Starting phenix.real_space_refine
on Sun Dec 29 06:59:43 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jqh_36572/12_2024/8jqh_36572_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jqh_36572/12_2024/8jqh_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_36572/12_2024/8jqh_36572.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jqh_36572/12_2024/8jqh_36572.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jqh_36572/12_2024/8jqh_36572_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jqh_36572/12_2024/8jqh_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-5532/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: 7.09, per 1000 atoms: 0.71
  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: 2.54
  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: 1.81
  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: 4.72

  Time building geometry restraints manager: 2.94 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:             0.660
  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:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     29.310
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.060
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.710
-------------------------------------------------------------------------------
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  : 1.185 
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: 0.2673
  time to fit residues: 94.9758
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  : 1.169 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
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 : 20.07
  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  : 1.127 
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: 0.8631 (tpt) cc_final: 0.8220 (tpp)
REVERT: A   49 THR cc_start: 0.9548 (p) cc_final: 0.9300 (t)
REVERT: A   59 ASP cc_start: 0.8777 (p0) cc_final: 0.8252 (p0)
REVERT: A  306 TYR cc_start: 0.8367 (m-10) cc_final: 0.7666 (m-10)
REVERT: A  313 ASP cc_start: 0.8554 (m-30) cc_final: 0.8133 (m-30)
REVERT: A  325 SER cc_start: 0.9179 (m) cc_final: 0.8978 (m)
REVERT: A  382 PHE cc_start: 0.8645 (t80) cc_final: 0.8129 (t80)
REVERT: A  417 MET cc_start: 0.9376 (mmm) cc_final: 0.9129 (mmm)
REVERT: A  481 LEU cc_start: 0.8906 (mt) cc_final: 0.7962 (mt)
REVERT: A  496 CYS cc_start: 0.9220 (m) cc_final: 0.8579 (m)
REVERT: A  507 ASP cc_start: 0.8413 (t0) cc_final: 0.8000 (t70)
REVERT: A  661 MET cc_start: 0.9472 (mmp) cc_final: 0.9266 (mmm)
REVERT: A  671 ILE cc_start: 0.9079 (mt) cc_final: 0.8669 (tp)
REVERT: A  687 ARG cc_start: 0.8327 (tpp80) cc_final: 0.7882 (mmm-85)
REVERT: A  710 PHE cc_start: 0.8242 (m-10) cc_final: 0.7949 (m-10)
REVERT: A  729 MET cc_start: 0.8822 (tmm) cc_final: 0.8523 (tmm)
REVERT: A  745 MET cc_start: 0.7741 (tmm) cc_final: 0.7491 (tmm)
REVERT: A  825 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7608 (tm-30)
REVERT: A  841 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8535 (mt-10)
REVERT: A  938 LYS cc_start: 0.9381 (pttt) cc_final: 0.9133 (pttp)
REVERT: A  974 LEU cc_start: 0.9577 (tp) cc_final: 0.9366 (tt)
REVERT: A 1009 MET cc_start: 0.8016 (ttm) cc_final: 0.7366 (ttm)
REVERT: A 1012 LEU cc_start: 0.9195 (mt) cc_final: 0.8995 (mt)
REVERT: A 1015 GLN cc_start: 0.9068 (pm20) cc_final: 0.8514 (pm20)
REVERT: A 1027 LEU cc_start: 0.9809 (tp) cc_final: 0.9587 (tt)
REVERT: A 1107 ASN cc_start: 0.8977 (t0) cc_final: 0.8594 (t0)
REVERT: A 1122 PHE cc_start: 0.8473 (m-80) cc_final: 0.7865 (m-80)
REVERT: A 1202 GLN cc_start: 0.9473 (mt0) cc_final: 0.9249 (tt0)
REVERT: A 1205 ARG cc_start: 0.9018 (tmt170) cc_final: 0.8667 (tpt90)
REVERT: A 1212 ASN cc_start: 0.9236 (t0) cc_final: 0.9017 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 230
  average time/residue: 0.2265
  time to fit residues: 72.3362
Evaluate side-chains
  175 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 60 optimal weight:   20.0000
   chunk 33 optimal weight:    0.9980
   chunk 90 optimal weight:    5.9990
   chunk 74 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 109 optimal weight:    0.9980
   chunk 117 optimal weight:   10.0000
   chunk 97 optimal weight:    3.9990
   chunk 108 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    2.1986

