Starting phenix.real_space_refine
on Thu Nov 14 14:51:41 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1r_35931/11_2024/8j1r_35931.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1r_35931/11_2024/8j1r_35931.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1r_35931/11_2024/8j1r_35931.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1r_35931/11_2024/8j1r_35931.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1r_35931/11_2024/8j1r_35931.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1r_35931/11_2024/8j1r_35931.cif"
  }
  resolution = 3.52
  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=   0.000 sd=   0.002
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      25      5.16       5
     C    4187      2.51       5
     N    1060      2.21       5
     O    1225      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 6497
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 677, 5375
          Classifications: {'peptide': 677}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 22, 'TRANS': 654}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 24
    Chain: "C"
      Number of atoms: 1122
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1122
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 15, 'TRANS': 130}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 16
  Time building chain proxies: 4.20, per 1000 atoms: 0.65
  Number of scatterers: 6497
  At special positions: 0
  Unit cell: (110.622, 95.586, 81.624, 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      25     16.00
     O    1225      8.00
     N    1060      7.00
     C    4187      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.54
  Conformation dependent library (CDL) restraints added in 893.4 milliseconds
  

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1556

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 4 sheets defined
      54.1% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 710 through 726
      removed outlier: 4.327A  pdb=" N   GLN A 716 " --> pdb=" O   GLU A 712 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   ILE A 717 " --> pdb=" O   GLU A 713 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLU A 718 " --> pdb=" O   LEU A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 733 through 749
    Processing helix  chain 'A' and resid 756 through 763
      removed outlier: 3.994A  pdb=" N   THR A 761 " --> pdb=" O   GLY A 757 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   THR A 763 " --> pdb=" O   GLU A 759 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 764 through 775
      removed outlier: 3.728A  pdb=" N   ARG A 772 " --> pdb=" O   SER A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 779 through 792
      removed outlier: 4.018A  pdb=" N   VAL A 790 " --> pdb=" O   SER A 786 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU A 792 " --> pdb=" O   LEU A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 810
      removed outlier: 4.299A  pdb=" N   ILE A 801 " --> pdb=" O   ARG A 797 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU A 802 " --> pdb=" O   PHE A 798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 824 through 828
      removed outlier: 3.516A  pdb=" N   LEU A 828 " --> pdb=" O   VAL A 825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 926 through 938
      removed outlier: 4.025A  pdb=" N   VAL A 930 " --> pdb=" O   THR A 926 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ILE A 931 " --> pdb=" O   VAL A 927 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ASN A 933 " --> pdb=" O   GLY A 929 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ARG A 938 " --> pdb=" O   THR A 934 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 991 through 993
      No H-bonds generated for 'chain 'A' and resid 991 through 993'
    Processing helix  chain 'A' and resid 994 through 1007
    Processing helix  chain 'A' and resid 1016 through 1029
    Processing helix  chain 'A' and resid 1029 through 1035
      removed outlier: 4.038A  pdb=" N   VAL A1033 " --> pdb=" O   GLU A1029 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1039 through 1049
    Processing helix  chain 'A' and resid 1050 through 1053
      removed outlier: 4.104A  pdb=" N   PHE A1053 " --> pdb=" O   PRO A1050 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1050 through 1053'
    Processing helix  chain 'A' and resid 1054 through 1066
    Processing helix  chain 'A' and resid 1068 through 1082
      removed outlier: 4.076A  pdb=" N   GLN A1074 " --> pdb=" O   GLY A1070 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLY A1082 " --> pdb=" O   ASN A1078 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1090 through 1096
    Processing helix  chain 'A' and resid 1109 through 1121
    Processing helix  chain 'A' and resid 1139 through 1154
      removed outlier: 4.166A  pdb=" N   THR A1143 " --> pdb=" O   GLY A1139 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   SER A1151 " --> pdb=" O   TYR A1147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1197 through 1217
    Processing helix  chain 'A' and resid 1226 through 1238
      removed outlier: 3.766A  pdb=" N   PHE A1230 " --> pdb=" O   SER A1226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1247 through 1256
      removed outlier: 3.630A  pdb=" N   CYS A1251 " --> pdb=" O   ASP A1247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1259 through 1272
