Starting phenix.real_space_refine
on Tue Mar  3 13:56:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xun_33475/03_2026/7xun_33475.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xun_33475/03_2026/7xun_33475.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xun_33475/03_2026/7xun_33475.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xun_33475/03_2026/7xun_33475.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xun_33475/03_2026/7xun_33475.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xun_33475/03_2026/7xun_33475.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      36      5.16       5
     C    3595      2.51       5
     N     948      2.21       5
     O    1012      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5591
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 741, 5591
          Classifications: {'peptide': 741}
          Link IDs: {'PTRANS': 30, 'TRANS': 710}
          Chain breaks: 1
  Time building chain proxies: 1.13, per 1000 atoms: 0.20
  Number of scatterers: 5591
  At special positions: 0
  Unit cell: (141.96, 92.274, 77.064, 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      36     16.00
     O    1012      8.00
     N     948      7.00
     C    3595      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.27
  Conformation dependent library (CDL) restraints added in 210.2 milliseconds
  

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1370

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 6 sheets defined
      56.3% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 638 through 643
      removed outlier: 3.968A  pdb=" N   HIS A 643 " --> pdb=" O   HIS A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 673
      removed outlier: 3.637A  pdb=" N   VAL A 659 " --> pdb=" O   LEU A 655 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   PHE A 660 " --> pdb=" O   CYS A 656 " (cutoff:3.500A)
      Proline residue:  A 663  - end of helix
    Processing helix  chain 'A' and resid 682 through 685
      removed outlier: 3.691A  pdb=" N   ASP A 685 " --> pdb=" O   MET A 682 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 682 through 685'
    Processing helix  chain 'A' and resid 694 through 710
      removed outlier: 3.572A  pdb=" N   PHE A 705 " --> pdb=" O   ILE A 701 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   VAL A 706 " --> pdb=" O   LEU A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 723
    Processing helix  chain 'A' and resid 728 through 754
      removed outlier: 3.662A  pdb=" N   LEU A 732 " --> pdb=" O   ASN A 728 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   SER A 744 " --> pdb=" O   ALA A 740 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LEU A 745 " --> pdb=" O   TYR A 741 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   LEU A 748 " --> pdb=" O   SER A 744 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ALA A 751 " --> pdb=" O   ILE A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 765 through 786
      removed outlier: 4.213A  pdb=" N   VAL A 772 " --> pdb=" O   PRO A 768 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE A 773 " --> pdb=" O   MET A 769 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLY A 777 " --> pdb=" O   PHE A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 797
    Processing helix  chain 'A' and resid 890 through 893
      removed outlier: 3.955A  pdb=" N   ASP A 893 " --> pdb=" O   VAL A 890 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 890 through 893'
    Processing helix  chain 'A' and resid 894 through 907
      removed outlier: 3.884A  pdb=" N   GLN A 907 " --> pdb=" O   VAL A 903 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 923
      removed outlier: 3.513A  pdb=" N   SER A 921 " --> pdb=" O   ALA A 917 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   TYR A 923 " --> pdb=" O   ARG A 919 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 924 through 946
      removed outlier: 3.541A  pdb=" N   THR A 935 " --> pdb=" O   MET A 931 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 946 through 952
      removed outlier: 4.382A  pdb=" N   VAL A 950 " --> pdb=" O   ASP A 946 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   ARG A 952 " --> pdb=" O   GLY A 948 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 962 through 982
      removed outlier: 3.778A  pdb=" N   ILE A 967 " --> pdb=" O   GLN A 963 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ARG A 969 " --> pdb=" O   GLU A 965 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA A 982 " --> pdb=" O   VAL A 978 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 989
      removed outlier: 3.839A  pdb=" N   LEU A 987 " --> pdb=" O   SER A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 989 through 1004
      removed outlier: 3.857A  pdb=" N   THR A 993 " --> pdb=" O   LEU A 989 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   ALA A 994 " --> pdb=" O   ALA A 990 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1012 through 1018
      removed outlier: 3.721A  pdb=" N   GLU A1016 " --> pdb=" O   GLY A1012 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1019 through 1021
      No H-bonds generated for 'chain 'A' and resid 1019 through 1021'
    Processing helix  chain 'A' and resid 1052 through 1065
      removed outlier: 4.491A  pdb=" N   LEU A1057 " --> pdb=" O   LEU A1053 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   ALA A1058 " --> pdb=" O   ARG A1054 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   VAL A1060 " --> pdb=" O   VAL A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1084
    Processing helix  chain 'A' and resid 1109 through 1114
      removed outlier: 3.622A  pdb=" N   LEU A1113 " --> pdb=" O   VAL A1109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1151 through 1155
      removed outlier: 3.945A  pdb=" N   LEU A1154 " --> pdb=" O   ARG A1151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1162 through 1174
      removed outlier: 3.584A  pdb=" N   SER A1166 " --> pdb=" O   SER A1162 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   HIS A1172 " --> pdb=" O   ALA A1168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1201 through 1213