-------------------------------------------------------------------------------
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 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: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.2987

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= 0.255
  Angle     :  0.664  15.596  13694  Z= 0.342
  Chirality :  0.043   0.166   1460
  Planarity :  0.004   0.046   1770
  Dihedral  :  5.033  17.261   1330
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 18.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.46 %
    Favored  : 96.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.24), residues: 1196
  helix:  0.23 (0.26), residues: 387
  sheet: -1.78 (0.31), residues: 224
  loop : -1.01 (0.26), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 361 
 HIS   0.011   0.002   HIS A 392 
 PHE   0.014   0.002   PHE A1142 
 TYR   0.013   0.002   TYR A1217 
 ARG   0.004   0.001   ARG A 984 

*********************** 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
  217 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 216
  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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 THR cc_start: 0.9511 (p) cc_final: 0.9260 (t)
REVERT: A   59 ASP cc_start: 0.8724 (p0) cc_final: 0.8199 (p0)
REVERT: A  306 TYR cc_start: 0.8443 (m-10) cc_final: 0.7804 (m-10)
REVERT: A  311 MET cc_start: 0.8911 (tpp) cc_final: 0.8651 (tpp)
REVERT: A  313 ASP cc_start: 0.8702 (m-30) cc_final: 0.8249 (m-30)
REVERT: A  339 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7277 (tm-30)
REVERT: A  382 PHE cc_start: 0.8557 (t80) cc_final: 0.7679 (t80)
REVERT: A  417 MET cc_start: 0.9407 (mmm) cc_final: 0.9193 (mmm)
REVERT: A  481 LEU cc_start: 0.9016 (mt) cc_final: 0.8144 (mt)
REVERT: A  496 CYS cc_start: 0.9219 (m) cc_final: 0.8609 (m)
REVERT: A  507 ASP cc_start: 0.8672 (t0) cc_final: 0.8127 (t0)
REVERT: A  661 MET cc_start: 0.9457 (mmp) cc_final: 0.9226 (mmm)
REVERT: A  671 ILE cc_start: 0.9041 (mt) cc_final: 0.8551 (tp)
REVERT: A  683 THR cc_start: 0.8774 (m) cc_final: 0.8562 (m)
REVERT: A  710 PHE cc_start: 0.8279 (m-10) cc_final: 0.7980 (m-10)
REVERT: A  729 MET cc_start: 0.8889 (tmm) cc_final: 0.8273 (tmm)
REVERT: A  825 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7663 (tm-30)
REVERT: A  841 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8567 (mt-10)
REVERT: A  938 LYS cc_start: 0.9450 (pttt) cc_final: 0.9239 (ptmm)
REVERT: A  993 ASP cc_start: 0.8934 (p0) cc_final: 0.8644 (p0)
REVERT: A 1009 MET cc_start: 0.8192 (ttm) cc_final: 0.7585 (ttm)
REVERT: A 1021 MET cc_start: 0.9595 (tpp) cc_final: 0.8609 (tpp)
REVERT: A 1043 MET cc_start: 0.8987 (mmp) cc_final: 0.8583 (mmp)
REVERT: A 1107 ASN cc_start: 0.9003 (t0) cc_final: 0.8565 (t0)
REVERT: A 1122 PHE cc_start: 0.8564 (m-80) cc_final: 0.8140 (m-80)
REVERT: A 1138 GLU cc_start: 0.7914 (pp20) cc_final: 0.7593 (pp20)
REVERT: A 1144 ASP cc_start: 0.9211 (t70) cc_final: 0.8957 (t0)
REVERT: A 1205 ARG cc_start: 0.8944 (tmt170) cc_final: 0.8574 (tpt90)
REVERT: A 1212 ASN cc_start: 0.9202 (t0) cc_final: 0.8964 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 216
  average time/residue: 0.2448
  time to fit residues: 73.1421
Evaluate side-chains
  175 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 107 optimal weight:    0.9990
   chunk 82 optimal weight:    8.9990
   chunk 56 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 73 optimal weight:    6.9990
   chunk 109 optimal weight:    3.9990
   chunk 115 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 103 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    2.5990

