Starting phenix.real_space_refine
on Fri Feb 14 09:48:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jqh_36572/02_2025/8jqh_36572_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jqh_36572/02_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_36572/02_2025/8jqh_36572.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jqh_36572/02_2025/8jqh_36572.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jqh_36572/02_2025/8jqh_36572_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jqh_36572/02_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-5592/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: 5.64, per 1000 atoms: 0.57
  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: 2.47
  Conformation dependent library (CDL) restraints added in 1.1 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: 1.74
  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: 4.19

  Time building geometry restraints manager: 2.87 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:             0.570
  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:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.100
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.220
-------------------------------------------------------------------------------
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= 0.368
  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 

*********************** 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  : 1.077 
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: 0.2547
  time to fit residues: 90.9144
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  : 1.136 
-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.094523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.070578 restraints weight = 34220.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.073062 restraints weight = 18690.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.074698 restraints weight = 12457.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3235
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    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 = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  10148  Z= 0.328
  Angle     :  0.747  17.550  13694  Z= 0.383
  Chirality :  0.044   0.188   1460
  Planarity :  0.005   0.068   1770
  Dihedral  :  5.236  18.632   1330
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 20.00
  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 

*********************** 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
  231 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 229
  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: symmetry clash
REVERT: A   28 MET cc_start: 0.8653 (tpt) cc_final: 0.8227 (tpp)
REVERT: A   49 THR cc_start: 0.9571 (p) cc_final: 0.9320 (t)
REVERT: A   59 ASP cc_start: 0.8860 (p0) cc_final: 0.8361 (p0)
REVERT: A  306 TYR cc_start: 0.8394 (m-10) cc_final: 0.7662 (m-10)
REVERT: A  313 ASP cc_start: 0.8553 (m-30) cc_final: 0.8134 (m-30)
REVERT: A  325 SER cc_start: 0.9148 (m) cc_final: 0.8937 (m)
REVERT: A  382 PHE cc_start: 0.8765 (t80) cc_final: 0.8278 (t80)
REVERT: A  417 MET cc_start: 0.9439 (mmm) cc_final: 0.9212 (mmm)
REVERT: A  481 LEU cc_start: 0.8946 (mt) cc_final: 0.8034 (mt)
REVERT: A  496 CYS cc_start: 0.9264 (m) cc_final: 0.8688 (m)
REVERT: A  507 ASP cc_start: 0.8452 (t0) cc_final: 0.8054 (t70)
REVERT: A  661 MET cc_start: 0.9534 (mmp) cc_final: 0.9313 (mmm)
REVERT: A  671 ILE cc_start: 0.9156 (mt) cc_final: 0.8690 (tp)
REVERT: A  687 ARG cc_start: 0.8420 (tpp80) cc_final: 0.7956 (mmm-85)
REVERT: A  710 PHE cc_start: 0.8163 (m-10) cc_final: 0.7883 (m-10)
REVERT: A  729 MET cc_start: 0.8750 (tmm) cc_final: 0.8485 (tmm)
REVERT: A  745 MET cc_start: 0.7799 (tmm) cc_final: 0.7545 (tmm)
REVERT: A  825 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7766 (tm-30)
REVERT: A  841 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8554 (mt-10)
REVERT: A  938 LYS cc_start: 0.9421 (pttt) cc_final: 0.9145 (pttp)
REVERT: A  974 LEU cc_start: 0.9594 (tp) cc_final: 0.9388 (tt)
REVERT: A 1009 MET cc_start: 0.8049 (ttm) cc_final: 0.7406 (ttm)
REVERT: A 1015 GLN cc_start: 0.9039 (pm20) cc_final: 0.8506 (pm20)
REVERT: A 1027 LEU cc_start: 0.9819 (tp) cc_final: 0.9609 (tt)
REVERT: A 1107 ASN cc_start: 0.9029 (t0) cc_final: 0.8640 (t0)
REVERT: A 1122 PHE cc_start: 0.8594 (m-80) cc_final: 0.8036 (m-80)
REVERT: A 1202 GLN cc_start: 0.9495 (mt0) cc_final: 0.9256 (tt0)
REVERT: A 1205 ARG cc_start: 0.9016 (tmt170) cc_final: 0.8625 (tpt90)
  outliers start: 2
  outliers final: 0
  residues processed: 230
  average time/residue: 0.2381
  time to fit residues: 76.0344
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  : 1.106 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 117 optimal weight:   10.0000
   chunk 92 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 45 optimal weight:    7.9990
   chunk 113 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 100 optimal weight:    7.9990
   chunk 61 optimal weight:    0.0020
   chunk 89 optimal weight:    8.9990
   overall best weight:    3.3996