      removed outlier: 3.614A  pdb=" N   VAL A1206 " --> pdb=" O   ALA A1202 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   HIS A1207 " --> pdb=" O   ALA A1203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1223 through 1235
      removed outlier: 3.734A  pdb=" N   GLN A1233 " --> pdb=" O   ALA A1229 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL A1234 " --> pdb=" O   ILE A1230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1251 through 1256
    Processing helix  chain 'A' and resid 1257 through 1259
      No H-bonds generated for 'chain 'A' and resid 1257 through 1259'
    Processing helix  chain 'A' and resid 1268 through 1270
      No H-bonds generated for 'chain 'A' and resid 1268 through 1270'
    Processing helix  chain 'A' and resid 1271 through 1278
    Processing helix  chain 'A' and resid 1304 through 1340
      removed outlier: 4.082A  pdb=" N   VAL A1308 " --> pdb=" O   LEU A1304 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE A1311 " --> pdb=" O   VAL A1307 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ARG A1316 " --> pdb=" O   HIS A1312 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ARG A1322 " --> pdb=" O   VAL A1318 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A1329 " --> pdb=" O   LEU A1325 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ASN A1332 " --> pdb=" O   ALA A1328 " (cutoff:3.500A)
      Proline residue:  A1337  - end of helix
    Processing helix  chain 'A' and resid 1351 through 1372
      removed outlier: 3.505A  pdb=" N   GLY A1355 " --> pdb=" O   GLN A1351 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   SER A1356 " --> pdb=" O   PRO A1352 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA A1357 " --> pdb=" O   TRP A1353 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA A1358 " --> pdb=" O   MET A1354 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   MET A1359 " --> pdb=" O   GLY A1355 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL A1364 " --> pdb=" O   ALA A1360 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER A1365 " --> pdb=" O   ALA A1361 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLN A1372 " --> pdb=" O   LEU A1368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1380 through 1388
      removed outlier: 3.606A  pdb=" N   ALA A1386 " --> pdb=" O   GLU A1382 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLN A1387 " --> pdb=" O   ARG A1383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1396 through 1400
    Processing sheet with id=AA1, first strand: chain 'A' and resid 687 through 689
      removed outlier: 3.931A  pdb=" N   ILE A 689 " --> pdb=" O   LEU A 692 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 814 through 821
      removed outlier: 6.655A  pdb=" N   THR A 807 " --> pdb=" O   ILE A 815 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   GLU A 817 " --> pdb=" O   VAL A 805 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   VAL A 805 " --> pdb=" O   GLU A 817 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLN A 819 " --> pdb=" O   ALA A 803 " (cutoff:3.500A)
      removed outlier: 5.490A  pdb=" N   ALA A 803 " --> pdb=" O   GLN A 819 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   THR A 804 " --> pdb=" O   LYS A 832 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   ILE A 830 " --> pdb=" O   VAL A 806 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   LEU A 884 " --> pdb=" O   LEU A 846 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   ASP A 842 " --> pdb=" O   THR A 888 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLY A 843 " --> pdb=" O   VAL A 872 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 838 through 839
      removed outlier: 3.759A  pdb=" N   SER A 876 " --> pdb=" O   PHE A 839 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 850 through 852
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1007 through 1009
      removed outlier: 3.783A  pdb=" N   VAL A1298 " --> pdb=" O   LEU A1008 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   VAL A1262 " --> pdb=" O   MET A1280 " (cutoff:3.500A)
      removed outlier: 8.414A  pdb=" N   VAL A1282 " --> pdb=" O   VAL A1262 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   MET A1264 " --> pdb=" O   VAL A1282 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   THR A1023 " --> pdb=" O   ALA A1263 " (cutoff:3.500A)
      removed outlier: 7.944A  pdb=" N   VAL A1265 " --> pdb=" O   THR A1023 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   MET A1025 " --> pdb=" O   VAL A1265 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   VAL A1216 " --> pdb=" O   LYS A1238 " (cutoff:3.500A)
      removed outlier: 8.686A  pdb=" N   PHE A1240 " --> pdb=" O   VAL A1216 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   LEU A1218 " --> pdb=" O   PHE A1240 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1038 through 1044
      removed outlier: 6.114A  pdb=" N   VAL A1039 " --> pdb=" O   ALA A1195 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   ALA A1195 " --> pdb=" O   VAL A1039 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   ARG A1041 " --> pdb=" O   ALA A1193 " (cutoff:3.500A)
      removed outlier: 5.422A  pdb=" N   LEU A1188 " --> pdb=" O   ILE A1184 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   ILE A1184 " --> pdb=" O   LEU A1188 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   GLY A1190 " --> pdb=" O   VAL A1182 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   VAL A1182 " --> pdb=" O   GLY A1190 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU A1181 " --> pdb=" O   GLY A1149 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   GLY A1149 " --> pdb=" O   LEU A1181 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ALA A1183 " --> pdb=" O   LEU A1147 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   GLY A1101 " --> pdb=" O   ALA A1096 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   ALA A1096 " --> pdb=" O   GLY A1101 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   GLY A1103 " --> pdb=" O   PHE A1094 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   PHE A1094 " --> pdb=" O   GLY A1103 " (cutoff:3.500A)