    Processing helix  chain 'A' and resid 1275 through 1283
    Processing helix  chain 'A' and resid 1306 through 1308
      No H-bonds generated for 'chain 'A' and resid 1306 through 1308'
    Processing helix  chain 'A' and resid 1309 through 1322
    Processing helix  chain 'A' and resid 1323 through 1339
      removed outlier: 4.763A  pdb=" N   LYS A1328 " --> pdb=" O   LYS A1324 " (cutoff:3.500A)
      removed outlier: 5.887A  pdb=" N   GLN A1329 " --> pdb=" O   GLY A1325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1342 through 1349
      removed outlier: 3.626A  pdb=" N   ILE A1348 " --> pdb=" O   ARG A1345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1350 through 1359
      removed outlier: 3.536A  pdb=" N   VAL A1355 " --> pdb=" O   PRO A1351 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   ASP A1356 " --> pdb=" O   ASP A1352 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ILE A1357 " --> pdb=" O   GLU A1353 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   PHE A1358 " --> pdb=" O   LEU A1354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1366 through 1373
    Processing helix  chain 'A' and resid 1384 through 1396
      removed outlier: 3.611A  pdb=" N   ALA A1396 " --> pdb=" O   SER A1392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1399 through 1410
      removed outlier: 3.542A  pdb=" N   ARG A1403 " --> pdb=" O   LYS A1399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1419 through 1423
    Processing helix  chain 'A' and resid 1461 through 1476
      removed outlier: 3.601A  pdb=" N   GLU A1474 " --> pdb=" O   CYS A1470 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 17
    Processing helix  chain 'C' and resid 99 through 111
      removed outlier: 3.915A  pdb=" N   LEU C 105 " --> pdb=" O   SER C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 129
      removed outlier: 3.719A  pdb=" N   ALA C 125 " --> pdb=" O   VAL C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 133 through 146
      removed outlier: 5.858A  pdb=" N   GLU C 141 " --> pdb=" O   ALA C 137 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   TRP C 142 " --> pdb=" O   THR C 138 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 853 through 858
      removed outlier: 3.529A  pdb=" N   ILE A 832 " --> pdb=" O   VAL A 858 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   HIS A 950 " --> pdb=" O   LYS A 833 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ILE A 952 " --> pdb=" O   LYS A 835 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL A 837 " --> pdb=" O   ILE A 952 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   PHE A 954 " --> pdb=" O   VAL A 837 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LYS A 953 " --> pdb=" O   PHE A 915 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   PHE A 914 " --> pdb=" O   VAL A 921 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1100 through 1105
      removed outlier: 6.578A  pdb=" N   ARG A1101 " --> pdb=" O   GLU A1129 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   GLU A1131 " --> pdb=" O   ARG A1101 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   LEU A1103 " --> pdb=" O   GLU A1131 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1375 through 1377
      removed outlier: 6.145A  pdb=" N   ASN A1375 " --> pdb=" O   VAL A1429 " (cutoff:3.500A)
      removed outlier: 7.647A  pdb=" N   LEU A1431 " --> pdb=" O   ASN A1375 " (cutoff:3.500A)
      removed outlier: 8.220A  pdb=" N   GLU A1377 " --> pdb=" O   LEU A1431 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   THR A1428 " --> pdb=" O   LEU A1454 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   LEU A1456 " --> pdb=" O   THR A1428 " (cutoff:3.500A)
      removed outlier: 6.042A  pdb=" N   VAL A1430 " --> pdb=" O   LEU A1456 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 23 through 26
      removed outlier: 3.679A  pdb=" N   ILE C  55 " --> pdb=" O   TRP C  34 " (cutoff:3.500A)

    283 hydrogen bonds defined for protein.
    822 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: 1.96

  Time building geometry restraints manager: 1.78 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2054
        1.34 -     1.46: 1443
        1.46 -     1.58: 3107
        1.58 -     1.69: 0
        1.69 -     1.81: 37
  Bond restraints: 6641
  Sorted by residual:
  bond pdb=" C   PRO A1188 "
       pdb=" N   GLU A1189 "
    ideal  model  delta    sigma   weight residual
    1.333  1.378 -0.045 2.74e-02 1.33e+03 2.74e+00
  bond pdb=" C   TYR C  61 "
       pdb=" N   PRO C  62 "
    ideal  model  delta    sigma   weight residual
    1.337  1.348 -0.011 1.06e-02 8.90e+03 1.15e+00
  bond pdb=" CG  LEU A1186 "
       pdb=" CD2 LEU A1186 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.23e-01
  bond pdb=" CB  ARG A1163 "
       pdb=" CG  ARG A1163 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.50e-01
  bond pdb=" CB  LEU A1186 "
       pdb=" CG  LEU A1186 "
    ideal  model  delta    sigma   weight residual
    1.530  1.512  0.018 2.00e-02 2.50e+03 8.07e-01
  ... (remaining 6636 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 8824
        1.75 -     3.49: 148
        3.49 -     5.24: 10
        5.24 -     6.98: 3
        6.98 -     8.73: 3
  Bond angle restraints: 8988
  Sorted by residual:
  angle pdb=" C   HIS A 820 "