-------------------------------------------------------------------------------
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 ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1013 ASN
** A1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1243 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.091582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.067721 restraints weight = 34823.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.070188 restraints weight = 18977.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.071791 restraints weight = 12664.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3180
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3180 r_free = 0.3180    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       28 |
|-----------------------------------------------------------------------------|
r_final: 0.3179
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.3335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070  10148  Z= 0.332
  Angle     :  0.713  15.142  13694  Z= 0.369
  Chirality :  0.044   0.175   1460
  Planarity :  0.005   0.045   1770
  Dihedral  :  5.193  18.263   1330
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 19.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  5.10 %
    Favored  : 94.81 %
  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: -1.34 (0.24), residues: 1196
  helix:  0.05 (0.26), residues: 387
  sheet: -1.71 (0.31), residues: 223
  loop : -1.10 (0.26), residues: 586

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   0.017   0.002   PHE A1142 
 TYR   0.019   0.002   TYR A 617 
 ARG   0.005   0.001   ARG A1204 

*********************** 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
  199 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 198
  time to evaluate  : 1.117 
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   59 ASP cc_start: 0.8918 (p0) cc_final: 0.8450 (p0)
REVERT: A  103 GLN cc_start: 0.8912 (mp10) cc_final: 0.8710 (mp10)
REVERT: A  122 TRP cc_start: 0.9362 (m100) cc_final: 0.8731 (m100)
REVERT: A  311 MET cc_start: 0.8884 (tpp) cc_final: 0.8681 (tpp)
REVERT: A  339 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7351 (tm-30)
REVERT: A  382 PHE cc_start: 0.8794 (t80) cc_final: 0.7946 (t80)
REVERT: A  481 LEU cc_start: 0.9137 (mt) cc_final: 0.8393 (mt)
REVERT: A  496 CYS cc_start: 0.9303 (m) cc_final: 0.8854 (m)
REVERT: A  507 ASP cc_start: 0.8791 (t0) cc_final: 0.8314 (t0)
REVERT: A  661 MET cc_start: 0.9526 (mmp) cc_final: 0.9269 (mmm)
REVERT: A  671 ILE cc_start: 0.9234 (mt) cc_final: 0.8736 (tp)
REVERT: A  710 PHE cc_start: 0.8255 (m-10) cc_final: 0.8041 (m-10)
REVERT: A  777 LEU cc_start: 0.8564 (mt) cc_final: 0.8293 (mt)
REVERT: A  825 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7949 (tm-30)
REVERT: A  841 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8644 (mt-10)
REVERT: A  993 ASP cc_start: 0.9081 (p0) cc_final: 0.8777 (p0)
REVERT: A 1009 MET cc_start: 0.8352 (ttm) cc_final: 0.7777 (ttm)
REVERT: A 1021 MET cc_start: 0.9656 (tpp) cc_final: 0.8362 (tpp)
REVERT: A 1107 ASN cc_start: 0.9099 (t0) cc_final: 0.8597 (t0)
REVERT: A 1144 ASP cc_start: 0.9326 (t70) cc_final: 0.9094 (t0)
REVERT: A 1202 GLN cc_start: 0.9474 (mt0) cc_final: 0.9271 (tt0)
REVERT: A 1205 ARG cc_start: 0.8991 (tmt170) cc_final: 0.8508 (tpt90)
  outliers start: 1
  outliers final: 0
  residues processed: 198
  average time/residue: 0.2345
  time to fit residues: 64.8138
Evaluate side-chains
  156 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.193 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 65 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9980
   chunk 105 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 84 optimal weight:    6.9990
   chunk 7 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 115 optimal weight:    9.9990
   overall best weight:    1.9786

-------------------------------------------------------------------------------
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 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 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**
A1097 ASN
** A1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1250 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.093401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.069787 restraints weight = 34296.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.072333 restraints weight = 18739.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.073977 restraints weight = 12481.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       28 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       33 |
|-----------------------------------------------------------------------------|
r_final: 0.3211
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10148  Z= 0.232
  Angle     :  0.631   8.174  13694  Z= 0.331
  Chirality :  0.043   0.228   1460
  Planarity :  0.005   0.126   1770
  Dihedral  :  5.026  16.592   1330
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 17.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.73 %
    Favored  : 96.09 %
  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: -1.16 (0.24), residues: 1196
  helix:  0.26 (0.27), residues: 389
  sheet: -1.70 (0.31), residues: 223
  loop : -1.00 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 532 
 HIS   0.006   0.001   HIS A 203 
 PHE   0.014   0.002   PHE A1142 
 TYR   0.016   0.002   TYR A 611 
 ARG   0.006   0.000   ARG A1252 