    271 hydrogen bonds defined for protein.
    786 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: 0.72

  Time building geometry restraints manager: 0.36 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1805
        1.34 -     1.46: 1039
        1.46 -     1.58: 2782
        1.58 -     1.69: 0
        1.69 -     1.81: 63
  Bond restraints: 5689
  Sorted by residual:
  bond pdb=" CA  ALA A 917 "
       pdb=" C   ALA A 917 "
    ideal  model  delta    sigma   weight residual
    1.522  1.507  0.015 1.40e-02 5.10e+03 1.20e+00
  bond pdb=" CG1 ILE A 929 "
       pdb=" CD1 ILE A 929 "
    ideal  model  delta    sigma   weight residual
    1.513  1.479  0.034 3.90e-02 6.57e+02 7.53e-01
  bond pdb=" C   THR A 991 "
       pdb=" N   PRO A 992 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.011 1.36e-02 5.41e+03 6.07e-01
  bond pdb=" CA  VAL A1036 "
       pdb=" CB  VAL A1036 "
    ideal  model  delta    sigma   weight residual
    1.535  1.542 -0.008 1.02e-02 9.61e+03 5.67e-01
  bond pdb=" N   VAL A 820 "
       pdb=" CA  VAL A 820 "
    ideal  model  delta    sigma   weight residual
    1.468  1.461  0.008 1.05e-02 9.07e+03 5.26e-01
  ... (remaining 5684 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 7613
        1.98 -     3.96: 94
        3.96 -     5.94: 18
        5.94 -     7.93: 1
        7.93 -     9.91: 1
  Bond angle restraints: 7727
  Sorted by residual:
  angle pdb=" CB  MET A1191 "
        pdb=" CG  MET A1191 "
        pdb=" SD  MET A1191 "
      ideal   model   delta    sigma   weight residual
     112.70  102.79    9.91 3.00e+00 1.11e-01 1.09e+01
  angle pdb=" C   ASN A 637 "
        pdb=" N   ALA A 638 "
        pdb=" CA  ALA A 638 "
      ideal   model   delta    sigma   weight residual
     121.54  126.06   -4.52 1.91e+00 2.74e-01 5.61e+00
  angle pdb=" N   THR A 991 "
        pdb=" CA  THR A 991 "
        pdb=" C   THR A 991 "
      ideal   model   delta    sigma   weight residual
     109.81  114.65   -4.84 2.21e+00 2.05e-01 4.80e+00
  angle pdb=" C   VAL A1036 "
        pdb=" CA  VAL A1036 "
        pdb=" CB  VAL A1036 "
      ideal   model   delta    sigma   weight residual
     111.18  113.54   -2.36 1.15e+00 7.56e-01 4.21e+00
  angle pdb=" N   LYS A 787 "
        pdb=" CA  LYS A 787 "
        pdb=" C   LYS A 787 "
      ideal   model   delta    sigma   weight residual
     113.72  110.74    2.98 1.52e+00 4.33e-01 3.84e+00
  ... (remaining 7722 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.73: 3028
       15.73 -    31.47: 326
       31.47 -    47.20: 59
       47.20 -    62.94: 12
       62.94 -    78.67: 6
  Dihedral angle restraints: 3431
    sinusoidal: 1309
      harmonic: 2122
  Sorted by residual:
  dihedral pdb=" CA  PHE A 954 "
           pdb=" C   PHE A 954 "
           pdb=" N   PRO A 955 "
           pdb=" CA  PRO A 955 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.79  -18.21     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  GLU A1254 "
           pdb=" C   GLU A1254 "
           pdb=" N   LEU A1255 "
           pdb=" CA  LEU A1255 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.88   18.12     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  LYS A 785 "
           pdb=" C   LYS A 785 "
           pdb=" N   SER A 786 "
           pdb=" CA  SER A 786 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.92   17.08     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 3428 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 476
       0.026 -    0.052: 274
       0.052 -    0.078: 112
       0.078 -    0.104: 58
       0.104 -    0.130: 30
  Chirality restraints: 950
  Sorted by residual:
  chirality pdb=" CA  THR A 766 "
            pdb=" N   THR A 766 "
            pdb=" C   THR A 766 "
            pdb=" CB  THR A 766 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.20e-01
  chirality pdb=" CA  ILE A1194 "
            pdb=" N   ILE A1194 "
            pdb=" C   ILE A1194 "
            pdb=" CB  ILE A1194 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.13e-01
  chirality pdb=" CG  LEU A1299 "
            pdb=" CB  LEU A1299 "
            pdb=" CD1 LEU A1299 "
            pdb=" CD2 LEU A1299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.04e-01
  ... (remaining 947 not shown)