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

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.3690

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= 0.273
  Angle     :  0.650   9.378  13694  Z= 0.341
  Chirality :  0.043   0.180   1460
  Planarity :  0.005   0.113   1770
  Dihedral  :  5.018  17.149   1330
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 17.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  5.19 %
    Favored  : 94.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.24), residues: 1196
  helix:  0.27 (0.26), residues: 386
  sheet: -1.75 (0.30), residues: 227
  loop : -1.01 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 532 
 HIS   0.007   0.002   HIS A 203 
 PHE   0.017   0.002   PHE A 425 
 TYR   0.016   0.002   TYR A1217 
 ARG   0.010   0.001   ARG A 956 

*********************** 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
  198 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 196
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.8750 (p0) cc_final: 0.8315 (p0)
REVERT: A  311 MET cc_start: 0.8927 (tpp) cc_final: 0.8695 (tpp)
REVERT: A  382 PHE cc_start: 0.8595 (t80) cc_final: 0.7619 (t80)
REVERT: A  481 LEU cc_start: 0.9111 (mt) cc_final: 0.8403 (mt)
REVERT: A  496 CYS cc_start: 0.9223 (m) cc_final: 0.8696 (m)
REVERT: A  661 MET cc_start: 0.9458 (mmp) cc_final: 0.9229 (mmm)
REVERT: A  710 PHE cc_start: 0.8314 (m-10) cc_final: 0.7995 (m-10)
REVERT: A  728 LYS cc_start: 0.9426 (mmpt) cc_final: 0.9074 (mmmt)
REVERT: A  729 MET cc_start: 0.8586 (tmm) cc_final: 0.8287 (tmm)
REVERT: A  777 LEU cc_start: 0.8543 (mt) cc_final: 0.8328 (mt)
REVERT: A  825 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7755 (tm-30)
REVERT: A  841 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8655 (mt-10)
REVERT: A  938 LYS cc_start: 0.9454 (pttt) cc_final: 0.9211 (ptmm)
REVERT: A  954 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8119 (mm-30)
REVERT: A  993 ASP cc_start: 0.9142 (p0) cc_final: 0.8870 (p0)
REVERT: A 1009 MET cc_start: 0.8226 (ttm) cc_final: 0.7581 (ttm)
REVERT: A 1013 ASN cc_start: 0.8874 (m110) cc_final: 0.8646 (m110)
REVERT: A 1015 GLN cc_start: 0.9003 (pm20) cc_final: 0.8717 (pm20)
REVERT: A 1021 MET cc_start: 0.9583 (tpp) cc_final: 0.8577 (tpp)
REVERT: A 1107 ASN cc_start: 0.9040 (t0) cc_final: 0.8519 (t0)
REVERT: A 1109 LEU cc_start: 0.9767 (tp) cc_final: 0.9566 (tt)
REVERT: A 1112 ILE cc_start: 0.8842 (tp) cc_final: 0.8638 (tt)
REVERT: A 1122 PHE cc_start: 0.8592 (m-80) cc_final: 0.8348 (m-80)
REVERT: A 1144 ASP cc_start: 0.9257 (t70) cc_final: 0.9008 (t0)
REVERT: A 1212 ASN cc_start: 0.9160 (t0) cc_final: 0.8938 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 197
  average time/residue: 0.2470
  time to fit residues: 68.7195
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  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 86 optimal weight:    0.5980
   chunk 47 optimal weight:    7.9990
   chunk 98 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9980
   chunk 59 optimal weight:    8.9990
   chunk 104 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1013 ASN
** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1238 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.3981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073  10148  Z= 0.223
  Angle     :  0.645  15.880  13694  Z= 0.335
  Chirality :  0.044   0.245   1460
  Planarity :  0.005   0.086   1770
  Dihedral  :  4.903  16.615   1330
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 16.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.82 %
    Favored  : 97.09 %
  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: -1.09 (0.24), residues: 1196
  helix:  0.35 (0.27), residues: 389
  sheet: -1.67 (0.31), residues: 219
  loop : -0.99 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1113 
 HIS   0.009   0.001   HIS A 203 
 PHE   0.012   0.001   PHE A1142 
 TYR   0.016   0.001   TYR A 611 
 ARG   0.013   0.001   ARG A 984 