        pdb=" N   ASP A 821 "
        pdb=" CA  ASP A 821 "
      ideal   model   delta    sigma   weight residual
     121.54  129.07   -7.53 1.91e+00 2.74e-01 1.55e+01
  angle pdb=" C   ASP C  60 "
        pdb=" N   TYR C  61 "
        pdb=" CA  TYR C  61 "
      ideal   model   delta    sigma   weight residual
     120.58  125.11   -4.53 1.32e+00 5.74e-01 1.18e+01
  angle pdb=" N   CYS A1450 "
        pdb=" CA  CYS A1450 "
        pdb=" C   CYS A1450 "
      ideal   model   delta    sigma   weight residual
     111.03  107.83    3.20 1.11e+00 8.12e-01 8.30e+00
  angle pdb=" C   VAL A1447 "
        pdb=" N   MET A1448 "
        pdb=" CA  MET A1448 "
      ideal   model   delta    sigma   weight residual
     122.08  126.22   -4.14 1.47e+00 4.63e-01 7.94e+00
  angle pdb=" CA  LEU A1186 "
        pdb=" CB  LEU A1186 "
        pdb=" CG  LEU A1186 "
      ideal   model   delta    sigma   weight residual
     116.30  125.03   -8.73 3.50e+00 8.16e-02 6.22e+00
  ... (remaining 8983 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.08: 3595
       15.08 -    30.15: 272
       30.15 -    45.23: 75
       45.23 -    60.30: 26
       60.30 -    75.37: 5
  Dihedral angle restraints: 3973
    sinusoidal: 1578
      harmonic: 2395
  Sorted by residual:
  dihedral pdb=" CA  ALA C 139 "
           pdb=" C   ALA C 139 "
           pdb=" N   ARG C 140 "
           pdb=" CA  ARG C 140 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.21  -25.79     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" CA  GLY A1068 "
           pdb=" C   GLY A1068 "
           pdb=" N   TYR A1069 "
           pdb=" CA  TYR A1069 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.40  -22.60     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  LEU A1185 "
           pdb=" C   LEU A1185 "
           pdb=" N   LEU A1186 "
           pdb=" CA  LEU A1186 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.38  -16.62     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 3970 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 506
       0.025 -    0.050: 312
       0.050 -    0.075: 128
       0.075 -    0.101: 50
       0.101 -    0.126: 26
  Chirality restraints: 1022
  Sorted by residual:
  chirality pdb=" CA  ILE A1297 "
            pdb=" N   ILE A1297 "
            pdb=" C   ILE A1297 "
            pdb=" CB  ILE A1297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.95e-01
  chirality pdb=" CA  VAL A1244 "
            pdb=" N   VAL A1244 "
            pdb=" C   VAL A1244 "
            pdb=" CB  VAL A1244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.54e-01
  chirality pdb=" CA  ILE A 834 "
            pdb=" N   ILE A 834 "
            pdb=" C   ILE A 834 "
            pdb=" CB  ILE A 834 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.48e-01
  ... (remaining 1019 not shown)

  Planarity restraints: 1136
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A1424 "   -0.032 5.00e-02 4.00e+02   4.77e-02 3.64e+00
        pdb=" N   PRO A1425 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A1425 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A1425 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  95 "    0.030 5.00e-02 4.00e+02   4.47e-02 3.20e+00
        pdb=" N   PRO C  96 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO C  96 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C  96 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A1238 "   -0.019 5.00e-02 4.00e+02   2.85e-02 1.30e+00
        pdb=" N   PRO A1239 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A1239 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A1239 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1133 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 709
        2.74 -     3.28: 6984
        3.28 -     3.82: 11062
        3.82 -     4.36: 12761
        4.36 -     4.90: 21116
  Nonbonded interactions: 52632
  Sorted by model distance:
  nonbonded pdb=" O   GLU A1435 "
            pdb=" OH  TYR A1443 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OH  TYR C  46 "
            pdb=" O   TYR C  75 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OE1 GLU A1256 "
            pdb=" NZ  LYS A1267 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" O   PRO A1054 "
            pdb=" OG1 THR A1057 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OG  SER C  23 "
            pdb=" OG  SER C  37 "
     model   vdw
     2.249 3.040
  ... (remaining 52627 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.990
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.950
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.010
  Internal consistency checks:             0.000
  Total:   22.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6641  Z= 0.267
  Angle     :  0.566   8.728   8988  Z= 0.308
  Chirality :  0.041   0.126   1022
  Planarity :  0.004   0.048   1136
  Dihedral  : 12.837  75.375   2417
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.72 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  :  8.02 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.31), residues: 805
  helix:  0.99 (0.27), residues: 395
  sheet: -0.04 (0.73), residues: 50
  loop : -0.67 (0.35), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1365 
 HIS   0.003   0.001   HIS A1378 
 PHE   0.014   0.002   PHE A1229 
 TYR   0.008   0.001   TYR A1147 