  Planarity restraints: 965
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 911 "    0.025 5.00e-02 4.00e+02   3.77e-02 2.28e+00
        pdb=" N   PRO A 912 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 912 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 912 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A1351 "   -0.021 5.00e-02 4.00e+02   3.24e-02 1.68e+00
        pdb=" N   PRO A1352 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A1352 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A1352 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A1069 "    0.020 5.00e-02 4.00e+02   2.97e-02 1.41e+00
        pdb=" N   PRO A1070 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO A1070 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A1070 "    0.017 5.00e-02 4.00e+02
  ... (remaining 962 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 110
        2.68 -     3.24: 5804
        3.24 -     3.79: 8544
        3.79 -     4.35: 11257
        4.35 -     4.90: 18202
  Nonbonded interactions: 43917
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 983 "
            pdb=" OG  SER A 986 "
     model   vdw
     2.129 3.040
  nonbonded pdb=" OG1 THR A 858 "
            pdb=" OE1 GLU A 860 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" OG  SER A1398 "
            pdb=" OE1 GLN A1399 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OE2 GLU A1173 "
            pdb=" OG1 THR A1226 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" NH2 ARG A1155 "
            pdb=" O   LEU A1159 "
     model   vdw
     2.281 3.120
  ... (remaining 43912 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.930
  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:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.520
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
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      :  0.002   0.034   5689  Z= 0.115
  Angle     :  0.575   9.908   7727  Z= 0.292
  Chirality :  0.044   0.130    950
  Planarity :  0.004   0.038    965
  Dihedral  : 13.724  78.672   2061
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.32), residues: 737
  helix: -0.13 (0.29), residues: 352
  sheet: -0.70 (0.61), residues: 76
  loop : -1.02 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1041 
 TYR   0.010   0.001   TYR A 713 
 PHE   0.010   0.001   PHE A 970 
 TRP   0.008   0.001   TRP A1153 
 HIS   0.004   0.001   HIS A1069 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 5689)
  covalent geometry    : angle       0.57456 ( 7727)
  hydrogen bonds       : bond        0.23238 (  271)
  hydrogen bonds       : angle       8.07580 (  786)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  945 ILE cc_start: 0.8320 (mm) cc_final: 0.7848 (pt)
REVERT: A 1169 MET cc_start: 0.8016 (ppp) cc_final: 0.7643 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.0597
  time to fit residues: 9.4922
Evaluate side-chains
  104 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.0870
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.2980
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0980
   overall best weight:    0.3758