*********************** 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
  197 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 196
  time to evaluate  : 1.124 
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: 0.8759 (p0) cc_final: 0.8360 (p0)
REVERT: A  210 MET cc_start: 0.8799 (mmm) cc_final: 0.8354 (mmm)
REVERT: A  217 ILE cc_start: 0.9541 (mm) cc_final: 0.9309 (mm)
REVERT: A  311 MET cc_start: 0.9344 (mmt) cc_final: 0.9048 (tpp)
REVERT: A  406 GLU cc_start: 0.7376 (tt0) cc_final: 0.7100 (tt0)
REVERT: A  481 LEU cc_start: 0.9121 (mt) cc_final: 0.8517 (mt)
REVERT: A  496 CYS cc_start: 0.9166 (m) cc_final: 0.8739 (m)
REVERT: A  507 ASP cc_start: 0.8794 (t0) cc_final: 0.8458 (t0)
REVERT: A  509 ILE cc_start: 0.8862 (mt) cc_final: 0.8642 (mt)
REVERT: A  661 MET cc_start: 0.9475 (mmp) cc_final: 0.9224 (mmm)
REVERT: A  710 PHE cc_start: 0.8491 (m-10) cc_final: 0.8156 (m-10)
REVERT: A  728 LYS cc_start: 0.9445 (mmpt) cc_final: 0.9075 (mmmt)
REVERT: A  729 MET cc_start: 0.8568 (tmm) cc_final: 0.8245 (tmm)
REVERT: A  745 MET cc_start: 0.7107 (tpp) cc_final: 0.6902 (tpp)
REVERT: A  825 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7795 (tm-30)
REVERT: A  841 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8653 (mt-10)
REVERT: A  938 LYS cc_start: 0.9468 (pttt) cc_final: 0.9056 (ptmm)
REVERT: A  954 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7954 (mm-30)
REVERT: A  993 ASP cc_start: 0.9139 (p0) cc_final: 0.8819 (p0)
REVERT: A 1008 GLN cc_start: 0.8783 (pm20) cc_final: 0.8111 (pm20)
REVERT: A 1009 MET cc_start: 0.8003 (ttm) cc_final: 0.7326 (ttm)
REVERT: A 1015 GLN cc_start: 0.9021 (pm20) cc_final: 0.8525 (pm20)
REVERT: A 1107 ASN cc_start: 0.9022 (t0) cc_final: 0.8580 (t0)
REVERT: A 1144 ASP cc_start: 0.9273 (t70) cc_final: 0.8995 (t0)
REVERT: A 1205 ARG cc_start: 0.8965 (tmt170) cc_final: 0.8433 (tpt90)
REVERT: A 1212 ASN cc_start: 0.9104 (t0) cc_final: 0.8870 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 196
  average time/residue: 0.2502
  time to fit residues: 67.8740
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  : 1.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 104 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 116 optimal weight:    2.9990
   chunk 96 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 60 optimal weight:   20.0000
   overall best weight:    3.1588

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1013 ASN
A1238 ASN
A1241 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.4504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079  10148  Z= 0.315
  Angle     :  0.699  11.620  13694  Z= 0.368
  Chirality :  0.045   0.199   1460
  Planarity :  0.005   0.084   1770
  Dihedral  :  5.165  18.851   1330
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 18.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.24), residues: 1196
  helix:  0.14 (0.26), residues: 387
  sheet: -1.80 (0.32), residues: 228
  loop : -1.06 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 532 
 HIS   0.009   0.002   HIS A 203 
 PHE   0.019   0.002   PHE A 202 
 TYR   0.018   0.002   TYR A1217 
 ARG   0.008   0.001   ARG A 984 

