0.8082 (m-10) cc_final: 0.7683 (m-10)
REVERT: A  825 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7504 (tm-30)
REVERT: A  938 LYS cc_start: 0.9216 (pttt) cc_final: 0.8849 (pptt)
REVERT: A  994 SER cc_start: 0.8861 (t) cc_final: 0.8347 (m)
REVERT: A 1027 LEU cc_start: 0.9689 (tp) cc_final: 0.9331 (tt)
REVERT: A 1036 TYR cc_start: 0.8433 (m-80) cc_final: 0.8201 (m-10)
REVERT: A 1088 GLU cc_start: 0.8103 (pp20) cc_final: 0.7519 (pp20)
REVERT: A 1107 ASN cc_start: 0.8782 (t0) cc_final: 0.8336 (t0)
REVERT: A 1202 GLN cc_start: 0.9532 (mt0) cc_final: 0.9261 (tt0)
REVERT: A 1205 ARG cc_start: 0.8978 (tmt170) cc_final: 0.8662 (tpt90)
REVERT: A 1245 TYR cc_start: 0.9099 (m-80) cc_final: 0.8872 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 264
  average time/residue: 0.2664
  time to fit residues: 96.6070
Evaluate side-chains
  192 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    6.9990
   chunk 90 optimal weight:    4.9990
   chunk 50 optimal weight:    9.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 57 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9990
   chunk 108 optimal weight:    2.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 135 ASN
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1013 ASN
A1238 ASN
A1241 GLN
A1243 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.094477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.070511 restraints weight = 34234.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.073007 restraints weight = 18695.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.074631 restraints weight = 12456.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3234
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3234 r_free = 0.3234    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3227 r_free = 0.3227    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3227
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  10148  Z= 0.239
  Angle     :  0.747  17.444  13694  Z= 0.383
  Chirality :  0.044   0.189   1460
  Planarity :  0.005   0.069   1770
  Dihedral  :  5.237  18.614   1330
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 20.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  5.73 %
    Favored  : 94.09 %
  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: -1.60 (0.23), residues: 1196
  helix: -0.28 (0.25), residues: 388
  sheet: -1.91 (0.30), residues: 234
  loop : -1.12 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A1113 
 HIS   0.006   0.002   HIS A 797 
 PHE   0.016   0.002   PHE A 228 
 TYR   0.022   0.002   TYR A 151 
 ARG   0.011   0.001   ARG A1252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04932 (  410)
  hydrogen bonds       : angle       6.55233 ( 1158)
  covalent geometry    : bond        0.00503 (10148)
  covalent geometry    : angle       0.74701 (13694)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 228
  time to evaluate  : 1.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.8648 (tpt) cc_final: 0.8243 (tpp)
REVERT: A   49 THR cc_start: 0.9572 (p) cc_final: 0.9321 (t)
REVERT: A   59 ASP cc_start: 0.8915 (p0) cc_final: 0.8383 (p0)
REVERT: A  306 TYR cc_start: 0.8395 (m-10) cc_final: 0.7658 (m-10)
REVERT: A  313 ASP cc_start: 0.8554 (m-30) cc_final: 0.8135 (m-30)
REVERT: A  325 SER cc_start: 0.9148 (m) cc_final: 0.8936 (m)
REVERT: A  382 PHE cc_start: 0.8771 (t80) cc_final: 0.8278 (t80)
REVERT: A  417 MET cc_start: 0.9439 (mmm) cc_final: 0.9219 (mmm)
REVERT: A  481 LEU cc_start: 0.8951 (mt) cc_final: 0.8039 (mt)
REVERT: A  496 CYS cc_start: 0.9273 (m) cc_final: 0.8702 (m)
REVERT: A  507 ASP cc_start: 0.8456 (t0) cc_final: 0.8060 (t70)
REVERT: A  661 MET cc_start: 0.9537 (mmp) cc_final: 0.9314 (mmm)
REVERT: A  671 ILE cc_start: 0.9159 (mt) cc_final: 0.8692 (tp)
REVERT: A  687 ARG cc_start: 0.8423 (tpp80) cc_final: 0.8005 (mmm-85)
REVERT: A  710 PHE cc_start: 0.8163 (m-10) cc_final: 0.7882 (m-10)
REVERT: A  729 MET cc_start: 0.8755 (tmm) cc_final: 0.8486 (tmm)
REVERT: A  745 MET cc_start: 0.7803 (tmm) cc_final: 0.7551 (tmm)
REVERT: A  825 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7773 (tm-30)
REVERT: A  841 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8554 (mt-10)
REVERT: A  938 LYS cc_start: 0.9419 (pttt) cc_final: 0.9144 (pttp)
REVERT: A  974 LEU cc_start: 0.9594 (tp) cc_final: 0.9389 (tt)
REVERT: A 1009 MET cc_start: 0.8043 (ttm) cc_final: 0.7398 (ttm)
REVERT: A 1015 GLN cc_start: 0.9078 (pm20) cc_final: 0.8559 (pm20)
REVERT: A 1027 LEU cc_start: 0.9819 (tp) cc_final: 0.9610 (tt)
REVERT: A 1107 ASN cc_start: 0.9030 (t0) cc_final: 0.8643 (t0)
REVERT: A 1122 PHE cc_start: 0.8589 (m-80) cc_final: 0.8035 (m-80)