*********************** 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
  200 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 198
  time to evaluate  : 1.217 
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   59 ASP cc_start: 0.8854 (p0) cc_final: 0.8446 (p0)
REVERT: A  122 TRP cc_start: 0.9331 (m100) cc_final: 0.8636 (m100)
REVERT: A  210 MET cc_start: 0.8943 (mmm) cc_final: 0.8546 (mmm)
REVERT: A  217 ILE cc_start: 0.9580 (mm) cc_final: 0.9379 (mm)
REVERT: A  311 MET cc_start: 0.8849 (tpp) cc_final: 0.8598 (tpp)
REVERT: A  313 ASP cc_start: 0.8922 (m-30) cc_final: 0.8471 (m-30)
REVERT: A  339 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7321 (tm-30)
REVERT: A  406 GLU cc_start: 0.7481 (tt0) cc_final: 0.7251 (tt0)
REVERT: A  481 LEU cc_start: 0.9136 (mt) cc_final: 0.8480 (mt)
REVERT: A  496 CYS cc_start: 0.9260 (m) cc_final: 0.8807 (m)
REVERT: A  507 ASP cc_start: 0.8771 (t0) cc_final: 0.8278 (t0)
REVERT: A  509 ILE cc_start: 0.8910 (mt) cc_final: 0.8700 (mt)
REVERT: A  661 MET cc_start: 0.9518 (mmp) cc_final: 0.9260 (mmm)
REVERT: A  710 PHE cc_start: 0.8439 (m-10) cc_final: 0.8086 (m-10)
REVERT: A  729 MET cc_start: 0.8902 (tmm) cc_final: 0.8392 (tmm)
REVERT: A  777 LEU cc_start: 0.8493 (mt) cc_final: 0.8236 (mt)
REVERT: A  825 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7948 (tm-30)
REVERT: A  841 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8714 (mt-10)
REVERT: A  887 GLU cc_start: 0.7901 (mp0) cc_final: 0.7698 (mp0)
REVERT: A  993 ASP cc_start: 0.9153 (p0) cc_final: 0.8922 (p0)
REVERT: A 1008 GLN cc_start: 0.8884 (pm20) cc_final: 0.8208 (pm20)
REVERT: A 1009 MET cc_start: 0.7969 (ttm) cc_final: 0.7057 (ttm)
REVERT: A 1086 GLU cc_start: 0.8303 (tt0) cc_final: 0.8101 (tt0)
REVERT: A 1107 ASN cc_start: 0.9102 (t0) cc_final: 0.8642 (t0)
REVERT: A 1144 ASP cc_start: 0.9318 (t70) cc_final: 0.9054 (t0)
REVERT: A 1205 ARG cc_start: 0.8949 (tmt170) cc_final: 0.8495 (tpt90)
  outliers start: 2
  outliers final: 0
  residues processed: 199
  average time/residue: 0.2364
  time to fit residues: 66.0548
Evaluate side-chains
  154 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 40 optimal weight:    0.9990
   chunk 42 optimal weight:    0.4980
   chunk 87 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 49 optimal weight:    0.1980
   chunk 41 optimal weight:    0.8980
   chunk 117 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 416 HIS
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1238 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.094745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.071001 restraints weight = 33920.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.073587 restraints weight = 18278.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.075331 restraints weight = 12090.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3229
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       33 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|
r_final: 0.3229
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.4090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  10148  Z= 0.197
  Angle     :  0.630  15.687  13694  Z= 0.329
  Chirality :  0.043   0.197   1460
  Planarity :  0.005   0.087   1770
  Dihedral  :  4.849  17.337   1330
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.73 %
    Favored  : 96.18 %
  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: -1.03 (0.24), residues: 1196
  helix:  0.36 (0.27), residues: 389
  sheet: -1.62 (0.31), residues: 221
  loop : -0.92 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 361 
 HIS   0.004   0.001   HIS A 797 
 PHE   0.011   0.001   PHE A 561 
 TYR   0.018   0.001   TYR A 611 
 ARG   0.005   0.000   ARG A 956 