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

Flipped N/Q/H residues before XYZ refinement:
A1277 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.157377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.120658 restraints weight = 9553.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3894 rms_B_bonded: 3.51
r_work: 0.3760 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5689  Z= 0.121
  Angle     :  0.607   9.623   7727  Z= 0.307
  Chirality :  0.045   0.154    950
  Planarity :  0.005   0.046    965
  Dihedral  :  4.130  18.046    775
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 12.07 %
    Favored  : 86.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.32), residues: 737
  helix:  0.29 (0.29), residues: 359
  sheet: -0.92 (0.54), residues: 96
  loop : -0.76 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1041 
 TYR   0.012   0.001   TYR A 713 
 PHE   0.011   0.001   PHE A 970 
 TRP   0.007   0.001   TRP A 939 
 HIS   0.003   0.001   HIS A 643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 5689)
  covalent geometry    : angle       0.60694 ( 7727)
  hydrogen bonds       : bond        0.04678 (  271)
  hydrogen bonds       : angle       5.11455 (  786)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 121
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  885 ILE cc_start: 0.8643 (pt) cc_final: 0.8423 (mp)
REVERT: A  929 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7685 (mp)
REVERT: A  945 ILE cc_start: 0.8306 (mm) cc_final: 0.7728 (pt)
REVERT: A 1154 LEU cc_start: 0.9363 (tp) cc_final: 0.9112 (tp)
REVERT: A 1155 ARG cc_start: 0.8903 (mmp80) cc_final: 0.8546 (mmp80)
  outliers start: 6
  outliers final: 4
  residues processed: 124
  average time/residue: 0.0642
  time to fit residues: 10.8801
Evaluate side-chains
  109 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  662 ILE
Chi-restraints excluded: chain A residue  929 ILE
Chi-restraints excluded: chain A residue 1174 MET
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1385 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 72 optimal weight:    0.8980
   chunk 31 optimal weight:    7.9990
   chunk 50 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A1247 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.153413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.116460 restraints weight = 9692.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3820 rms_B_bonded: 3.44
r_work: 0.3694 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5689  Z= 0.153
  Angle     :  0.602   8.381   7727  Z= 0.306
  Chirality :  0.045   0.133    950
  Planarity :  0.004   0.050    965
  Dihedral  :  4.217  18.870    775
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.82 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.32), residues: 737
  helix:  0.39 (0.29), residues: 350
  sheet: -0.93 (0.54), residues: 91
  loop : -0.77 (0.39), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1041 
 TYR   0.010   0.001   TYR A 713 
 PHE   0.013   0.001   PHE A 970 
 TRP   0.016   0.001   TRP A1153 
 HIS   0.005   0.001   HIS A 643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 5689)
  covalent geometry    : angle       0.60239 ( 7727)
  hydrogen bonds       : bond        0.04165 (  271)
  hydrogen bonds       : angle       4.91953 (  786)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
REVERT: A  781 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8802 (tm-30)
REVERT: A  885 ILE cc_start: 0.8619 (pt) cc_final: 0.8373 (mp)
REVERT: A  929 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7765 (mp)
REVERT: A 1154 LEU cc_start: 0.9394 (tp) cc_final: 0.8832 (tp)
REVERT: A 1164 ASP cc_start: 0.9498 (t0) cc_final: 0.9054 (p0)
  outliers start: 17
  outliers final: 11
  residues processed: 113
  average time/residue: 0.0580
  time to fit residues: 9.1809
Evaluate side-chains
  109 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  662 ILE
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  929 ILE
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue 1023 THR
Chi-restraints excluded: chain A residue 1174 MET
Chi-restraints excluded: chain A residue 1219 ILE
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1303 ASP
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1330 ILE
Chi-restraints excluded: chain A residue 1385 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 31 optimal weight:    8.9990
   chunk 30 optimal weight:    0.6980
   chunk 0 optimal weight:    9.9990
   chunk 9 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 889 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.154149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.117266 restraints weight = 9677.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3832 rms_B_bonded: 3.43
r_work: 0.3707 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5689  Z= 0.133
  Angle     :  0.596   7.592   7727  Z= 0.299
  Chirality :  0.045   0.147    950
  Planarity :  0.004   0.049    965
  Dihedral  :  4.182  18.993    775
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 18.11 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.32), residues: 737
  helix:  0.52 (0.29), residues: 349
  sheet: -1.05 (0.54), residues: 91
  loop : -0.84 (0.38), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1041 
 TYR   0.010   0.001   TYR A 713 
 PHE   0.013   0.001   PHE A 970 
 TRP   0.008   0.001   TRP A1153 
 HIS   0.004   0.001   HIS A 643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5689)
  covalent geometry    : angle       0.59612 ( 7727)
  hydrogen bonds       : bond        0.03791 (  271)
  hydrogen bonds       : angle       4.66751 (  786)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: A  781 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8523 (tm-30)
REVERT: A  885 ILE cc_start: 0.8603 (pt) cc_final: 0.8353 (mp)
REVERT: A  929 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7820 (mp)
REVERT: A  940 ILE cc_start: 0.7656 (tt) cc_final: 0.7374 (tt)
REVERT: A 1164 ASP cc_start: 0.9501 (t0) cc_final: 0.9062 (p0)
  outliers start: 21
  outliers final: 12
  residues processed: 116
  average time/residue: 0.0553
  time to fit residues: 9.1064
Evaluate side-chains
  114 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  662 ILE
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  929 ILE
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue 1023 THR
Chi-restraints excluded: chain A residue 1174 MET
Chi-restraints excluded: chain A residue 1178 THR
Chi-restraints excluded: chain A residue 1219 ILE
Chi-restraints excluded: chain A residue 1243 VAL
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1303 ASP
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1385 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0870
   chunk 59 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0770
   chunk 40 optimal weight:    6.9990
   chunk 53 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.4716