 ARG   0.003   0.000   ARG A1163 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 98
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1009 VAL cc_start: 0.6208 (OUTLIER) cc_final: 0.5829 (m)
REVERT: A 1022 LYS cc_start: 0.8645 (ttmt) cc_final: 0.8436 (ttpt)
REVERT: A 1029 GLU cc_start: 0.7648 (tp30) cc_final: 0.6926 (tm-30)
REVERT: A 1058 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7308 (mtm110)
REVERT: A 1185 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6455 (pp)
REVERT: A 1220 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7459 (pp)
REVERT: A 1349 LEU cc_start: 0.6287 (OUTLIER) cc_final: 0.6087 (mm)
REVERT: A 1370 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.7006 (mt)
REVERT: A 1423 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7589 (tt)
REVERT: A 1427 PHE cc_start: 0.7783 (t80) cc_final: 0.7581 (t80)
REVERT: C    9 LYS cc_start: 0.8411 (tmtt) cc_final: 0.7980 (tptp)
  outliers start: 44
  outliers final: 16
  residues processed: 136
  average time/residue: 0.2056
  time to fit residues: 36.4487
Evaluate side-chains
  96 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  928 PHE
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  947 ASP
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1012 ASP
Chi-restraints excluded: chain A residue 1058 ARG
Chi-restraints excluded: chain A residue 1067 PHE
Chi-restraints excluded: chain A residue 1126 ASP
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1204 PHE
Chi-restraints excluded: chain A residue 1214 SER
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1258 VAL
Chi-restraints excluded: chain A residue 1288 VAL
Chi-restraints excluded: chain A residue 1349 LEU
Chi-restraints excluded: chain A residue 1352 ASP
Chi-restraints excluded: chain A residue 1370 LEU
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1423 LEU
Chi-restraints excluded: chain A residue 1475 GLU
Chi-restraints excluded: chain C residue   67 LYS
Chi-restraints excluded: chain C residue  121 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 63 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 73 optimal weight:    7.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A1378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.1169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6641  Z= 0.279
  Angle     :  0.593   8.235   8988  Z= 0.308
  Chirality :  0.043   0.163   1022
  Planarity :  0.004   0.045   1136
  Dihedral  :  7.859  59.417    918
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 11.07 %
    Favored  : 84.23 %
  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: -0.03 (0.30), residues: 805
  helix:  0.66 (0.26), residues: 415
  sheet: -0.25 (0.69), residues: 56
  loop : -0.75 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 737 
 HIS   0.004   0.001   HIS A 780 
 PHE   0.016   0.002   PHE A1067 
 TYR   0.010   0.001   TYR A1069 
 ARG   0.002   0.000   ARG A1163 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 81
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
REVERT: A 1009 VAL cc_start: 0.6077 (OUTLIER) cc_final: 0.5693 (m)
REVERT: A 1029 GLU cc_start: 0.7820 (tp30) cc_final: 0.7188 (tm-30)
REVERT: A 1061 PHE cc_start: 0.8320 (t80) cc_final: 0.7834 (t80)
REVERT: A 1220 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7478 (pp)
REVERT: A 1279 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8238 (mm)
REVERT: A 1389 ASP cc_start: 0.8047 (m-30) cc_final: 0.7496 (m-30)
REVERT: C   13 ASP cc_start: 0.8645 (m-30) cc_final: 0.8358 (m-30)
  outliers start: 34
  outliers final: 15
  residues processed: 108
  average time/residue: 0.1858
  time to fit residues: 26.8931
Evaluate side-chains
  85 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1010 LYS
Chi-restraints excluded: chain A residue 1067 PHE
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1279 LEU
Chi-restraints excluded: chain A residue 1288 VAL
Chi-restraints excluded: chain A residue 1352 ASP
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1475 GLU
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   67 LYS
Chi-restraints excluded: chain C residue   84 ASN
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  121 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 50 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 65 optimal weight:    0.4980
   chunk 25 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A1276 ASN
** A1378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6641  Z= 0.195
  Angle     :  0.559   8.439   8988  Z= 0.283
  Chirality :  0.041   0.154   1022
  Planarity :  0.004   0.043   1136
  Dihedral  :  6.328  47.690    896
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 12.72 %
    Favored  : 83.26 %
  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:  0.13 (0.30), residues: 805
  helix:  0.80 (0.26), residues: 416
  sheet:  0.09 (0.72), residues: 50
  loop : -0.73 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 737 
 HIS   0.003   0.001   HIS A 780 
 PHE   0.015   0.001   PHE A1067 
 TYR   0.012   0.001   TYR A1206 
 ARG   0.002   0.000   ARG A1101 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 84
  time to evaluate  : 0.765 
Fit side-chains
REVERT: A 1009 VAL cc_start: 0.5940 (OUTLIER) cc_final: 0.5599 (m)
REVERT: A 1029 GLU cc_start: 0.7836 (tp30) cc_final: 0.7288 (tp30)
REVERT: A 1040 ASP cc_start: 0.7469 (m-30) cc_final: 0.6782 (t0)