*********************** 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  : 1.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.8848 (p0) cc_final: 0.8508 (p0)
REVERT: A  103 GLN cc_start: 0.8988 (mp10) cc_final: 0.8781 (mp10)
REVERT: A  111 LEU cc_start: 0.8920 (mm) cc_final: 0.8636 (mm)
REVERT: A  216 SER cc_start: 0.9405 (m) cc_final: 0.9129 (t)
REVERT: A  311 MET cc_start: 0.9397 (mmt) cc_final: 0.9072 (tpp)
REVERT: A  371 TYR cc_start: 0.8478 (p90) cc_final: 0.8110 (p90)
REVERT: A  406 GLU cc_start: 0.7323 (tt0) cc_final: 0.7038 (tt0)
REVERT: A  481 LEU cc_start: 0.9265 (mt) cc_final: 0.9002 (mt)
REVERT: A  509 ILE cc_start: 0.8835 (mt) cc_final: 0.8617 (mt)
REVERT: A  661 MET cc_start: 0.9513 (mmp) cc_final: 0.9232 (mmm)
REVERT: A  710 PHE cc_start: 0.8556 (m-10) cc_final: 0.8274 (m-10)
REVERT: A  725 LEU cc_start: 0.9334 (tp) cc_final: 0.8971 (tp)
REVERT: A  728 LYS cc_start: 0.9482 (mmpt) cc_final: 0.9098 (mmmt)
REVERT: A  729 MET cc_start: 0.8674 (tmm) cc_final: 0.8092 (tmm)
REVERT: A  777 LEU cc_start: 0.8653 (mt) cc_final: 0.8384 (mt)
REVERT: A  825 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7814 (tm-30)
REVERT: A  841 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8685 (mt-10)
REVERT: A  876 LEU cc_start: 0.8957 (tp) cc_final: 0.8754 (tt)
REVERT: A  974 LEU cc_start: 0.9525 (tt) cc_final: 0.9074 (tt)
REVERT: A  993 ASP cc_start: 0.9240 (p0) cc_final: 0.9002 (p0)
REVERT: A 1008 GLN cc_start: 0.8952 (pm20) cc_final: 0.8271 (pm20)
REVERT: A 1009 MET cc_start: 0.8181 (ttm) cc_final: 0.7883 (ttm)
REVERT: A 1021 MET cc_start: 0.9533 (tpp) cc_final: 0.9015 (tpp)
REVERT: A 1107 ASN cc_start: 0.9036 (t0) cc_final: 0.8449 (t0)
REVERT: A 1138 GLU cc_start: 0.7972 (pp20) cc_final: 0.7671 (pp20)
REVERT: A 1144 ASP cc_start: 0.9264 (t70) cc_final: 0.8927 (t0)
REVERT: A 1228 ARG cc_start: 0.6710 (ptt180) cc_final: 0.6058 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.2340
  time to fit residues: 57.8740
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  : 1.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 111 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 84 optimal weight:    0.4980
   chunk 65 optimal weight:    7.9990
   chunk 97 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 115 optimal weight:   10.0000
   chunk 72 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 416 HIS
** 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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.4679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10148  Z= 0.183
  Angle     :  0.619   7.280  13694  Z= 0.328
  Chirality :  0.044   0.209   1460
  Planarity :  0.004   0.061   1770
  Dihedral  :  4.906  17.739   1330
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 15.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  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: -1.01 (0.24), residues: 1196
  helix:  0.39 (0.27), residues: 383
  sheet: -1.64 (0.33), residues: 221
  loop : -0.90 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 899 
 HIS   0.006   0.001   HIS A 797 
 PHE   0.020   0.001   PHE A 202 
 TYR   0.016   0.001   TYR A1217 
 ARG   0.004   0.000   ARG A1057 