REVERT: A 1202 GLN cc_start: 0.9495 (mt0) cc_final: 0.9257 (tt0)
REVERT: A 1205 ARG cc_start: 0.9004 (tmt170) cc_final: 0.8615 (tpt90)
  outliers start: 2
  outliers final: 0
  residues processed: 229
  average time/residue: 0.2387
  time to fit residues: 76.0377
Evaluate side-chains
  178 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 83 optimal weight:    9.9990
   chunk 117 optimal weight:    6.9990
   chunk 92 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 45 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0070
   chunk 89 optimal weight:   10.0000
   overall best weight:    1.5804

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 203 HIS
** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1243 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.095428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.071594 restraints weight = 33860.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.074200 restraints weight = 18247.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.075912 restraints weight = 12026.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3259
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  10148  Z= 0.154
  Angle     :  0.646  14.678  13694  Z= 0.332
  Chirality :  0.043   0.167   1460
  Planarity :  0.004   0.047   1770
  Dihedral  :  4.970  17.282   1330
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 17.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.18 %
    Favored  : 96.72 %
  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: -1.17 (0.24), residues: 1196
  helix:  0.26 (0.26), residues: 387
  sheet: -1.78 (0.31), residues: 224
  loop : -0.99 (0.26), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 361 
 HIS   0.011   0.002   HIS A 392 
 PHE   0.012   0.002   PHE A1142 
 TYR   0.017   0.001   TYR A 617 
 ARG   0.004   0.000   ARG A 984 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04237 (  410)
  hydrogen bonds       : angle       6.18424 ( 1158)
  covalent geometry    : bond        0.00335 (10148)
  covalent geometry    : angle       0.64646 (13694)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 224
  time to evaluate  : 1.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 THR cc_start: 0.9491 (p) cc_final: 0.9236 (t)
REVERT: A   59 ASP cc_start: 0.8826 (p0) cc_final: 0.8317 (p0)
REVERT: A  306 TYR cc_start: 0.8397 (m-10) cc_final: 0.7719 (m-10)
REVERT: A  311 MET cc_start: 0.8787 (tpp) cc_final: 0.8527 (tpp)
REVERT: A  313 ASP cc_start: 0.8668 (m-30) cc_final: 0.8207 (m-30)
REVERT: A  339 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7358 (tm-30)
REVERT: A  382 PHE cc_start: 0.8600 (t80) cc_final: 0.8063 (t80)
REVERT: A  481 LEU cc_start: 0.8987 (mt) cc_final: 0.8162 (mt)
REVERT: A  496 CYS cc_start: 0.9282 (m) cc_final: 0.8806 (m)
REVERT: A  507 ASP cc_start: 0.8698 (t0) cc_final: 0.8188 (t70)
REVERT: A  661 MET cc_start: 0.9526 (mmp) cc_final: 0.9289 (mmm)
REVERT: A  671 ILE cc_start: 0.9047 (mt) cc_final: 0.8502 (tp)
REVERT: A  683 THR cc_start: 0.8767 (m) cc_final: 0.8513 (m)
REVERT: A  687 ARG cc_start: 0.8495 (tpp80) cc_final: 0.8287 (tpt170)
REVERT: A  710 PHE cc_start: 0.8218 (m-10) cc_final: 0.7880 (m-10)
REVERT: A  729 MET cc_start: 0.8829 (tmm) cc_final: 0.8525 (tmm)
REVERT: A  825 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7818 (tm-30)
REVERT: A  841 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8579 (mt-10)
REVERT: A  938 LYS cc_start: 0.9484 (pttt) cc_final: 0.9251 (ptmm)
REVERT: A  984 ARG cc_start: 0.9022 (mmm-85) cc_final: 0.8162 (mmm-85)
REVERT: A  993 ASP cc_start: 0.8978 (p0) cc_final: 0.8735 (p0)
REVERT: A 1009 MET cc_start: 0.8134 (ttm) cc_final: 0.7354 (ttm)
REVERT: A 1021 MET cc_start: 0.9599 (tpp) cc_final: 0.8614 (tpp)
REVERT: A 1043 MET cc_start: 0.9038 (mmp) cc_final: 0.8644 (mmp)
REVERT: A 1107 ASN cc_start: 0.8937 (t0) cc_final: 0.8538 (t0)
REVERT: A 1122 PHE cc_start: 0.8662 (m-80) cc_final: 0.8261 (m-80)
REVERT: A 1144 ASP cc_start: 0.9295 (t70) cc_final: 0.9021 (t0)
REVERT: A 1184 CYS cc_start: 0.8862 (t) cc_final: 0.8653 (t)
REVERT: A 1205 ARG cc_start: 0.8919 (tmt170) cc_final: 0.8526 (tpt90)
REVERT: A 1245 TYR cc_start: 0.8849 (m-80) cc_final: 0.8411 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 224
  average time/residue: 0.3563
  time to fit residues: 111.4621
Evaluate side-chains
  177 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 2.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0170
   chunk 19 optimal weight:    4.9990
   chunk 105 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 84 optimal weight:    0.2980
   chunk 7 optimal weight:    0.0030
   chunk 11 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 69 optimal weight:    0.4980