REVERT: A 1220 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7456 (pp)
REVERT: A 1279 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8189 (mm)
REVERT: A 1382 MET cc_start: 0.7090 (mmm) cc_final: 0.6858 (tpt)
REVERT: A 1389 ASP cc_start: 0.7883 (m-30) cc_final: 0.7469 (m-30)
REVERT: A 1423 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7765 (tt)
  outliers start: 29
  outliers final: 18
  residues processed: 110
  average time/residue: 0.1972
  time to fit residues: 29.1762
Evaluate side-chains
  93 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 1.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  865 THR
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  997 ILE
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain A residue 1067 PHE
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1214 SER
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1279 LEU
Chi-restraints excluded: chain A residue 1288 VAL
Chi-restraints excluded: chain A residue 1352 ASP
Chi-restraints excluded: chain A residue 1415 LEU
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1423 LEU
Chi-restraints excluded: chain A residue 1475 GLU
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   67 LYS
Chi-restraints excluded: chain C residue   84 ASN
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  121 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 55 optimal weight:    0.0970
   chunk 38 optimal weight:    0.0970
   chunk 8 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 73 optimal weight:   10.0000
   chunk 78 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0980
   overall best weight:    0.3976

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

Flipped N/Q/H residues before XYZ refinement:
A1276 ASN
** A1378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6641  Z= 0.162
  Angle     :  0.552   7.552   8988  Z= 0.275
  Chirality :  0.041   0.264   1022
  Planarity :  0.004   0.040   1136
  Dihedral  :  5.883  50.651    894
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 13.97 %
    Favored  : 82.02 %
  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:  0.30 (0.30), residues: 805
  helix:  0.95 (0.26), residues: 417
  sheet: -0.08 (0.67), residues: 57
  loop : -0.65 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 737 
 HIS   0.003   0.001   HIS A 780 
 PHE   0.013   0.001   PHE A1067 
 TYR   0.015   0.001   TYR A1206 
 ARG   0.002   0.000   ARG A1101 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 86
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
REVERT: A 1009 VAL cc_start: 0.5919 (OUTLIER) cc_final: 0.5627 (m)
REVERT: A 1029 GLU cc_start: 0.7907 (tp30) cc_final: 0.7542 (tp30)
REVERT: A 1040 ASP cc_start: 0.7416 (m-30) cc_final: 0.6984 (t70)
REVERT: A 1045 LEU cc_start: 0.8000 (mt) cc_final: 0.7752 (mt)
REVERT: A 1061 PHE cc_start: 0.8299 (t80) cc_final: 0.7838 (t80)
REVERT: A 1220 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7469 (pp)
REVERT: A 1279 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7900 (mm)
REVERT: A 1389 ASP cc_start: 0.7844 (m-30) cc_final: 0.7469 (m-30)
REVERT: A 1423 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7625 (tt)
REVERT: C  145 LYS cc_start: 0.8816 (pttm) cc_final: 0.8562 (pttm)
  outliers start: 29
  outliers final: 18
  residues processed: 111
  average time/residue: 0.1894
  time to fit residues: 28.0391
Evaluate side-chains
  89 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 67
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  854 THR
Chi-restraints excluded: chain A residue  865 THR
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  997 ILE
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain A residue 1067 PHE
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1214 SER
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1234 HIS
Chi-restraints excluded: chain A residue 1276 ASN
Chi-restraints excluded: chain A residue 1279 LEU
Chi-restraints excluded: chain A residue 1352 ASP
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1415 LEU
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1423 LEU
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  121 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 1 optimal weight:    0.0470
   chunk 58 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   chunk 54 optimal weight:    0.4980
   chunk 0 optimal weight:    6.9990
   chunk 39 optimal weight:    0.3980
   chunk 70 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
** A1378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6641  Z= 0.162
  Angle     :  0.564  10.499   8988  Z= 0.277
  Chirality :  0.041   0.219   1022
  Planarity :  0.004   0.039   1136
  Dihedral  :  5.287  51.368    884
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 14.80 %
    Favored  : 81.05 %
  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:  0.30 (0.30), residues: 805
  helix:  0.94 (0.26), residues: 417
  sheet: -0.06 (0.66), residues: 57
  loop : -0.63 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1162 
 HIS   0.003   0.001   HIS A1005 
 PHE   0.023   0.001   PHE A1427 
 TYR   0.017   0.001   TYR A1069 
 ARG   0.003   0.000   ARG A1101 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 72
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
REVERT: A  716 GLN cc_start: 0.6641 (OUTLIER) cc_final: 0.6171 (pm20)
