Starting phenix.real_space_refine
on Fri Apr  5 21:12:27 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xun_33475/04_2024/7xun_33475.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xun_33475/04_2024/7xun_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xun_33475/04_2024/7xun_33475.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xun_33475/04_2024/7xun_33475.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xun_33475/04_2024/7xun_33475.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xun_33475/04_2024/7xun_33475.pdb"
  }
  resolution = 3.4
  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=   0.001
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
    Residue "A TYR  670": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  713": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  719": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  854": "OE1" <-> "OE2"
    Residue "A PHE  920": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP 1164": "OD1" <-> "OD2"
    Residue "A TYR 1331": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/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: 3.40, per 1000 atoms: 0.61
  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  - 3.50
        Amino acid           : False - 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: 1.89
  Conformation dependent library (CDL) restraints added in 975.6 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: 0.78
  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: 1.74

  Time building geometry restraints manager: 2.10 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:
       98.55 -   105.65: 128
      105.65 -   112.74: 3227
      112.74 -   119.84: 1819
      119.84 -   126.93: 2490
      126.93 -   134.03: 63
  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 2.440
  nonbonded pdb=" OG1 THR A 858 "
            pdb=" OE1 GLU A 860 "
     model   vdw
     2.147 2.440
  nonbonded pdb=" OG  SER A1398 "
            pdb=" OE1 GLN A1399 "
     model   vdw
     2.219 2.440
  nonbonded pdb=" OE2 GLU A1173 "
            pdb=" OG1 THR A1226 "
     model   vdw
     2.228 2.440
  nonbonded pdb=" NH2 ARG A1155 "
            pdb=" O   LEU A1159 "
     model   vdw
     2.281 2.520
  ... (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:             0.580
  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:          3.050
  Check model and map are aligned:         0.080
  Set scattering table:                    0.060
  Process input model:                     18.870
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  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:2.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.330
-------------------------------------------------------------------------------
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= 0.162
  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 (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: -0.92 (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
 TRP   0.008   0.001   TRP A1153 
 HIS   0.004   0.001   HIS A1069 
 PHE   0.010   0.001   PHE A 970 
 TYR   0.010   0.001   TYR A 713 
 ARG   0.007   0.001   ARG A1041 

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.575 
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: 0.1496
  time to fit residues: 23.3902
Evaluate side-chains
  104 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    0.0980
   chunk 56 optimal weight:    0.5980
   chunk 31 optimal weight:    0.2980
   chunk 19 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    7.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.1279

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= 0.166
  Angle     :  0.589   9.154   7727  Z= 0.297
  Chirality :  0.044   0.147    950
  Planarity :  0.004   0.043    965
  Dihedral  :  4.090  17.717    775
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 12.56 %
    Favored  : 86.46 %
  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: -0.46 (0.33), residues: 737
  helix:  0.26 (0.29), residues: 356
  sheet: -0.78 (0.58), residues: 86
  loop : -0.69 (0.39), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 939 
 HIS   0.003   0.001   HIS A 643 
 PHE   0.011   0.001   PHE A 970 
 TYR   0.012   0.001   TYR A 713 
 ARG   0.004   0.000   ARG A1151 

*********************** 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
  125 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 119
  time to evaluate  : 0.656 
Fit side-chains
REVERT: A  929 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7561 (mp)
REVERT: A  945 ILE cc_start: 0.8232 (mm) cc_final: 0.7668 (pt)
REVERT: A 1242 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6791 (mp0)
  outliers start: 6
  outliers final: 3
  residues processed: 123
  average time/residue: 0.1498
  time to fit residues: 24.8774
Evaluate side-chains
  107 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0870
   chunk 55 optimal weight:    0.9990
   chunk 45 optimal weight:    9.9990
   chunk 18 optimal weight:    0.6980
   chunk 67 optimal weight:    0.8980
   chunk 72 optimal weight:    0.7980
   chunk 59 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A1177 GLN
** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5689  Z= 0.167
  Angle     :  0.580  10.349   7727  Z= 0.289
  Chirality :  0.044   0.131    950
  Planarity :  0.004   0.049    965
  Dihedral  :  4.034  17.760    775
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.99 %
    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 (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: -0.35 (0.32), residues: 737
  helix:  0.44 (0.29), residues: 359
  sheet: -0.76 (0.54), residues: 96
  loop : -0.77 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1153 
 HIS   0.003   0.001   HIS A 643 
 PHE   0.012   0.001   PHE A 970 
 TYR   0.011   0.001   TYR A 713 
 ARG   0.006   0.001   ARG A1155 