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

Flipped N/Q/H residues before XYZ refinement:
** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.156532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.119920 restraints weight = 9787.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3878 rms_B_bonded: 3.50
r_work: 0.3750 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5689  Z= 0.111
  Angle     :  0.597  12.776   7727  Z= 0.295
  Chirality :  0.045   0.187    950
  Planarity :  0.004   0.048    965
  Dihedral  :  4.081  18.668    775
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 20.39 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.32), residues: 737
  helix:  0.64 (0.29), residues: 359
  sheet: -1.23 (0.53), residues: 91
  loop : -0.92 (0.38), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1316 
 TYR   0.015   0.001   TYR A 713 
 PHE   0.012   0.001   PHE A 970 
 TRP   0.007   0.001   TRP A1353 
 HIS   0.009   0.001   HIS A1312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 5689)
  covalent geometry    : angle       0.59664 ( 7727)
  hydrogen bonds       : bond        0.03514 (  271)
  hydrogen bonds       : angle       4.41935 (  786)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  781 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8653 (tm-30)
REVERT: A  885 ILE cc_start: 0.8526 (pt) cc_final: 0.8317 (mp)
REVERT: A  929 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7803 (mp)
REVERT: A  940 ILE cc_start: 0.7553 (tt) cc_final: 0.7282 (tt)
REVERT: A 1164 ASP cc_start: 0.9474 (t0) cc_final: 0.9047 (p0)
REVERT: A 1267 ASP cc_start: 0.8184 (p0) cc_final: 0.7862 (p0)
  outliers start: 14
  outliers final: 10
  residues processed: 112
  average time/residue: 0.0492
  time to fit residues: 7.9310
Evaluate side-chains
  115 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  662 ILE
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  929 ILE
Chi-restraints excluded: chain A residue 1023 THR
Chi-restraints excluded: chain A residue 1174 MET
Chi-restraints excluded: chain A residue 1219 ILE
Chi-restraints excluded: chain A residue 1243 VAL
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1303 ASP
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1385 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 64 optimal weight:    0.0770
   chunk 32 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0030
   chunk 61 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.4348

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

Flipped N/Q/H residues before XYZ refinement:
** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.157636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.121127 restraints weight = 9758.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 3.50
r_work: 0.3766 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5689  Z= 0.106
  Angle     :  0.577   7.694   7727  Z= 0.287
  Chirality :  0.044   0.145    950
  Planarity :  0.004   0.047    965
  Dihedral  :  3.980  18.310    775
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 22.19 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.32), residues: 737
  helix:  0.73 (0.29), residues: 360
  sheet: -1.00 (0.55), residues: 81
  loop : -0.86 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1041 
 TYR   0.013   0.001   TYR A 713 
 PHE   0.011   0.001   PHE A 970 
 TRP   0.010   0.001   TRP A1153 
 HIS   0.008   0.001   HIS A1312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 5689)
  covalent geometry    : angle       0.57727 ( 7727)
  hydrogen bonds       : bond        0.03365 (  271)
  hydrogen bonds       : angle       4.31171 (  786)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  781 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8578 (tm-30)
REVERT: A  885 ILE cc_start: 0.8566 (pt) cc_final: 0.8346 (mp)
REVERT: A  929 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7832 (mp)
REVERT: A  940 ILE cc_start: 0.7470 (tt) cc_final: 0.7212 (tt)
REVERT: A 1164 ASP cc_start: 0.9481 (t0) cc_final: 0.9057 (p0)
REVERT: A 1267 ASP cc_start: 0.8153 (p0) cc_final: 0.7866 (p0)
  outliers start: 13
  outliers final: 11
  residues processed: 114
  average time/residue: 0.0571
  time to fit residues: 9.0458
Evaluate side-chains
  114 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  662 ILE
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  929 ILE
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue 1174 MET
Chi-restraints excluded: chain A residue 1219 ILE
Chi-restraints excluded: chain A residue 1243 VAL
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1303 ASP
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1330 ILE
Chi-restraints excluded: chain A residue 1385 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0470
   chunk 53 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.6478