REVERT: A 1009 VAL cc_start: 0.6084 (OUTLIER) cc_final: 0.5805 (m)
REVERT: A 1029 GLU cc_start: 0.7953 (tp30) cc_final: 0.7576 (tp30)
REVERT: A 1040 ASP cc_start: 0.7452 (m-30) cc_final: 0.7051 (t70)
REVERT: A 1045 LEU cc_start: 0.8027 (mt) cc_final: 0.7764 (mt)
REVERT: A 1061 PHE cc_start: 0.8294 (t80) cc_final: 0.8009 (t80)
REVERT: A 1185 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6758 (pp)
REVERT: A 1220 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7461 (pp)
REVERT: A 1279 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7788 (mm)
REVERT: A 1282 LEU cc_start: 0.8598 (tt) cc_final: 0.8120 (tt)
REVERT: A 1284 LEU cc_start: 0.8399 (mm) cc_final: 0.7966 (tp)
REVERT: A 1382 MET cc_start: 0.7481 (tpt) cc_final: 0.7108 (tpp)
REVERT: A 1389 ASP cc_start: 0.7895 (m-30) cc_final: 0.7550 (m-30)
REVERT: A 1423 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7626 (tt)
  outliers start: 30
  outliers final: 20
  residues processed: 100
  average time/residue: 0.2108
  time to fit residues: 29.5132
Evaluate side-chains
  88 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 62
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 GLN
Chi-restraints excluded: chain A residue  854 THR
Chi-restraints excluded: chain A residue  865 THR
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  997 ILE
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain A residue 1067 PHE
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1214 SER
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1234 HIS
Chi-restraints excluded: chain A residue 1279 LEU
Chi-restraints excluded: chain A residue 1288 VAL
Chi-restraints excluded: chain A residue 1352 ASP
Chi-restraints excluded: chain A residue 1415 LEU
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1423 LEU
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  121 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0270
   chunk 65 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 75 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0010
   chunk 44 optimal weight:    0.0010
   overall best weight:    0.2450

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

Flipped N/Q/H residues before XYZ refinement:
A1276 ASN
A1373 ASN
** A1378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6641  Z= 0.146
  Angle     :  0.539   8.611   8988  Z= 0.266
  Chirality :  0.040   0.150   1022
  Planarity :  0.003   0.039   1136
  Dihedral  :  5.100  53.968    884
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 14.80 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  0.42 (0.30), residues: 805
  helix:  1.06 (0.26), residues: 419
  sheet: -0.45 (0.63), residues: 69
  loop : -0.51 (0.37), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 737 
 HIS   0.004   0.001   HIS C  76 
 PHE   0.020   0.001   PHE A1427 
 TYR   0.014   0.001   TYR A1069 
 ARG   0.003   0.000   ARG A1101 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 83
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
REVERT: A  716 GLN cc_start: 0.6578 (OUTLIER) cc_final: 0.6211 (pm20)
REVERT: A 1009 VAL cc_start: 0.6198 (OUTLIER) cc_final: 0.5928 (m)
REVERT: A 1029 GLU cc_start: 0.7950 (tp30) cc_final: 0.7527 (tp30)
REVERT: A 1040 ASP cc_start: 0.7438 (m-30) cc_final: 0.7058 (t70)
REVERT: A 1045 LEU cc_start: 0.7954 (mt) cc_final: 0.7666 (mt)
REVERT: A 1185 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6728 (pp)
REVERT: A 1207 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6749 (tp)
REVERT: A 1220 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7445 (pp)
REVERT: A 1279 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7793 (mm)
REVERT: A 1382 MET cc_start: 0.7560 (tpt) cc_final: 0.7229 (tpp)
REVERT: A 1389 ASP cc_start: 0.7834 (m-30) cc_final: 0.7523 (m-30)
REVERT: A 1423 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7592 (tt)
  outliers start: 32
  outliers final: 18
  residues processed: 110
  average time/residue: 0.1955
  time to fit residues: 28.6527
Evaluate side-chains
  96 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 GLN
Chi-restraints excluded: chain A residue  854 THR
Chi-restraints excluded: chain A residue  865 THR
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1067 PHE
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1207 LEU
Chi-restraints excluded: chain A residue 1214 SER
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1234 HIS
Chi-restraints excluded: chain A residue 1276 ASN
Chi-restraints excluded: chain A residue 1279 LEU
Chi-restraints excluded: chain A residue 1288 VAL
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1423 LEU
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  121 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0010
   chunk 43 optimal weight:    0.5980
   chunk 78 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 46 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
A1276 ASN
A1378 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6641  Z= 0.169
  Angle     :  0.576   9.352   8988  Z= 0.282
  Chirality :  0.042   0.281   1022
  Planarity :  0.004   0.040   1136
  Dihedral  :  5.087  56.326    882
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 17.15 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  0.36 (0.30), residues: 805
  helix:  1.00 (0.26), residues: 418
  sheet: -0.53 (0.63), residues: 69