   chunk 115 optimal weight:    2.9990
   overall best weight:    0.3428

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1097 ASN
** A1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1250 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.098040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.074261 restraints weight = 33582.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.076981 restraints weight = 17884.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.078742 restraints weight = 11715.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3310
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
r_final: 0.3310
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10148  Z= 0.120
  Angle     :  0.601   9.992  13694  Z= 0.315
  Chirality :  0.043   0.177   1460
  Planarity :  0.004   0.089   1770
  Dihedral  :  4.792  16.779   1330
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  4.19 %
    Favored  : 95.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.24), residues: 1196
  helix:  0.36 (0.27), residues: 388
  sheet: -1.73 (0.31), residues: 218
  loop : -0.97 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 361 
 HIS   0.004   0.001   HIS A 203 
 PHE   0.019   0.001   PHE A 382 
 TYR   0.014   0.001   TYR A 977 
 ARG   0.005   0.000   ARG A 730 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03906 (  410)
  hydrogen bonds       : angle       5.81849 ( 1158)
  covalent geometry    : bond        0.00258 (10148)
  covalent geometry    : angle       0.60077 (13694)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 226
  time to evaluate  : 1.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 THR cc_start: 0.9377 (p) cc_final: 0.9129 (t)
REVERT: A   59 ASP cc_start: 0.8808 (p0) cc_final: 0.8278 (p0)
REVERT: A  210 MET cc_start: 0.9000 (mmm) cc_final: 0.8736 (mmm)
REVERT: A  216 SER cc_start: 0.9259 (m) cc_final: 0.8727 (p)
REVERT: A  313 ASP cc_start: 0.8700 (m-30) cc_final: 0.8283 (m-30)
REVERT: A  481 LEU cc_start: 0.8942 (mt) cc_final: 0.8082 (mt)
REVERT: A  496 CYS cc_start: 0.9288 (m) cc_final: 0.8806 (m)
REVERT: A  507 ASP cc_start: 0.8735 (t0) cc_final: 0.8243 (t70)
REVERT: A  661 MET cc_start: 0.9510 (mmp) cc_final: 0.9287 (mmm)
REVERT: A  683 THR cc_start: 0.8795 (m) cc_final: 0.8560 (m)
REVERT: A  710 PHE cc_start: 0.8382 (m-10) cc_final: 0.7989 (m-10)
REVERT: A  728 LYS cc_start: 0.9353 (mmpt) cc_final: 0.9016 (mmmt)
REVERT: A  729 MET cc_start: 0.8459 (tmm) cc_final: 0.7991 (tmm)
REVERT: A  825 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7787 (tm-30)
REVERT: A  841 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8639 (mt-10)
REVERT: A  938 LYS cc_start: 0.9439 (pttt) cc_final: 0.9170 (ptmm)
REVERT: A  984 ARG cc_start: 0.8897 (mmm-85) cc_final: 0.7991 (mmm-85)
REVERT: A  993 ASP cc_start: 0.9065 (p0) cc_final: 0.8842 (p0)
REVERT: A 1009 MET cc_start: 0.7985 (ttm) cc_final: 0.7095 (ttm)
REVERT: A 1021 MET cc_start: 0.9503 (tpp) cc_final: 0.9039 (tpp)
REVERT: A 1043 MET cc_start: 0.8987 (mmp) cc_final: 0.8678 (mmp)
REVERT: A 1107 ASN cc_start: 0.8825 (t0) cc_final: 0.8431 (t0)
REVERT: A 1122 PHE cc_start: 0.8567 (m-80) cc_final: 0.8219 (m-80)
REVERT: A 1123 GLU cc_start: 0.8579 (mp0) cc_final: 0.8320 (mp0)
REVERT: A 1144 ASP cc_start: 0.9318 (t70) cc_final: 0.9026 (t0)
REVERT: A 1153 TYR cc_start: 0.8521 (m-80) cc_final: 0.8180 (m-80)
REVERT: A 1184 CYS cc_start: 0.8778 (t) cc_final: 0.8538 (t)
  outliers start: 2
  outliers final: 0
  residues processed: 227
  average time/residue: 0.2510
  time to fit residues: 80.8077
Evaluate side-chains
  167 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 87 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0050
   chunk 59 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0030
   chunk 41 optimal weight:    0.8980
   chunk 117 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   overall best weight:    1.5808

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1238 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.095347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.071291 restraints weight = 33858.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.073855 restraints weight = 18388.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.075575 restraints weight = 12196.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3243
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3243 r_free = 0.3243    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3243 r_free = 0.3243    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       33 |
|-----------------------------------------------------------------------------|
r_final: 0.3243