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.156785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.120244 restraints weight = 9802.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 3.51
r_work: 0.3755 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5689  Z= 0.117
  Angle     :  0.592  10.178   7727  Z= 0.291
  Chirality :  0.044   0.143    950
  Planarity :  0.004   0.047    965
  Dihedral  :  3.995  18.444    775
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 21.86 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.32), residues: 737
  helix:  0.64 (0.29), residues: 366
  sheet: -1.04 (0.54), residues: 81
  loop : -0.93 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1316 
 TYR   0.012   0.001   TYR A 713 
 PHE   0.011   0.001   PHE A 970 
 TRP   0.007   0.001   TRP A 712 
 HIS   0.008   0.001   HIS A1312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 5689)
  covalent geometry    : angle       0.59151 ( 7727)
  hydrogen bonds       : bond        0.03403 (  271)
  hydrogen bonds       : angle       4.29659 (  786)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  929 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7884 (mp)
REVERT: A  940 ILE cc_start: 0.7540 (tt) cc_final: 0.7283 (tt)
REVERT: A 1021 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8155 (mp)
REVERT: A 1040 MET cc_start: 0.5799 (mtm) cc_final: 0.5238 (pmm)
REVERT: A 1164 ASP cc_start: 0.9460 (t0) cc_final: 0.9023 (p0)
REVERT: A 1169 MET cc_start: 0.8184 (ppp) cc_final: 0.7583 (ppp)
REVERT: A 1267 ASP cc_start: 0.8121 (p0) cc_final: 0.7836 (p0)
  outliers start: 15
  outliers final: 12
  residues processed: 111
  average time/residue: 0.0527
  time to fit residues: 8.3210
Evaluate side-chains
  115 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  662 ILE
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  929 ILE
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue 1021 ILE
Chi-restraints excluded: chain A residue 1153 TRP
Chi-restraints excluded: chain A residue 1174 MET
Chi-restraints excluded: chain A residue 1219 ILE
Chi-restraints excluded: chain A residue 1243 VAL
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1303 ASP
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1330 ILE
Chi-restraints excluded: chain A residue 1385 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0570
   chunk 36 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.6898

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.156900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.119712 restraints weight = 9758.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3884 rms_B_bonded: 3.56
r_work: 0.3758 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5689  Z= 0.120
  Angle     :  0.606   9.912   7727  Z= 0.295
  Chirality :  0.044   0.139    950
  Planarity :  0.004   0.048    965
  Dihedral  :  3.999  18.152    775
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 22.35 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.32), residues: 737
  helix:  0.68 (0.29), residues: 367
  sheet: -1.10 (0.54), residues: 81
  loop : -0.96 (0.38), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1155 
 TYR   0.012   0.001   TYR A 713 
 PHE   0.011   0.001   PHE A 970 
 TRP   0.008   0.001   TRP A 712 
 HIS   0.008   0.001   HIS A1312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 5689)
  covalent geometry    : angle       0.60567 ( 7727)
  hydrogen bonds       : bond        0.03385 (  271)
  hydrogen bonds       : angle       4.28841 (  786)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  781 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8970 (tm-30)
REVERT: A  929 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7817 (mp)
REVERT: A  940 ILE cc_start: 0.7534 (tt) cc_final: 0.7279 (tt)
REVERT: A 1021 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8161 (mp)
REVERT: A 1040 MET cc_start: 0.5745 (mtm) cc_final: 0.5127 (pmm)
REVERT: A 1164 ASP cc_start: 0.9465 (t0) cc_final: 0.9018 (p0)
REVERT: A 1169 MET cc_start: 0.8230 (ppp) cc_final: 0.7678 (ppp)
REVERT: A 1267 ASP cc_start: 0.8091 (p0) cc_final: 0.7810 (p0)
  outliers start: 15
  outliers final: 13
  residues processed: 110
  average time/residue: 0.0513
  time to fit residues: 8.0028
Evaluate side-chains
  116 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  662 ILE
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  929 ILE
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue 1021 ILE
Chi-restraints excluded: chain A residue 1144 PHE
Chi-restraints excluded: chain A residue 1153 TRP
Chi-restraints excluded: chain A residue 1174 MET
Chi-restraints excluded: chain A residue 1219 ILE
Chi-restraints excluded: chain A residue 1243 VAL
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1303 ASP
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1330 ILE
Chi-restraints excluded: chain A residue 1385 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 45 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   chunk 5 optimal weight:    0.3980
   chunk 16 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0170
   chunk 70 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.4818