  loop : -0.49 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 737 
 HIS   0.003   0.001   HIS A1005 
 PHE   0.037   0.001   PHE A1061 
 TYR   0.014   0.001   TYR C  75 
 ARG   0.005   0.000   ARG C  16 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 76
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
REVERT: A  716 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.6202 (pm20)
REVERT: A 1009 VAL cc_start: 0.6203 (OUTLIER) cc_final: 0.5914 (m)
REVERT: A 1029 GLU cc_start: 0.7960 (tp30) cc_final: 0.7521 (tp30)
REVERT: A 1040 ASP cc_start: 0.7393 (m-30) cc_final: 0.6998 (t70)
REVERT: A 1185 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6752 (pp)
REVERT: A 1220 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7481 (pp)
REVERT: A 1279 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7987 (mm)
REVERT: A 1382 MET cc_start: 0.7515 (tpt) cc_final: 0.7207 (tpp)
REVERT: A 1389 ASP cc_start: 0.7825 (m-30) cc_final: 0.7520 (m-30)
REVERT: A 1423 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7556 (tt)
  outliers start: 29
  outliers final: 21
  residues processed: 99
  average time/residue: 0.1834
  time to fit residues: 25.0442
Evaluate side-chains
  97 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 GLN
Chi-restraints excluded: chain A residue  854 THR
Chi-restraints excluded: chain A residue  865 THR
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  997 ILE
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain A residue 1067 PHE
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1214 SER
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1234 HIS
Chi-restraints excluded: chain A residue 1276 ASN
Chi-restraints excluded: chain A residue 1279 LEU
Chi-restraints excluded: chain A residue 1288 VAL
Chi-restraints excluded: chain A residue 1415 LEU
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1423 LEU
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  121 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 71 optimal weight:    9.9990
   chunk 74 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A1373 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6641  Z= 0.207
  Angle     :  0.606  11.504   8988  Z= 0.294
  Chirality :  0.043   0.327   1022
  Planarity :  0.004   0.039   1136
  Dihedral  :  5.252  59.400    882
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 17.29 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  0.33 (0.30), residues: 805
  helix:  0.95 (0.26), residues: 418
  sheet: -0.51 (0.65), residues: 69
  loop : -0.49 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1162 
 HIS   0.004   0.001   HIS A1005 
 PHE   0.021   0.001   PHE A1427 
 TYR   0.012   0.001   TYR A1069 
 ARG   0.005   0.000   ARG C  16 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 73
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
REVERT: A  716 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.6209 (pm20)
REVERT: A 1009 VAL cc_start: 0.6186 (OUTLIER) cc_final: 0.5856 (m)
REVERT: A 1029 GLU cc_start: 0.7984 (tp30) cc_final: 0.7579 (tp30)
REVERT: A 1040 ASP cc_start: 0.7383 (m-30) cc_final: 0.6947 (t70)
REVERT: A 1185 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6795 (pp)
REVERT: A 1220 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7484 (pp)
REVERT: A 1279 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8054 (mm)
REVERT: A 1382 MET cc_start: 0.7486 (tpt) cc_final: 0.7168 (tpp)
REVERT: A 1389 ASP cc_start: 0.7820 (m-30) cc_final: 0.7521 (m-30)
REVERT: A 1423 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7566 (tt)
  outliers start: 30
  outliers final: 22
  residues processed: 97
  average time/residue: 0.1814
  time to fit residues: 24.0721
Evaluate side-chains
  99 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 71
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 GLN
Chi-restraints excluded: chain A residue  854 THR
Chi-restraints excluded: chain A residue  865 THR
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  997 ILE
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1010 LYS
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain A residue 1067 PHE
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1214 SER
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1234 HIS
Chi-restraints excluded: chain A residue 1279 LEU
Chi-restraints excluded: chain A residue 1288 VAL
Chi-restraints excluded: chain A residue 1415 LEU
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1423 LEU
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   84 ASN
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  121 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0050
   chunk 68 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    1.1598

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

Flipped N/Q/H residues before XYZ refinement:
A1276 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6641  Z= 0.262
  Angle     :  0.663  11.104   8988  Z= 0.317
  Chirality :  0.045   0.371   1022
  Planarity :  0.004   0.040   1136
  Dihedral  :  5.527  58.049    882
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 17.57 %
    Favored  : 78.84 %
  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:  0.10 (0.30), residues: 805
  helix:  0.74 (0.26), residues: 423
  sheet:  0.40 (0.75), residues: 50
  loop : -0.78 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1162 
 HIS   0.004   0.001   HIS A1005 