*********************** 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
  193 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 192
  time to evaluate  : 1.104 
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   59 ASP cc_start: 0.8941 (p0) cc_final: 0.8552 (p0)
REVERT: A  122 TRP cc_start: 0.9324 (m100) cc_final: 0.8762 (m100)
REVERT: A  217 ILE cc_start: 0.9547 (mm) cc_final: 0.9346 (mm)
REVERT: A  311 MET cc_start: 0.9234 (mmt) cc_final: 0.8957 (tpp)
REVERT: A  481 LEU cc_start: 0.9160 (mt) cc_final: 0.8663 (mt)
REVERT: A  496 CYS cc_start: 0.9212 (m) cc_final: 0.8862 (m)
REVERT: A  507 ASP cc_start: 0.8852 (t0) cc_final: 0.8501 (t0)
REVERT: A  509 ILE cc_start: 0.8849 (mt) cc_final: 0.8598 (mt)
REVERT: A  617 TYR cc_start: 0.8801 (m-80) cc_final: 0.8416 (m-80)
REVERT: A  661 MET cc_start: 0.9564 (mmp) cc_final: 0.9275 (mmm)
REVERT: A  683 THR cc_start: 0.8828 (m) cc_final: 0.8612 (m)
REVERT: A  710 PHE cc_start: 0.8484 (m-10) cc_final: 0.8139 (m-10)
REVERT: A  729 MET cc_start: 0.8849 (tmm) cc_final: 0.8233 (tmm)
REVERT: A  745 MET cc_start: 0.7139 (tpp) cc_final: 0.6924 (tpp)
REVERT: A  825 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7720 (tm-30)
REVERT: A  841 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8658 (mt-10)
REVERT: A  993 ASP cc_start: 0.9140 (p0) cc_final: 0.8910 (p0)
REVERT: A 1043 MET cc_start: 0.9159 (mmp) cc_final: 0.8914 (mmp)
REVERT: A 1086 GLU cc_start: 0.8239 (tt0) cc_final: 0.8006 (tt0)
REVERT: A 1107 ASN cc_start: 0.9061 (t0) cc_final: 0.8609 (t0)
REVERT: A 1122 PHE cc_start: 0.8658 (m-80) cc_final: 0.8393 (m-80)
REVERT: A 1144 ASP cc_start: 0.9342 (t70) cc_final: 0.9066 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 192
  average time/residue: 0.2269
  time to fit residues: 61.7526
Evaluate side-chains
  147 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.225 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 64 optimal weight:    4.9990
   chunk 50 optimal weight:    8.9990
   chunk 59 optimal weight:    6.9990
   chunk 114 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 83 optimal weight:    8.9990
   chunk 53 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    2.5586

-------------------------------------------------------------------------------
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**
** A1013 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 = 0.3571 r_free = 0.3571 target = 0.091994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.068125 restraints weight = 34577.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.070573 restraints weight = 18991.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.072192 restraints weight = 12814.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3174
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
r_final: 0.3174
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.4468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  10148  Z= 0.273
  Angle     :  0.654   7.958  13694  Z= 0.345
  Chirality :  0.043   0.172   1460
  Planarity :  0.005   0.079   1770
  Dihedral  :  4.999  17.877   1330
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 17.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  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: -1.16 (0.24), residues: 1196
  helix:  0.25 (0.27), residues: 387
  sheet: -1.63 (0.32), residues: 223
  loop : -1.03 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 361 
 HIS   0.008   0.002   HIS A 797 
 PHE   0.016   0.002   PHE A 561 
 TYR   0.016   0.002   TYR A1217 
 ARG   0.005   0.000   ARG A1201 