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.3793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  10148  Z= 0.147
  Angle     :  0.627  13.681  13694  Z= 0.324
  Chirality :  0.043   0.246   1460
  Planarity :  0.004   0.073   1770
  Dihedral  :  4.731  17.123   1330
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.37 %
    Favored  : 96.45 %
  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: -0.93 (0.24), residues: 1196
  helix:  0.50 (0.27), residues: 390
  sheet: -1.76 (0.30), residues: 223
  loop : -0.83 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 361 
 HIS   0.006   0.001   HIS A 203 
 PHE   0.013   0.001   PHE A 382 
 TYR   0.013   0.001   TYR A1217 
 ARG   0.004   0.000   ARG A 956 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03926 (  410)
  hydrogen bonds       : angle       5.74646 ( 1158)
  covalent geometry    : bond        0.00323 (10148)
  covalent geometry    : angle       0.62680 (13694)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 207
  time to evaluate  : 1.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 THR cc_start: 0.9456 (p) cc_final: 0.9234 (t)
REVERT: A   59 ASP cc_start: 0.8841 (p0) cc_final: 0.8397 (p0)
REVERT: A  111 LEU cc_start: 0.9034 (mm) cc_final: 0.8816 (mp)
REVERT: A  210 MET cc_start: 0.8854 (mmm) cc_final: 0.8633 (mmm)
REVERT: A  216 SER cc_start: 0.9293 (m) cc_final: 0.8797 (p)
REVERT: A  313 ASP cc_start: 0.8819 (m-30) cc_final: 0.8506 (m-30)
REVERT: A  406 GLU cc_start: 0.7282 (tt0) cc_final: 0.6836 (tt0)
REVERT: A  481 LEU cc_start: 0.9026 (mt) cc_final: 0.8274 (mt)
REVERT: A  496 CYS cc_start: 0.9255 (m) cc_final: 0.8790 (m)
REVERT: A  507 ASP cc_start: 0.8867 (t0) cc_final: 0.8580 (t70)
REVERT: A  509 ILE cc_start: 0.8792 (mt) cc_final: 0.8576 (mt)
REVERT: A  661 MET cc_start: 0.9505 (mmp) cc_final: 0.9262 (mmm)
REVERT: A  710 PHE cc_start: 0.8376 (m-10) cc_final: 0.7949 (m-10)
REVERT: A  728 LYS cc_start: 0.9373 (mmpt) cc_final: 0.9022 (mmmt)
REVERT: A  729 MET cc_start: 0.8482 (tmm) cc_final: 0.8100 (tmm)
REVERT: A  753 TYR cc_start: 0.5340 (m-10) cc_final: 0.4990 (m-10)
REVERT: A  825 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7865 (tm-30)
REVERT: A  841 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8620 (mt-10)
REVERT: A  993 ASP cc_start: 0.9142 (p0) cc_final: 0.8911 (p0)
REVERT: A 1009 MET cc_start: 0.8007 (ttm) cc_final: 0.7360 (ttm)
REVERT: A 1021 MET cc_start: 0.9585 (tpp) cc_final: 0.9157 (tpp)
REVERT: A 1107 ASN cc_start: 0.8902 (t0) cc_final: 0.8515 (t0)
REVERT: A 1123 GLU cc_start: 0.8521 (mp0) cc_final: 0.8253 (mp0)
REVERT: A 1138 GLU cc_start: 0.8032 (pp20) cc_final: 0.7712 (pp20)
REVERT: A 1144 ASP cc_start: 0.9389 (t70) cc_final: 0.9131 (t0)
REVERT: A 1153 TYR cc_start: 0.8675 (m-80) cc_final: 0.8454 (m-80)
REVERT: A 1218 ASP cc_start: 0.7673 (t70) cc_final: 0.7242 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 208
  average time/residue: 0.2254
  time to fit residues: 65.9631
Evaluate side-chains
  160 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 55 optimal weight:   20.0000
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 114 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 83 optimal weight:    0.0670
   chunk 53 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    1.0124

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

Flipped N/Q/H residues before XYZ refinement:
A 130 HIS
A 131 GLN
A 135 ASN
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1241 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.096345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.072170 restraints weight = 33782.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.074748 restraints weight = 18353.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.076490 restraints weight = 12213.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3272
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3272 r_free = 0.3272    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       33 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3272 r_free = 0.3272    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
r_final: 0.3272
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.4087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10148  Z= 0.125
  Angle     :  0.604   7.877  13694  Z= 0.319
  Chirality :  0.043   0.192   1460
  Planarity :  0.004   0.061   1770
  Dihedral  :  4.731  16.909   1330
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  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: -0.93 (0.24), residues: 1196
  helix:  0.43 (0.27), residues: 389
  sheet: -1.63 (0.31), residues: 220
  loop : -0.83 (0.26), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 361 