*********************** 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
  183 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.110 
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: 0.8235 (ttp) cc_final: 0.7578 (tmm)
REVERT: A   47 MET cc_start: 0.8234 (tmm) cc_final: 0.7712 (tmm)
REVERT: A   59 ASP cc_start: 0.8839 (p0) cc_final: 0.8475 (p0)
REVERT: A  210 MET cc_start: 0.8794 (mmm) cc_final: 0.8495 (mmm)
REVERT: A  311 MET cc_start: 0.9291 (mmt) cc_final: 0.8978 (tpp)
REVERT: A  371 TYR cc_start: 0.8406 (p90) cc_final: 0.8130 (p90)
REVERT: A  406 GLU cc_start: 0.7293 (tt0) cc_final: 0.7077 (tt0)
REVERT: A  481 LEU cc_start: 0.9084 (mt) cc_final: 0.8834 (mt)
REVERT: A  661 MET cc_start: 0.9482 (mmp) cc_final: 0.9186 (mmm)
REVERT: A  710 PHE cc_start: 0.8493 (m-10) cc_final: 0.8154 (m-10)
REVERT: A  728 LYS cc_start: 0.9469 (mmpt) cc_final: 0.9083 (mmmt)
REVERT: A  777 LEU cc_start: 0.8678 (mt) cc_final: 0.8439 (mt)
REVERT: A  825 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7773 (tm-30)
REVERT: A  841 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8689 (mt-10)
REVERT: A  974 LEU cc_start: 0.9566 (tt) cc_final: 0.9106 (tt)
REVERT: A  979 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8662 (tm-30)
REVERT: A  984 ARG cc_start: 0.7797 (tpp80) cc_final: 0.7251 (ttp80)
REVERT: A  993 ASP cc_start: 0.9156 (p0) cc_final: 0.8886 (p0)
REVERT: A 1008 GLN cc_start: 0.8623 (pm20) cc_final: 0.8255 (pm20)
REVERT: A 1009 MET cc_start: 0.8035 (ttm) cc_final: 0.7469 (ttm)
REVERT: A 1015 GLN cc_start: 0.9182 (pm20) cc_final: 0.8717 (pm20)
REVERT: A 1107 ASN cc_start: 0.9045 (t0) cc_final: 0.8541 (t0)
REVERT: A 1138 GLU cc_start: 0.7941 (pp20) cc_final: 0.7638 (pp20)
REVERT: A 1144 ASP cc_start: 0.9282 (t70) cc_final: 0.8900 (t0)
REVERT: A 1228 ARG cc_start: 0.6859 (ptt180) cc_final: 0.6089 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.2337
  time to fit residues: 59.9228
Evaluate side-chains
  155 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 1.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:    0.0060
   chunk 46 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0270
   chunk 73 optimal weight:    4.9990
   chunk 78 optimal weight:   20.0000
   chunk 57 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 90 optimal weight:    0.4980
   chunk 105 optimal weight:    0.4980
   overall best weight:    0.3654

-------------------------------------------------------------------------------
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 327 HIS ** 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: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.4844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10148  Z= 0.165
  Angle     :  0.620   7.999  13694  Z= 0.327
  Chirality :  0.043   0.206   1460
  Planarity :  0.004   0.052   1770
  Dihedral  :  4.814  17.461   1330
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  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: -0.95 (0.24), residues: 1196
  helix:  0.40 (0.27), residues: 383
  sheet: -1.55 (0.33), residues: 214
  loop : -0.88 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP A 361 
 HIS   0.009   0.001   HIS A 392 
 PHE   0.023   0.001   PHE A 202 
 TYR   0.016   0.001   TYR A1217 
 ARG   0.006   0.000   ARG A 587 