*********************** 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
  177 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.8968 (p0) cc_final: 0.8649 (p0)
REVERT: A  111 LEU cc_start: 0.8963 (mm) cc_final: 0.8692 (mm)
REVERT: A  122 TRP cc_start: 0.9351 (m100) cc_final: 0.8689 (m100)
REVERT: A  210 MET cc_start: 0.8861 (mmm) cc_final: 0.8636 (mmm)
REVERT: A  216 SER cc_start: 0.9392 (m) cc_final: 0.9093 (t)
REVERT: A  217 ILE cc_start: 0.9573 (mm) cc_final: 0.9355 (mm)
REVERT: A  311 MET cc_start: 0.9316 (mmt) cc_final: 0.9023 (tpp)
REVERT: A  371 TYR cc_start: 0.8308 (p90) cc_final: 0.8070 (p90)
REVERT: A  481 LEU cc_start: 0.9125 (mt) cc_final: 0.8686 (mt)
REVERT: A  496 CYS cc_start: 0.9191 (m) cc_final: 0.8795 (m)
REVERT: A  509 ILE cc_start: 0.8870 (mt) cc_final: 0.8631 (mt)
REVERT: A  617 TYR cc_start: 0.8831 (m-80) cc_final: 0.8446 (m-80)
REVERT: A  661 MET cc_start: 0.9556 (mmp) cc_final: 0.9261 (mmm)
REVERT: A  683 THR cc_start: 0.8861 (m) cc_final: 0.8658 (m)
REVERT: A  710 PHE cc_start: 0.8473 (m-10) cc_final: 0.8187 (m-10)
REVERT: A  725 LEU cc_start: 0.9235 (tp) cc_final: 0.8982 (tp)
REVERT: A  729 MET cc_start: 0.8858 (tmm) cc_final: 0.8318 (tmm)
REVERT: A  825 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7911 (tm-30)
REVERT: A  841 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8689 (mt-10)
REVERT: A  974 LEU cc_start: 0.9496 (tt) cc_final: 0.9028 (tt)
REVERT: A 1009 MET cc_start: 0.7689 (ttm) cc_final: 0.7062 (ttm)
REVERT: A 1021 MET cc_start: 0.9497 (tpp) cc_final: 0.9127 (tpp)
REVERT: A 1043 MET cc_start: 0.9180 (mmp) cc_final: 0.8944 (mmp)
REVERT: A 1107 ASN cc_start: 0.9128 (t0) cc_final: 0.8645 (t0)
REVERT: A 1138 GLU cc_start: 0.7945 (pp20) cc_final: 0.7667 (pp20)
REVERT: A 1144 ASP cc_start: 0.9345 (t70) cc_final: 0.8994 (t0)
REVERT: A 1206 ARG cc_start: 0.8471 (tpp-160) cc_final: 0.7969 (tpp-160)
REVERT: A 1228 ARG cc_start: 0.6344 (ptt180) cc_final: 0.5558 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.2266
  time to fit residues: 56.7437
Evaluate side-chains
  139 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.247 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 5 optimal weight:    7.9990
   chunk 96 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 117 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 8 optimal weight:    7.9990
   chunk 95 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 55 optimal weight:    7.9990
   chunk 90 optimal weight:    9.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 130 HIS
** 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**
** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1241 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.091841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.067985 restraints weight = 34990.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.070438 restraints weight = 19019.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.072025 restraints weight = 12738.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3165
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3165 r_free = 0.3165    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3165 r_free = 0.3165    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
r_final: 0.3165
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.4788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10148  Z= 0.271
  Angle     :  0.660   8.279  13694  Z= 0.352
  Chirality :  0.044   0.254   1460
  Planarity :  0.005   0.070   1770
  Dihedral  :  5.054  19.799   1330
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 17.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    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: -1.16 (0.24), residues: 1196
  helix:  0.20 (0.27), residues: 383
  sheet: -1.57 (0.33), residues: 221
  loop : -1.01 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A1113 
 HIS   0.007   0.001   HIS A 797 
 PHE   0.021   0.002   PHE A 382 
 TYR   0.018   0.002   TYR A1217 
 ARG   0.016   0.001   ARG A1205 

*********************** 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
  170 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 1.279 
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: 0.7963 (ttp) cc_final: 0.7358 (tmm)
REVERT: A   59 ASP cc_start: 0.8979 (p0) cc_final: 0.8675 (p0)
REVERT: A  122 TRP cc_start: 0.9349 (m100) cc_final: 0.8776 (m100)
REVERT: A  210 MET cc_start: 0.8853 (mmm) cc_final: 0.8497 (mmm)
REVERT: A  311 MET cc_start: 0.9331 (mmt) cc_final: 0.9061 (tpp)
REVERT: A  325 SER cc_start: 0.9035 (m) cc_final: 0.8828 (m)
REVERT: A  371 TYR cc_start: 0.8621 (p90) cc_final: 0.8262 (p90)
REVERT: A  617 TYR cc_start: 0.8816 (m-80) cc_final: 0.8416 (m-80)
REVERT: A  661 MET cc_start: 0.9572 (mmp) cc_final: 0.9250 (mmm)
REVERT: A  710 PHE cc_start: 0.8503 (m-10) cc_final: 0.8243 (m-10)
REVERT: A  725 LEU cc_start: 0.9339 (tp) cc_final: 0.9103 (tp)
REVERT: A  729 MET cc_start: 0.8869 (tmm) cc_final: 0.8337 (tmm)
REVERT: A  777 LEU cc_start: 0.8587 (mt) cc_final: 0.8335 (mt)
REVERT: A  825 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7930 (tm-30)
REVERT: A  841 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8661 (mt-10)
REVERT: A  974 LEU cc_start: 0.9534 (tt) cc_final: 0.9021 (tt)
REVERT: A 1009 MET cc_start: 0.7823 (ttm) cc_final: 0.7110 (ttm)
REVERT: A 1021 MET cc_start: 0.9539 (tpp) cc_final: 0.9145 (tpp)
REVERT: A 1107 ASN cc_start: 0.9106 (t0) cc_final: 0.8459 (t0)
REVERT: A 1138 GLU cc_start: 0.7931 (pp20) cc_final: 0.7617 (pp20)
REVERT: A 1144 ASP cc_start: 0.9300 (t70) cc_final: 0.8942 (t0)
REVERT: A 1228 ARG cc_start: 0.6514 (ptt180) cc_final: 0.5727 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.2302
  time to fit residues: 54.6614
Evaluate side-chains
  137 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 1.118 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 100 optimal weight:    0.0670
   chunk 25 optimal weight:    3.9990
   chunk 117 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 83 optimal weight:    0.7980
   chunk 65 optimal weight:    7.9990
   chunk 85 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    1.7722