 HIS   0.006   0.001   HIS A 616 
 PHE   0.020   0.001   PHE A 382 
 TYR   0.019   0.001   TYR A 371 
 ARG   0.004   0.000   ARG A 956 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03831 (  410)
  hydrogen bonds       : angle       5.61692 ( 1158)
  covalent geometry    : bond        0.00279 (10148)
  covalent geometry    : angle       0.60368 (13694)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.8048 (ttp) cc_final: 0.7502 (tmm)
REVERT: A   47 MET cc_start: 0.8324 (tmm) cc_final: 0.7699 (tmm)
REVERT: A   49 THR cc_start: 0.9418 (p) cc_final: 0.9177 (t)
REVERT: A   59 ASP cc_start: 0.8869 (p0) cc_final: 0.8423 (p0)
REVERT: A  216 SER cc_start: 0.9258 (m) cc_final: 0.8774 (p)
REVERT: A  313 ASP cc_start: 0.8929 (m-30) cc_final: 0.8560 (m-30)
REVERT: A  481 LEU cc_start: 0.9004 (mt) cc_final: 0.8385 (mt)
REVERT: A  496 CYS cc_start: 0.9209 (m) cc_final: 0.8711 (m)
REVERT: A  507 ASP cc_start: 0.9039 (t0) cc_final: 0.8555 (t70)
REVERT: A  509 ILE cc_start: 0.8791 (mt) cc_final: 0.8568 (mt)
REVERT: A  617 TYR cc_start: 0.8781 (m-80) cc_final: 0.8411 (m-80)
REVERT: A  661 MET cc_start: 0.9494 (mmp) cc_final: 0.9245 (mmm)
REVERT: A  683 THR cc_start: 0.8888 (m) cc_final: 0.8656 (m)
REVERT: A  710 PHE cc_start: 0.8360 (m-10) cc_final: 0.7916 (m-10)
REVERT: A  728 LYS cc_start: 0.9355 (mmpt) cc_final: 0.9045 (mmmt)
REVERT: A  825 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7818 (tm-30)
REVERT: A  841 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8614 (mt-10)
REVERT: A  974 LEU cc_start: 0.9532 (tt) cc_final: 0.8986 (tt)
REVERT: A  993 ASP cc_start: 0.9106 (p0) cc_final: 0.8845 (p0)
REVERT: A 1009 MET cc_start: 0.8029 (ttm) cc_final: 0.7393 (ttm)
REVERT: A 1013 ASN cc_start: 0.9180 (m-40) cc_final: 0.8754 (m-40)
REVERT: A 1043 MET cc_start: 0.8972 (mmp) cc_final: 0.8663 (mmp)
REVERT: A 1094 TYR cc_start: 0.8121 (p90) cc_final: 0.7863 (p90)
REVERT: A 1107 ASN cc_start: 0.8899 (t0) cc_final: 0.8452 (t0)
REVERT: A 1123 GLU cc_start: 0.8467 (mp0) cc_final: 0.8154 (mp0)
REVERT: A 1138 GLU cc_start: 0.7902 (pp20) cc_final: 0.7682 (pp20)
REVERT: A 1144 ASP cc_start: 0.9376 (t70) cc_final: 0.9080 (t0)
REVERT: A 1228 ARG cc_start: 0.6653 (ptt180) cc_final: 0.5934 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.2224
  time to fit residues: 61.7447
Evaluate side-chains
  157 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 117 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:   20.0000
   chunk 90 optimal weight:   10.0000
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 260 GLN
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 416 HIS
A 621 HIS
** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.093932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.069696 restraints weight = 34783.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.072215 restraints weight = 19081.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.073896 restraints weight = 12838.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3224
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|
r_final: 0.3224
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.4494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10148  Z= 0.161
  Angle     :  0.619   7.550  13694  Z= 0.327
  Chirality :  0.043   0.209   1460
  Planarity :  0.005   0.060   1770
  Dihedral  :  4.771  16.345   1330
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.24), residues: 1196
  helix:  0.49 (0.27), residues: 383
  sheet: -1.57 (0.32), residues: 219
  loop : -0.85 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A1113 
 HIS   0.005   0.001   HIS A1150 
 PHE   0.023   0.002   PHE A 382 
 TYR   0.016   0.002   TYR A1217 
 ARG   0.012   0.001   ARG A 984 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03822 (  410)
  hydrogen bonds       : angle       5.64730 ( 1158)
  covalent geometry    : bond        0.00350 (10148)
  covalent geometry    : angle       0.61905 (13694)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.8201 (ttp) cc_final: 0.7361 (tmm)
REVERT: A   47 MET cc_start: 0.8318 (tmm) cc_final: 0.7745 (tmm)
REVERT: A   59 ASP cc_start: 0.8869 (p0) cc_final: 0.8469 (p0)
REVERT: A  216 SER cc_start: 0.9282 (m) cc_final: 0.8747 (p)
REVERT: A  217 ILE cc_start: 0.9500 (mm) cc_final: 0.9232 (mm)
REVERT: A  481 LEU cc_start: 0.9124 (mt) cc_final: 0.8599 (mt)
REVERT: A  496 CYS cc_start: 0.9239 (m) cc_final: 0.8791 (m)
REVERT: A  507 ASP cc_start: 0.9082 (t0) cc_final: 0.8626 (t70)
REVERT: A  509 ILE cc_start: 0.8772 (mt) cc_final: 0.8545 (mt)
REVERT: A  661 MET cc_start: 0.9523 (mmp) cc_final: 0.9264 (mmm)
REVERT: A  710 PHE cc_start: 0.8380 (m-10) cc_final: 0.7948 (m-10)