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.158352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.121510 restraints weight = 9707.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3901 rms_B_bonded: 3.55
r_work: 0.3777 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5689  Z= 0.106
  Angle     :  0.602  10.130   7727  Z= 0.291
  Chirality :  0.044   0.144    950
  Planarity :  0.004   0.047    965
  Dihedral  :  3.894  17.819    775
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 22.68 %
    Favored  : 75.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.32), residues: 737
  helix:  0.83 (0.28), residues: 367
  sheet: -1.09 (0.54), residues: 81
  loop : -0.95 (0.38), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1316 
 TYR   0.012   0.001   TYR A 713 
 PHE   0.010   0.001   PHE A 970 
 TRP   0.008   0.001   TRP A1353 
 HIS   0.007   0.001   HIS A1312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 5689)
  covalent geometry    : angle       0.60172 ( 7727)
  hydrogen bonds       : bond        0.03212 (  271)
  hydrogen bonds       : angle       4.17014 (  786)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  781 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8957 (tm-30)
REVERT: A  929 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7817 (mp)
REVERT: A  940 ILE cc_start: 0.7450 (tt) cc_final: 0.7207 (tt)
REVERT: A 1021 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8190 (mp)
REVERT: A 1022 LYS cc_start: 0.8217 (mmtt) cc_final: 0.8010 (mmtt)
REVERT: A 1040 MET cc_start: 0.5842 (mtm) cc_final: 0.5144 (pmm)
REVERT: A 1164 ASP cc_start: 0.9438 (t0) cc_final: 0.9015 (p0)
REVERT: A 1169 MET cc_start: 0.8254 (ppp) cc_final: 0.7705 (ppp)
REVERT: A 1191 MET cc_start: 0.8531 (mmm) cc_final: 0.7945 (mmm)
REVERT: A 1267 ASP cc_start: 0.8084 (p0) cc_final: 0.7804 (p0)
  outliers start: 14
  outliers final: 11
  residues processed: 120
  average time/residue: 0.0557
  time to fit residues: 9.1263
Evaluate side-chains
  117 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  929 ILE
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue 1021 ILE
Chi-restraints excluded: chain A residue 1144 PHE
Chi-restraints excluded: chain A residue 1174 MET
Chi-restraints excluded: chain A residue 1219 ILE
Chi-restraints excluded: chain A residue 1243 VAL
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1303 ASP
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1359 MET
Chi-restraints excluded: chain A residue 1385 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 42 optimal weight:    9.9990
   chunk 32 optimal weight:    0.0670
   chunk 26 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.6118

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.157721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.121387 restraints weight = 9792.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 3.42
r_work: 0.3767 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5689  Z= 0.119
  Angle     :  0.633  10.240   7727  Z= 0.306
  Chirality :  0.045   0.140    950
  Planarity :  0.004   0.047    965
  Dihedral  :  3.929  17.850    775
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 23.98 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.32), residues: 737
  helix:  0.77 (0.29), residues: 367
  sheet: -1.08 (0.54), residues: 81
  loop : -0.99 (0.38), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1041 
 TYR   0.012   0.001   TYR A 713 
 PHE   0.011   0.001   PHE A 970 
 TRP   0.008   0.001   TRP A 712 
 HIS   0.008   0.001   HIS A1312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 5689)
  covalent geometry    : angle       0.63335 ( 7727)
  hydrogen bonds       : bond        0.03284 (  271)
  hydrogen bonds       : angle       4.16479 (  786)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  781 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8948 (tm-30)
REVERT: A  929 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7915 (mp)
REVERT: A  940 ILE cc_start: 0.7517 (tt) cc_final: 0.7270 (tt)
REVERT: A 1021 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8237 (mp)
REVERT: A 1022 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7982 (mmtt)
REVERT: A 1164 ASP cc_start: 0.9464 (t0) cc_final: 0.9045 (p0)
REVERT: A 1169 MET cc_start: 0.8311 (ppp) cc_final: 0.7754 (ppp)
REVERT: A 1191 MET cc_start: 0.8595 (mmm) cc_final: 0.7963 (mmm)
REVERT: A 1267 ASP cc_start: 0.8018 (p0) cc_final: 0.7773 (p0)
  outliers start: 14
  outliers final: 12
  residues processed: 107
  average time/residue: 0.0567
  time to fit residues: 8.4119
Evaluate side-chains
  113 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  929 ILE
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue 1021 ILE
Chi-restraints excluded: chain A residue 1144 PHE
Chi-restraints excluded: chain A residue 1174 MET
Chi-restraints excluded: chain A residue 1219 ILE
Chi-restraints excluded: chain A residue 1243 VAL
Chi-restraints excluded: chain A residue 1264 MET
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1303 ASP
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1359 MET
Chi-restraints excluded: chain A residue 1385 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0170
   chunk 31 optimal weight:    0.0980
   chunk 43 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0060
   chunk 65 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 47 optimal weight:    8.9990
   chunk 25 optimal weight:    0.0030
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.2044

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.161037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.124694 restraints weight = 9685.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 3.45
r_work: 0.3821 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5689  Z= 0.102
  Angle     :  0.610  10.129   7727  Z= 0.293
  Chirality :  0.044   0.141    950
  Planarity :  0.004   0.048    965
  Dihedral  :  3.785  16.908    775
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 24.63 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.32), residues: 737
  helix:  0.94 (0.29), residues: 359
  sheet: -1.09 (0.53), residues: 83
  loop : -0.92 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1041 
 TYR   0.012   0.001   TYR A 713 
 PHE   0.009   0.001   PHE A 970 
 TRP   0.010   0.001   TRP A1353 
 HIS   0.006   0.001   HIS A1312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 5689)
  covalent geometry    : angle       0.60998 ( 7727)
  hydrogen bonds       : bond        0.03014 (  271)
  hydrogen bonds       : angle       4.00268 (  786)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1465.86 seconds
wall clock time: 25 minutes 44.14 seconds (1544.14 seconds total)