*********************** 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
  125 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.633 
Fit side-chains
REVERT: A  929 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7538 (mp)
REVERT: A  940 ILE cc_start: 0.7526 (tt) cc_final: 0.7209 (tt)
REVERT: A 1154 LEU cc_start: 0.9307 (tp) cc_final: 0.8951 (tp)
REVERT: A 1155 ARG cc_start: 0.8862 (mmm160) cc_final: 0.8320 (mmp-170)
REVERT: A 1164 ASP cc_start: 0.9310 (t0) cc_final: 0.8897 (p0)
  outliers start: 16
  outliers final: 10
  residues processed: 116
  average time/residue: 0.1363
  time to fit residues: 21.6626
Evaluate side-chains
  114 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
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  804 THR
Chi-restraints excluded: chain A residue  929 ILE
Chi-restraints excluded: chain A residue  937 VAL
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 1299 LEU
Chi-restraints excluded: chain A residue 1303 ASP
Chi-restraints excluded: chain A residue 1326 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 34 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 67 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.1848

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= 0.183
  Angle     :  0.587   8.262   7727  Z= 0.289
  Chirality :  0.044   0.147    950
  Planarity :  0.004   0.046    965
  Dihedral  :  4.056  18.089    775
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 19.09 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.33), residues: 737
  helix:  0.50 (0.29), residues: 360
  sheet: -0.87 (0.53), residues: 96
  loop : -0.85 (0.40), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1153 
 HIS   0.003   0.001   HIS A 643 
 PHE   0.012   0.001   PHE A 970 
 TYR   0.010   0.001   TYR A 713 
 ARG   0.005   0.000   ARG A1041 

*********************** 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
  127 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.628 
Fit side-chains
REVERT: A  929 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7607 (mp)
REVERT: A  940 ILE cc_start: 0.7512 (tt) cc_final: 0.7211 (tt)
REVERT: A 1164 ASP cc_start: 0.9346 (t0) cc_final: 0.8915 (p0)
REVERT: A 1191 MET cc_start: 0.8834 (mmm) cc_final: 0.8621 (mmm)
  outliers start: 19
  outliers final: 11
  residues processed: 120
  average time/residue: 0.1424
  time to fit residues: 23.3971
Evaluate side-chains
  114 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
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  804 THR
Chi-restraints excluded: chain A residue  929 ILE
Chi-restraints excluded: chain A residue  937 VAL
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 1 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 49 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0770
   overall best weight:    0.6340

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

Flipped N/Q/H residues before XYZ refinement:
** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.2026

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= 0.172
  Angle     :  0.592  12.861   7727  Z= 0.290
  Chirality :  0.044   0.167    950
  Planarity :  0.004   0.049    965
  Dihedral  :  4.052  18.000    775
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 20.39 %
    Favored  : 76.84 %
  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: -0.34 (0.32), residues: 737
  helix:  0.59 (0.29), residues: 360
  sheet: -1.01 (0.52), residues: 96
  loop : -0.87 (0.40), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1153 
 HIS   0.009   0.001   HIS A1312 
 PHE   0.012   0.001   PHE A 970 
 TYR   0.015   0.001   TYR A 713 
 ARG   0.005   0.000   ARG A1316 