REVERT: A  725 LEU cc_start: 0.8924 (tp) cc_final: 0.8629 (tp)
REVERT: A  728 LYS cc_start: 0.9450 (mmpt) cc_final: 0.9107 (mmmt)
REVERT: A  825 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7829 (tm-30)
REVERT: A  841 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8633 (mt-10)
REVERT: A  993 ASP cc_start: 0.9141 (p0) cc_final: 0.8867 (p0)
REVERT: A 1013 ASN cc_start: 0.9069 (m-40) cc_final: 0.8560 (m-40)
REVERT: A 1021 MET cc_start: 0.9495 (tpp) cc_final: 0.9266 (tpp)
REVERT: A 1043 MET cc_start: 0.9066 (mmp) cc_final: 0.8840 (mmp)
REVERT: A 1094 TYR cc_start: 0.8477 (p90) cc_final: 0.7762 (p90)
REVERT: A 1107 ASN cc_start: 0.8940 (t0) cc_final: 0.8467 (t0)
REVERT: A 1123 GLU cc_start: 0.8415 (mp0) cc_final: 0.8100 (mp0)
REVERT: A 1138 GLU cc_start: 0.7865 (pp20) cc_final: 0.7664 (pp20)
REVERT: A 1144 ASP cc_start: 0.9382 (t70) cc_final: 0.9029 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.2229
  time to fit residues: 56.4371
Evaluate side-chains
  148 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 100 optimal weight:    0.0670
   chunk 25 optimal weight:    0.0060
   chunk 117 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 83 optimal weight:    8.9990
   chunk 65 optimal weight:    6.9990
   chunk 85 optimal weight:    5.9990
   chunk 81 optimal weight:   10.0000
   overall best weight:    1.2140

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.096048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.071851 restraints weight = 34068.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.074369 restraints weight = 18577.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.076106 restraints weight = 12349.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3248
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|
r_final: 0.3248
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.4689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10148  Z= 0.131
  Angle     :  0.626   9.086  13694  Z= 0.331
  Chirality :  0.043   0.260   1460
  Planarity :  0.004   0.054   1770
  Dihedral  :  4.772  16.720   1330
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  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: -0.96 (0.24), residues: 1196
  helix:  0.37 (0.27), residues: 383
  sheet: -1.52 (0.33), residues: 213
  loop : -0.88 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 361 
 HIS   0.007   0.001   HIS A 392 
 PHE   0.032   0.002   PHE A 421 
 TYR   0.016   0.001   TYR A 611 
 ARG   0.005   0.000   ARG A 956 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03814 (  410)
  hydrogen bonds       : angle       5.60947 ( 1158)
  covalent geometry    : bond        0.00292 (10148)
  covalent geometry    : angle       0.62596 (13694)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 1.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.8213 (ttp) cc_final: 0.7492 (tmm)
REVERT: A   47 MET cc_start: 0.8294 (tmm) cc_final: 0.7697 (tmm)
REVERT: A   59 ASP cc_start: 0.8887 (p0) cc_final: 0.8491 (p0)
REVERT: A  216 SER cc_start: 0.9283 (m) cc_final: 0.8781 (p)
REVERT: A  217 ILE cc_start: 0.9550 (mm) cc_final: 0.9292 (mm)
REVERT: A  391 ASP cc_start: 0.8700 (t70) cc_final: 0.8251 (t0)
REVERT: A  481 LEU cc_start: 0.9003 (mt) cc_final: 0.8568 (mt)
REVERT: A  496 CYS cc_start: 0.9228 (m) cc_final: 0.8869 (m)
REVERT: A  509 ILE cc_start: 0.8830 (mt) cc_final: 0.8610 (mt)
REVERT: A  657 GLU cc_start: 0.9106 (mp0) cc_final: 0.8754 (mp0)
REVERT: A  661 MET cc_start: 0.9515 (mmp) cc_final: 0.9220 (mmm)
REVERT: A  710 PHE cc_start: 0.8384 (m-10) cc_final: 0.7990 (m-10)
REVERT: A  728 LYS cc_start: 0.9450 (mmpt) cc_final: 0.9095 (mmmt)
REVERT: A  729 MET cc_start: 0.8620 (tmm) cc_final: 0.8283 (tmm)
REVERT: A  825 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7786 (tm-30)
REVERT: A  841 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8649 (mt-10)
REVERT: A  964 ASP cc_start: 0.9210 (t0) cc_final: 0.9010 (t0)
REVERT: A  993 ASP cc_start: 0.9135 (p0) cc_final: 0.8878 (p0)
REVERT: A 1008 GLN cc_start: 0.8706 (pm20) cc_final: 0.8246 (pm20)
REVERT: A 1043 MET cc_start: 0.9118 (mmp) cc_final: 0.8914 (mmp)
REVERT: A 1086 GLU cc_start: 0.8251 (tt0) cc_final: 0.8030 (tt0)
REVERT: A 1094 TYR cc_start: 0.8567 (p90) cc_final: 0.7775 (p90)
REVERT: A 1107 ASN cc_start: 0.8895 (t0) cc_final: 0.8420 (t0)
REVERT: A 1123 GLU cc_start: 0.8365 (mp0) cc_final: 0.8138 (mp0)
REVERT: A 1138 GLU cc_start: 0.7888 (pp20) cc_final: 0.7198 (pp20)
REVERT: A 1144 ASP cc_start: 0.9367 (t70) cc_final: 0.9008 (t0)
REVERT: A 1228 ARG cc_start: 0.6645 (ptt180) cc_final: 0.5733 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.2223
  time to fit residues: 57.1474