-------------------------------------------------------------------------------
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 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1013 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 = 0.3592 r_free = 0.3592 target = 0.092901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.068839 restraints weight = 34606.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.071275 restraints weight = 18993.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.072882 restraints weight = 12754.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       39 |
|-----------------------------------------------------------------------------|
r_final: 0.3184
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.4971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10148  Z= 0.223
  Angle     :  0.628   7.705  13694  Z= 0.333
  Chirality :  0.043   0.186   1460
  Planarity :  0.004   0.060   1770
  Dihedral  :  4.956  18.483   1330
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  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: -1.03 (0.24), residues: 1196
  helix:  0.35 (0.27), residues: 383
  sheet: -1.53 (0.34), residues: 198
  loop : -1.00 (0.25), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 361 
 HIS   0.006   0.001   HIS A 797 
 PHE   0.022   0.002   PHE A 202 
 TYR   0.018   0.001   TYR A1217 
 ARG   0.006   0.000   ARG A 956 

*********************** 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
  183 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.8044 (ttp) cc_final: 0.7341 (tmm)
REVERT: A   47 MET cc_start: 0.8216 (tmm) cc_final: 0.7848 (tmm)
REVERT: A   59 ASP cc_start: 0.9008 (p0) cc_final: 0.8697 (p0)
REVERT: A  122 TRP cc_start: 0.9286 (m100) cc_final: 0.8818 (m100)
REVERT: A  210 MET cc_start: 0.8831 (mmm) cc_final: 0.8515 (mmm)
REVERT: A  311 MET cc_start: 0.9293 (mmt) cc_final: 0.9032 (tpp)
REVERT: A  325 SER cc_start: 0.8985 (m) cc_final: 0.8778 (m)
REVERT: A  357 GLU cc_start: 0.7194 (tt0) cc_final: 0.6801 (tt0)
REVERT: A  371 TYR cc_start: 0.8697 (p90) cc_final: 0.8314 (p90)
REVERT: A  617 TYR cc_start: 0.8775 (m-80) cc_final: 0.8365 (m-80)
REVERT: A  661 MET cc_start: 0.9562 (mmp) cc_final: 0.9229 (mmm)
REVERT: A  683 THR cc_start: 0.8929 (m) cc_final: 0.8719 (m)
REVERT: A  710 PHE cc_start: 0.8467 (m-10) cc_final: 0.8213 (m-10)
REVERT: A  725 LEU cc_start: 0.9328 (tp) cc_final: 0.9126 (tp)
REVERT: A  729 MET cc_start: 0.8859 (tmm) cc_final: 0.8337 (tmm)
REVERT: A  777 LEU cc_start: 0.8655 (mt) cc_final: 0.8395 (mt)
REVERT: A  825 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7901 (tm-30)
REVERT: A  841 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8735 (mt-10)
REVERT: A  974 LEU cc_start: 0.9516 (tt) cc_final: 0.9012 (tt)
REVERT: A 1005 CYS cc_start: 0.8999 (t) cc_final: 0.8760 (t)
REVERT: A 1009 MET cc_start: 0.7788 (ttm) cc_final: 0.7084 (ttm)
REVERT: A 1021 MET cc_start: 0.9529 (tpp) cc_final: 0.9098 (tpp)
REVERT: A 1086 GLU cc_start: 0.8557 (pt0) cc_final: 0.8352 (pt0)
REVERT: A 1107 ASN cc_start: 0.9049 (t0) cc_final: 0.8353 (t0)
REVERT: A 1109 LEU cc_start: 0.9729 (tp) cc_final: 0.9516 (tp)
REVERT: A 1144 ASP cc_start: 0.9280 (t70) cc_final: 0.8884 (t0)
REVERT: A 1228 ARG cc_start: 0.6503 (ptt180) cc_final: 0.5693 (ptt90)
REVERT: A 1245 TYR cc_start: 0.8886 (m-80) cc_final: 0.8356 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.2313
  time to fit residues: 59.0880
Evaluate side-chains
  145 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 59 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 74 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 88 optimal weight:   10.0000
   chunk 90 optimal weight:    2.9990
   chunk 95 optimal weight:    0.7980
   overall best weight:    0.9588