*********************** 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
  193 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.8256 (ttp) cc_final: 0.7635 (tmm)
REVERT: A   47 MET cc_start: 0.8197 (tmm) cc_final: 0.7528 (tmm)
REVERT: A   59 ASP cc_start: 0.8819 (p0) cc_final: 0.8429 (p0)
REVERT: A  210 MET cc_start: 0.8783 (mmm) cc_final: 0.8516 (mmm)
REVERT: A  311 MET cc_start: 0.9193 (mmt) cc_final: 0.8993 (tpp)
REVERT: A  357 GLU cc_start: 0.7226 (tt0) cc_final: 0.6999 (tt0)
REVERT: A  391 ASP cc_start: 0.8597 (t70) cc_final: 0.8319 (t0)
REVERT: A  406 GLU cc_start: 0.7416 (tt0) cc_final: 0.7193 (tt0)
REVERT: A  481 LEU cc_start: 0.9017 (mt) cc_final: 0.8685 (mt)
REVERT: A  496 CYS cc_start: 0.9066 (m) cc_final: 0.8770 (m)
REVERT: A  657 GLU cc_start: 0.8964 (mp0) cc_final: 0.8756 (mp0)
REVERT: A  661 MET cc_start: 0.9455 (mmp) cc_final: 0.9165 (mmm)
REVERT: A  710 PHE cc_start: 0.8438 (m-10) cc_final: 0.8062 (m-10)
REVERT: A  728 LYS cc_start: 0.9472 (mmpt) cc_final: 0.9065 (mmmt)
REVERT: A  729 MET cc_start: 0.8550 (tmm) cc_final: 0.8338 (tmm)
REVERT: A  753 TYR cc_start: 0.5376 (m-10) cc_final: 0.5026 (m-10)
REVERT: A  825 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7784 (tm-30)
REVERT: A  841 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8668 (mt-10)
REVERT: A  974 LEU cc_start: 0.9538 (tt) cc_final: 0.9047 (tt)
REVERT: A  979 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8640 (tm-30)
REVERT: A  993 ASP cc_start: 0.9131 (p0) cc_final: 0.8819 (p0)
REVERT: A 1005 CYS cc_start: 0.8768 (t) cc_final: 0.8480 (t)
REVERT: A 1009 MET cc_start: 0.7936 (ttm) cc_final: 0.7702 (ttm)
REVERT: A 1107 ASN cc_start: 0.8845 (t0) cc_final: 0.8377 (t0)
REVERT: A 1144 ASP cc_start: 0.9290 (t70) cc_final: 0.8906 (t0)
REVERT: A 1153 TYR cc_start: 0.8674 (m-80) cc_final: 0.8417 (m-80)
REVERT: A 1228 ARG cc_start: 0.6892 (ptt180) cc_final: 0.6131 (ptt90)
REVERT: A 1245 TYR cc_start: 0.8721 (m-80) cc_final: 0.8213 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.2304
  time to fit residues: 63.0680
Evaluate side-chains
  151 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 101 optimal weight:    4.9990
   chunk 107 optimal weight:    0.7980
   chunk 64 optimal weight:    0.7980
   chunk 46 optimal weight:   10.0000
   chunk 84 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 70 optimal weight:    4.9990
   chunk 113 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 771 GLN
A1013 ASN
** A1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.5063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10148  Z= 0.174
  Angle     :  0.625   8.134  13694  Z= 0.329
  Chirality :  0.044   0.261   1460
  Planarity :  0.005   0.099   1770
  Dihedral  :  4.816  16.401   1330
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.24), residues: 1196
  helix:  0.35 (0.27), residues: 384
  sheet: -1.66 (0.32), residues: 216
  loop : -0.94 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 361 
 HIS   0.004   0.001   HIS A 203 
 PHE   0.023   0.001   PHE A 382 
 TYR   0.019   0.001   TYR A1197 
 ARG   0.004   0.000   ARG A 587 