 PHE   0.046   0.002   PHE A1061 
 TYR   0.015   0.001   TYR C  75 
 ARG   0.006   0.000   ARG C  16 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 70
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
REVERT: A 1009 VAL cc_start: 0.6166 (OUTLIER) cc_final: 0.5732 (m)
REVERT: A 1029 GLU cc_start: 0.7918 (tp30) cc_final: 0.7576 (tp30)
REVERT: A 1040 ASP cc_start: 0.7352 (m-30) cc_final: 0.6860 (t70)
REVERT: A 1220 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7451 (pp)
REVERT: A 1279 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8163 (mm)
REVERT: A 1382 MET cc_start: 0.7535 (tpt) cc_final: 0.7192 (tpp)
REVERT: A 1389 ASP cc_start: 0.7828 (m-30) cc_final: 0.7531 (m-30)
  outliers start: 26
  outliers final: 21
  residues processed: 91
  average time/residue: 0.1801
  time to fit residues: 22.4956
Evaluate side-chains
  87 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 63
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  865 THR
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  997 ILE
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1010 LYS
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain A residue 1067 PHE
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1214 SER
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1276 ASN
Chi-restraints excluded: chain A residue 1279 LEU
Chi-restraints excluded: chain A residue 1288 VAL
Chi-restraints excluded: chain A residue 1415 LEU
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   84 ASN
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  121 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 74 optimal weight:    0.4980
   chunk 64 optimal weight:    0.4980
   chunk 6 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 39 optimal weight:    0.4980
   chunk 51 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 59 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A1276 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6641  Z= 0.185
  Angle     :  0.633  12.253   8988  Z= 0.300
  Chirality :  0.043   0.367   1022
  Planarity :  0.004   0.043   1136
  Dihedral  :  5.356  55.671    882
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 17.84 %
    Favored  : 79.11 %
  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:  0.32 (0.30), residues: 805
  helix:  0.87 (0.26), residues: 418
  sheet:  0.56 (0.75), residues: 48
  loop : -0.60 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1162 
 HIS   0.005   0.001   HIS A1005 
 PHE   0.039   0.002   PHE A1061 
 TYR   0.012   0.001   TYR A1069 
 ARG   0.010   0.000   ARG C  16 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
REVERT: A 1009 VAL cc_start: 0.6172 (OUTLIER) cc_final: 0.5815 (m)
REVERT: A 1029 GLU cc_start: 0.7934 (tp30) cc_final: 0.7588 (tp30)
REVERT: A 1040 ASP cc_start: 0.7341 (m-30) cc_final: 0.6888 (t70)
REVERT: A 1220 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7446 (pp)
REVERT: A 1279 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8032 (mm)
REVERT: A 1382 MET cc_start: 0.7493 (tpt) cc_final: 0.7166 (tpp)
REVERT: A 1389 ASP cc_start: 0.7817 (m-30) cc_final: 0.7496 (m-30)
  outliers start: 22
  outliers final: 19
  residues processed: 90
  average time/residue: 0.1802
  time to fit residues: 22.1104
Evaluate side-chains
  87 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 65
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  865 THR
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  997 ILE
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain A residue 1067 PHE
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1214 SER
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1276 ASN
Chi-restraints excluded: chain A residue 1279 LEU
Chi-restraints excluded: chain A residue 1288 VAL
Chi-restraints excluded: chain A residue 1415 LEU
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  121 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 17 optimal weight:    0.0050
   chunk 64 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0050
   chunk 66 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 11 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.4808

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

Flipped N/Q/H residues before XYZ refinement:
A1276 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.129888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.096596 restraints weight = 13870.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.100043 restraints weight = 7635.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.102351 restraints weight = 5231.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6641  Z= 0.174
  Angle     :  0.623  12.150   8988  Z= 0.297
  Chirality :  0.043   0.352   1022
  Planarity :  0.004   0.042   1136
  Dihedral  :  5.290  54.331    882
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 17.98 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.30), residues: 805
  helix:  0.89 (0.26), residues: 418
  sheet: -0.41 (0.71), residues: 62
  loop : -0.49 (0.36), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1162 
 HIS   0.003   0.001   HIS A1005 
 PHE   0.037   0.001   PHE A1061 
 TYR   0.017   0.001   TYR C  75 
 ARG   0.011   0.000   ARG C  16 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1764.47 seconds
wall clock time: 33 minutes 21.43 seconds (2001.43 seconds total)