-------------------------------------------------------------------------------
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 214 GLN
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.094576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.070653 restraints weight = 34144.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.073175 restraints weight = 18527.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.074840 restraints weight = 12361.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3226
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       39 |
|-----------------------------------------------------------------------------|
|-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:       38 |
|-----------------------------------------------------------------------------|
r_final: 0.3227
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.5169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10148  Z= 0.189
  Angle     :  0.630   7.664  13694  Z= 0.336
  Chirality :  0.043   0.208   1460
  Planarity :  0.004   0.054   1770
  Dihedral  :  4.871  17.383   1330
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 14.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  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:  0.30 (0.27), residues: 381
  sheet: -1.33 (0.35), residues: 194
  loop : -0.94 (0.25), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 361 
 HIS   0.007   0.001   HIS A 392 
 PHE   0.025   0.001   PHE A 202 
 TYR   0.018   0.001   TYR A1217 
 ARG   0.006   0.000   ARG A 956 

*********************** 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
  181 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.8085 (ttp) cc_final: 0.7645 (tmm)
REVERT: A   59 ASP cc_start: 0.9026 (p0) cc_final: 0.8697 (p0)
REVERT: A  122 TRP cc_start: 0.9243 (m100) cc_final: 0.8792 (m100)
REVERT: A  325 SER cc_start: 0.9024 (m) cc_final: 0.8811 (m)
REVERT: A  357 GLU cc_start: 0.7046 (tt0) cc_final: 0.6779 (tt0)
REVERT: A  371 TYR cc_start: 0.8636 (p90) cc_final: 0.8209 (p90)
REVERT: A  391 ASP cc_start: 0.8733 (t70) cc_final: 0.8489 (t0)
REVERT: A  617 TYR cc_start: 0.8734 (m-80) cc_final: 0.8315 (m-80)
REVERT: A  661 MET cc_start: 0.9558 (mmp) cc_final: 0.9219 (mmm)
REVERT: A  683 THR cc_start: 0.8970 (m) cc_final: 0.8754 (m)
REVERT: A  710 PHE cc_start: 0.8481 (m-10) cc_final: 0.8220 (m-10)
REVERT: A  729 MET cc_start: 0.8816 (tmm) cc_final: 0.8276 (tmm)
REVERT: A  777 LEU cc_start: 0.8686 (mt) cc_final: 0.8441 (mt)
REVERT: A  825 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7947 (tm-30)
REVERT: A  841 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8722 (mt-10)
REVERT: A  974 LEU cc_start: 0.9471 (tt) cc_final: 0.8892 (tt)
REVERT: A 1005 CYS cc_start: 0.8926 (t) cc_final: 0.8605 (t)
REVERT: A 1009 MET cc_start: 0.7702 (ttm) cc_final: 0.7022 (ttm)
REVERT: A 1021 MET cc_start: 0.9490 (tpp) cc_final: 0.9096 (tpp)
REVERT: A 1075 LYS cc_start: 0.8782 (ptmt) cc_final: 0.8579 (ptpt)
REVERT: A 1107 ASN cc_start: 0.8983 (t0) cc_final: 0.8466 (t0)
REVERT: A 1144 ASP cc_start: 0.9315 (t70) cc_final: 0.8898 (t0)
REVERT: A 1228 ARG cc_start: 0.6590 (ptt180) cc_final: 0.5768 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.2265
  time to fit residues: 58.2233
Evaluate side-chains
  145 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 47 optimal weight:    9.9990
   chunk 42 optimal weight:    0.2980
   chunk 0 optimal weight:   10.0000
   chunk 110 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0050
   chunk 93 optimal weight:    0.5980
   chunk 96 optimal weight:    0.7980
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
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 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1013 ASN
** 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 = 0.3649 r_free = 0.3649 target = 0.096211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.072311 restraints weight = 33786.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.074898 restraints weight = 18386.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.076596 restraints weight = 12280.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3259
|-occupancy refinement: start-------------------------------------------------|
| 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:       38 |
|-----------------------------------------------------------------------------|
|-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:       39 |
|-----------------------------------------------------------------------------|
r_final: 0.3259
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.5330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10148  Z= 0.175
  Angle     :  0.624   8.265  13694  Z= 0.329
  Chirality :  0.044   0.283   1460
  Planarity :  0.004   0.045   1770
  Dihedral  :  4.759  16.853   1330
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  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: -1.01 (0.24), residues: 1196
  helix:  0.21 (0.27), residues: 384
  sheet: -1.45 (0.33), residues: 208
  loop : -0.87 (0.26), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 361 
 HIS   0.012   0.001   HIS A1150 
 PHE   0.027   0.001   PHE A 202 
 TYR   0.018   0.001   TYR A1197 
 ARG   0.005   0.000   ARG A 956 