*********************** 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
  182 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  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: A   28 MET cc_start: 0.8188 (ttp) cc_final: 0.7738 (tmm)
REVERT: A   47 MET cc_start: 0.8210 (tmm) cc_final: 0.7922 (tmm)
REVERT: A   59 ASP cc_start: 0.8841 (p0) cc_final: 0.8450 (p0)
REVERT: A  348 CYS cc_start: 0.9037 (m) cc_final: 0.8345 (t)
REVERT: A  481 LEU cc_start: 0.9024 (mt) cc_final: 0.8680 (mt)
REVERT: A  496 CYS cc_start: 0.9005 (m) cc_final: 0.8697 (m)
REVERT: A  509 ILE cc_start: 0.9131 (mm) cc_final: 0.8668 (mt)
REVERT: A  657 GLU cc_start: 0.8991 (mp0) cc_final: 0.8730 (mp0)
REVERT: A  661 MET cc_start: 0.9457 (mmp) cc_final: 0.9189 (mmm)
REVERT: A  710 PHE cc_start: 0.8481 (m-10) cc_final: 0.8134 (m-10)
REVERT: A  728 LYS cc_start: 0.9466 (mmpt) cc_final: 0.9071 (mmmt)
REVERT: A  825 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7759 (tm-30)
REVERT: A  839 ILE cc_start: 0.9070 (mm) cc_final: 0.8839 (mt)
REVERT: A  841 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8678 (mt-10)
REVERT: A  974 LEU cc_start: 0.9544 (tt) cc_final: 0.8963 (tt)
REVERT: A  979 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8638 (tm-30)
REVERT: A  993 ASP cc_start: 0.9123 (p0) cc_final: 0.8815 (p0)
REVERT: A 1005 CYS cc_start: 0.8756 (t) cc_final: 0.8222 (t)
REVERT: A 1013 ASN cc_start: 0.8996 (m110) cc_final: 0.8494 (m-40)
REVERT: A 1107 ASN cc_start: 0.8866 (t0) cc_final: 0.8408 (t0)
REVERT: A 1144 ASP cc_start: 0.9255 (t70) cc_final: 0.8875 (t0)
REVERT: A 1153 TYR cc_start: 0.8641 (m-80) cc_final: 0.8418 (m-80)
REVERT: A 1228 ARG cc_start: 0.6867 (ptt180) cc_final: 0.6067 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2183
  time to fit residues: 56.4735
Evaluate side-chains
  143 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 79 optimal weight:   20.0000
   chunk 119 optimal weight:    1.9990
   chunk 110 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9980
   chunk 58 optimal weight:   30.0000
   chunk 75 optimal weight:    6.9990
   chunk 101 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 103 GLN
** 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**
** A1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.5190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10148  Z= 0.190
  Angle     :  0.623   8.699  13694  Z= 0.329
  Chirality :  0.043   0.170   1460
  Planarity :  0.005   0.094   1770
  Dihedral  :  4.833  19.288   1330
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 15.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.24), residues: 1196
  helix:  0.43 (0.27), residues: 384
  sheet: -1.65 (0.33), residues: 212
  loop : -0.91 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 361 
 HIS   0.005   0.001   HIS A 203 
 PHE   0.026   0.002   PHE A 382 
 TYR   0.030   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
  177 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.383 
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: 0.8157 (ttp) cc_final: 0.7591 (tmm)
REVERT: A   47 MET cc_start: 0.8531 (tmm) cc_final: 0.7694 (tmm)
REVERT: A   59 ASP cc_start: 0.8849 (p0) cc_final: 0.8472 (p0)
REVERT: A  348 CYS cc_start: 0.9023 (m) cc_final: 0.8325 (t)
REVERT: A  481 LEU cc_start: 0.9008 (mt) cc_final: 0.8662 (mt)
REVERT: A  657 GLU cc_start: 0.8986 (mp0) cc_final: 0.8689 (mp0)
REVERT: A  661 MET cc_start: 0.9454 (mmp) cc_final: 0.9196 (mmm)
REVERT: A  710 PHE cc_start: 0.8493 (m-10) cc_final: 0.8175 (m-10)
REVERT: A  728 LYS cc_start: 0.9474 (mmpt) cc_final: 0.9092 (mmmt)
REVERT: A  825 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7760 (tm-30)
REVERT: A  839 ILE cc_start: 0.9065 (mm) cc_final: 0.8838 (mt)
REVERT: A  841 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8664 (mt-10)
REVERT: A  979 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8709 (tm-30)
REVERT: A  993 ASP cc_start: 0.9112 (p0) cc_final: 0.8843 (p0)
REVERT: A 1107 ASN cc_start: 0.8842 (t0) cc_final: 0.8365 (t0)
REVERT: A 1144 ASP cc_start: 0.9158 (t70) cc_final: 0.8792 (t0)
REVERT: A 1150 HIS cc_start: 0.8904 (p90) cc_final: 0.8675 (p90)
REVERT: A 1153 TYR cc_start: 0.8615 (m-80) cc_final: 0.8357 (m-80)
REVERT: A 1228 ARG cc_start: 0.6821 (ptt180) cc_final: 0.6078 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.2408
  time to fit residues: 61.2534
Evaluate side-chains
  144 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 14 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 83 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 392 HIS
** A 534 HIS ** 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 = 0.3665 r_free = 0.3665 target = 0.096938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.072942 restraints weight = 33611.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.075506 restraints weight = 18494.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.077222 restraints weight = 12431.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3270
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       25 |
|-----------------------------------------------------------------------------|
r_final: 0.3263
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.5321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  10148  Z= 0.196
  Angle     :  0.637   8.329  13694  Z= 0.338
  Chirality :  0.044   0.238   1460
  Planarity :  0.005   0.081   1770
  Dihedral  :  4.823  21.505   1330
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.24), residues: 1196
  helix:  0.40 (0.27), residues: 383
  sheet: -1.56 (0.33), residues: 209
  loop : -0.89 (0.26), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 361 
 HIS   0.004   0.001   HIS A 203 
 PHE   0.025   0.001   PHE A 382 
 TYR   0.050   0.002   TYR A 206 
 ARG   0.013   0.000   ARG A 984 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2234.96 seconds
wall clock time: 42 minutes 1.62 seconds (2521.62 seconds total)