Evaluate side-chains
  149 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 59 optimal weight:    8.9990
   chunk 14 optimal weight:    4.9990
   chunk 85 optimal weight:    9.9990
   chunk 19 optimal weight:    0.7980
   chunk 74 optimal weight:    6.9990
   chunk 64 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 88 optimal weight:    9.9990
   chunk 90 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1238 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.093518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.069300 restraints weight = 34868.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.071722 restraints weight = 19110.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.073292 restraints weight = 12882.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3189
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|
r_final: 0.3189
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.4952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10148  Z= 0.184
  Angle     :  0.657   8.324  13694  Z= 0.348
  Chirality :  0.044   0.258   1460
  Planarity :  0.005   0.063   1770
  Dihedral  :  4.862  16.281   1330
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 15.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.64 %
    Favored  : 99.27 %
  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: -1.04 (0.24), residues: 1196
  helix:  0.24 (0.27), residues: 383
  sheet: -1.48 (0.33), residues: 223
  loop : -0.90 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 361 
 HIS   0.007   0.001   HIS A 392 
 PHE   0.032   0.002   PHE A 382 
 TYR   0.021   0.002   TYR A1217 
 ARG   0.006   0.001   ARG A 742 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03965 (  410)
  hydrogen bonds       : angle       5.77697 ( 1158)
  covalent geometry    : bond        0.00402 (10148)
  covalent geometry    : angle       0.65737 (13694)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 172
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.8175 (ttp) cc_final: 0.7486 (tmm)
REVERT: A   47 MET cc_start: 0.8348 (tmm) cc_final: 0.7653 (tmm)
REVERT: A   48 GLU cc_start: 0.9010 (pm20) cc_final: 0.8751 (pm20)
REVERT: A   59 ASP cc_start: 0.8913 (p0) cc_final: 0.8580 (p0)
REVERT: A  216 SER cc_start: 0.9344 (m) cc_final: 0.9026 (t)
REVERT: A  217 ILE cc_start: 0.9529 (mm) cc_final: 0.9306 (mm)
REVERT: A  325 SER cc_start: 0.9256 (m) cc_final: 0.8695 (m)
REVERT: A  481 LEU cc_start: 0.9084 (mt) cc_final: 0.8709 (mt)
REVERT: A  496 CYS cc_start: 0.9270 (m) cc_final: 0.8950 (m)
REVERT: A  661 MET cc_start: 0.9525 (mmp) cc_final: 0.9241 (mmm)
REVERT: A  710 PHE cc_start: 0.8426 (m-10) cc_final: 0.8047 (m-10)
REVERT: A  725 LEU cc_start: 0.9207 (tp) cc_final: 0.8961 (tp)
REVERT: A  728 LYS cc_start: 0.9449 (mmpt) cc_final: 0.9095 (mmmt)
REVERT: A  729 MET cc_start: 0.8675 (tmm) cc_final: 0.8469 (tmm)
REVERT: A  825 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7942 (tm-30)
REVERT: A  841 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8678 (mt-10)
REVERT: A  964 ASP cc_start: 0.9185 (t0) cc_final: 0.8958 (t0)
REVERT: A  974 LEU cc_start: 0.9485 (tt) cc_final: 0.9048 (tt)
REVERT: A  993 ASP cc_start: 0.9154 (p0) cc_final: 0.8921 (p0)
REVERT: A 1005 CYS cc_start: 0.8961 (t) cc_final: 0.8743 (t)
REVERT: A 1008 GLN cc_start: 0.8825 (pm20) cc_final: 0.8327 (pm20)
REVERT: A 1009 MET cc_start: 0.7196 (ttp) cc_final: 0.6911 (tmm)
REVERT: A 1021 MET cc_start: 0.9487 (tpp) cc_final: 0.9097 (tpp)
REVERT: A 1107 ASN cc_start: 0.9020 (t0) cc_final: 0.8509 (t0)
REVERT: A 1123 GLU cc_start: 0.8372 (mp0) cc_final: 0.8164 (mp0)
REVERT: A 1138 GLU cc_start: 0.7575 (pp20) cc_final: 0.7227 (pp20)
REVERT: A 1144 ASP cc_start: 0.9267 (t70) cc_final: 0.8877 (t0)
REVERT: A 1220 HIS cc_start: 0.7903 (m90) cc_final: 0.7702 (m90)
REVERT: A 1228 ARG cc_start: 0.6650 (ptt180) cc_final: 0.5695 (ptt90)
REVERT: A 1233 LYS cc_start: 0.9539 (pptt) cc_final: 0.9317 (ptpt)
  outliers start: 1
  outliers final: 1
  residues processed: 173
  average time/residue: 0.2353
  time to fit residues: 59.3987
Evaluate side-chains
  148 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 147
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 47 optimal weight:    8.9990
   chunk 42 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 110 optimal weight:    0.9980
   chunk 83 optimal weight:    6.9990
   chunk 112 optimal weight:    0.2980
   chunk 54 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.095811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.071647 restraints weight = 33989.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.074192 restraints weight = 18575.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.075890 restraints weight = 12441.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3248