********************** 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
  184 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 1.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.8037 (ttp) cc_final: 0.7590 (tmm)
REVERT: A   59 ASP cc_start: 0.8973 (p0) cc_final: 0.8639 (p0)
REVERT: A  122 TRP cc_start: 0.9208 (m100) cc_final: 0.8897 (m100)
REVERT: A  210 MET cc_start: 0.8847 (mmm) cc_final: 0.8627 (mmm)
REVERT: A  348 CYS cc_start: 0.9145 (m) cc_final: 0.8436 (t)
REVERT: A  371 TYR cc_start: 0.8529 (p90) cc_final: 0.8215 (p90)
REVERT: A  661 MET cc_start: 0.9523 (mmp) cc_final: 0.9232 (mmm)
REVERT: A  683 THR cc_start: 0.8896 (m) cc_final: 0.8682 (m)
REVERT: A  710 PHE cc_start: 0.8370 (m-10) cc_final: 0.8100 (m-10)
REVERT: A  725 LEU cc_start: 0.9070 (tp) cc_final: 0.8776 (tp)
REVERT: A  728 LYS cc_start: 0.9407 (mmpt) cc_final: 0.9075 (mmmt)
REVERT: A  729 MET cc_start: 0.8802 (tmm) cc_final: 0.8224 (tmm)
REVERT: A  825 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7843 (tm-30)
REVERT: A  841 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8718 (mt-10)
REVERT: A  974 LEU cc_start: 0.9447 (tt) cc_final: 0.8892 (tt)
REVERT: A  993 ASP cc_start: 0.9102 (p0) cc_final: 0.8885 (p0)
REVERT: A 1005 CYS cc_start: 0.8932 (t) cc_final: 0.8547 (t)
REVERT: A 1009 MET cc_start: 0.7642 (ttm) cc_final: 0.6951 (ttm)
REVERT: A 1022 GLN cc_start: 0.9074 (mt0) cc_final: 0.8637 (tt0)
REVERT: A 1107 ASN cc_start: 0.8899 (t0) cc_final: 0.8396 (t0)
REVERT: A 1144 ASP cc_start: 0.9281 (t70) cc_final: 0.9029 (t0)
REVERT: A 1150 HIS cc_start: 0.8912 (p90) cc_final: 0.8020 (p90)
REVERT: A 1228 ARG cc_start: 0.6563 (ptt180) cc_final: 0.5653 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.2174
  time to fit residues: 56.9027
Evaluate side-chains
  146 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 76 optimal weight:    8.9990
   chunk 108 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 534 HIS ** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.095406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.071381 restraints weight = 34279.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.073914 restraints weight = 18852.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.075578 restraints weight = 12704.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3245
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       39 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       40 |
|-----------------------------------------------------------------------------|
r_final: 0.3245
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.5527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10148  Z= 0.195
  Angle     :  0.627   7.584  13694  Z= 0.331
  Chirality :  0.044   0.219   1460
  Planarity :  0.004   0.046   1770
  Dihedral  :  4.753  15.903   1330
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  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:  0.24 (0.27), residues: 384
  sheet: -1.37 (0.34), residues: 210
  loop : -0.86 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A1113 
 HIS   0.003   0.001   HIS A 797 
 PHE   0.027   0.002   PHE A 382 
 TYR   0.018   0.001   TYR A1217 
 ARG   0.005   0.000   ARG A 956 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3149.92 seconds
wall clock time: 57 minutes 33.25 seconds (3453.25 seconds total)