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
r_final: 0.3248
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.5098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10148  Z= 0.121
  Angle     :  0.630   8.113  13694  Z= 0.330
  Chirality :  0.043   0.231   1460
  Planarity :  0.004   0.045   1770
  Dihedral  :  4.759  16.253   1330
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  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: -0.89 (0.24), residues: 1196
  helix:  0.39 (0.27), residues: 383
  sheet: -1.35 (0.34), residues: 214
  loop : -0.87 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 361 
 HIS   0.004   0.001   HIS A 797 
 PHE   0.026   0.001   PHE A 202 
 TYR   0.044   0.002   TYR A 206 
 ARG   0.005   0.000   ARG A 956 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03759 (  410)
  hydrogen bonds       : angle       5.50492 ( 1158)
  covalent geometry    : bond        0.00274 (10148)
  covalent geometry    : angle       0.62979 (13694)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.8262 (ttp) cc_final: 0.7528 (tmm)
REVERT: A   47 MET cc_start: 0.8334 (tmm) cc_final: 0.7623 (tmm)
REVERT: A   48 GLU cc_start: 0.8969 (pm20) cc_final: 0.8713 (pm20)
REVERT: A   59 ASP cc_start: 0.8895 (p0) cc_final: 0.8551 (p0)
REVERT: A  216 SER cc_start: 0.9281 (m) cc_final: 0.8730 (p)
REVERT: A  217 ILE cc_start: 0.9551 (mm) cc_final: 0.9263 (mm)
REVERT: A  325 SER cc_start: 0.9162 (m) cc_final: 0.8610 (m)
REVERT: A  481 LEU cc_start: 0.9022 (mt) cc_final: 0.8688 (mt)
REVERT: A  496 CYS cc_start: 0.9147 (m) cc_final: 0.8861 (m)
REVERT: A  661 MET cc_start: 0.9497 (mmp) cc_final: 0.9218 (mmm)
REVERT: A  710 PHE cc_start: 0.8378 (m-10) cc_final: 0.8071 (m-10)
REVERT: A  725 LEU cc_start: 0.9120 (tp) cc_final: 0.8914 (tp)
REVERT: A  728 LYS cc_start: 0.9478 (mmpt) cc_final: 0.9105 (mmmt)
REVERT: A  825 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7767 (tm-30)
REVERT: A  841 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8629 (mt-10)
REVERT: A  964 ASP cc_start: 0.9165 (t0) cc_final: 0.8949 (t0)
REVERT: A  974 LEU cc_start: 0.9464 (tt) cc_final: 0.8996 (tt)
REVERT: A  979 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8643 (tm-30)
REVERT: A  993 ASP cc_start: 0.9081 (p0) cc_final: 0.8787 (p0)
REVERT: A 1005 CYS cc_start: 0.8865 (t) cc_final: 0.8615 (t)
REVERT: A 1043 MET cc_start: 0.9124 (mmp) cc_final: 0.8660 (mmp)
REVERT: A 1048 TYR cc_start: 0.8198 (t80) cc_final: 0.7655 (t80)
REVERT: A 1107 ASN cc_start: 0.8914 (t0) cc_final: 0.8374 (t0)
REVERT: A 1123 GLU cc_start: 0.8394 (mp0) cc_final: 0.8163 (mp0)
REVERT: A 1144 ASP cc_start: 0.9206 (t70) cc_final: 0.8818 (t0)
REVERT: A 1228 ARG cc_start: 0.6571 (ptt180) cc_final: 0.5648 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2159
  time to fit residues: 55.6601
Evaluate side-chains
  151 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 85 optimal weight:   10.0000
   chunk 92 optimal weight:    3.9990
   chunk 71 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0970
   chunk 108 optimal weight:    0.8980
   chunk 94 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1238 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.096499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.072363 restraints weight = 34078.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.074924 restraints weight = 18512.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.076659 restraints weight = 12398.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.5259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10148  Z= 0.123
  Angle     :  0.630   8.572  13694  Z= 0.331
  Chirality :  0.042   0.173   1460
  Planarity :  0.004   0.046   1770
  Dihedral  :  4.702  16.511   1330
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.00 %
    Favored  : 99.91 %
  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: -0.91 (0.24), residues: 1196
  helix:  0.38 (0.27), residues: 383
  sheet: -1.30 (0.34), residues: 208
  loop : -0.92 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 361 
 HIS   0.005   0.001   HIS A1072 
 PHE   0.022   0.001   PHE A 202 
 TYR   0.032   0.001   TYR A 206 
 ARG   0.006   0.000   ARG A1204 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03753 (  410)
  hydrogen bonds       : angle       5.49137 ( 1158)
  covalent geometry    : bond        0.00277 (10148)
  covalent geometry    : angle       0.62967 (13694)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3661.62 seconds
wall clock time: 65 minutes 12.72 seconds (3912.72 seconds total)