*********************** 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
  127 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.631 
Fit side-chains
REVERT: A  929 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7629 (mp)
REVERT: A  940 ILE cc_start: 0.7472 (tt) cc_final: 0.7181 (tt)
REVERT: A 1164 ASP cc_start: 0.9334 (t0) cc_final: 0.8921 (p0)
REVERT: A 1359 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6694 (ttp)
  outliers start: 17
  outliers final: 12
  residues processed: 119
  average time/residue: 0.1393
  time to fit residues: 23.1436
Evaluate side-chains
  119 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
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  792 LEU
Chi-restraints excluded: chain A residue  804 THR
Chi-restraints excluded: chain A residue  929 ILE
Chi-restraints excluded: chain A residue  937 VAL
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 1359 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 71 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    0.2980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A1177 GLN
A1247 HIS
** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5689  Z= 0.180
  Angle     :  0.580   6.950   7727  Z= 0.288
  Chirality :  0.044   0.146    950
  Planarity :  0.004   0.048    965
  Dihedral  :  4.043  18.085    775
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 21.70 %
    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 (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: -0.23 (0.33), residues: 737
  helix:  0.68 (0.29), residues: 358
  sheet: -0.97 (0.52), residues: 96
  loop : -0.81 (0.40), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A1153 
 HIS   0.008   0.001   HIS A1312 
 PHE   0.012   0.001   PHE A 970 
 TYR   0.013   0.001   TYR A 713 
 ARG   0.006   0.000   ARG A1041 

*********************** 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
  127 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.797 
Fit side-chains
REVERT: A  929 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7605 (mp)
REVERT: A  940 ILE cc_start: 0.7463 (tt) cc_final: 0.7181 (tt)
REVERT: A 1021 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8193 (mp)
REVERT: A 1040 MET cc_start: 0.5152 (mpp) cc_final: 0.4945 (pmm)
REVERT: A 1164 ASP cc_start: 0.9282 (t0) cc_final: 0.8854 (p0)
REVERT: A 1359 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6703 (ttp)
  outliers start: 19
  outliers final: 15
  residues processed: 118
  average time/residue: 0.1517
  time to fit residues: 24.5985
Evaluate side-chains
  124 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
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  792 LEU
Chi-restraints excluded: chain A residue  804 THR
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 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 1330 ILE
Chi-restraints excluded: chain A residue 1359 MET
Chi-restraints excluded: chain A residue 1380 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 71 optimal weight:    0.0670
   chunk 44 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 28 optimal weight:    0.2980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A1177 GLN
** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5689  Z= 0.168
  Angle     :  0.588   7.268   7727  Z= 0.290
  Chirality :  0.044   0.140    950
  Planarity :  0.004   0.048    965
  Dihedral  :  4.014  17.803    775
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 22.19 %
    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 (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: -0.11 (0.33), residues: 737
  helix:  0.73 (0.29), residues: 360
  sheet: -0.67 (0.54), residues: 86
  loop : -0.78 (0.39), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1153 
 HIS   0.008   0.001   HIS A1312 
 PHE   0.012   0.001   PHE A 970 
 TYR   0.012   0.001   TYR A 713 
 ARG   0.005   0.000   ARG A1316 

*********************** 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
  125 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.574 
Fit side-chains
REVERT: A  929 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7601 (mp)
REVERT: A  931 MET cc_start: 0.7446 (tmm) cc_final: 0.7236 (tmm)
REVERT: A  940 ILE cc_start: 0.7431 (tt) cc_final: 0.7163 (tt)
REVERT: A 1021 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8191 (mp)
REVERT: A 1164 ASP cc_start: 0.9299 (t0) cc_final: 0.8894 (p0)
REVERT: A 1191 MET cc_start: 0.8580 (mmm) cc_final: 0.8050 (mmm)
REVERT: A 1359 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6681 (ttp)
  outliers start: 17
  outliers final: 13
  residues processed: 117
  average time/residue: 0.1455
  time to fit residues: 23.3570
Evaluate side-chains
  121 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
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  804 THR
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 1359 MET
Chi-restraints excluded: chain A residue 1380 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0000
   chunk 6 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
A1177 GLN
** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5689  Z= 0.188
  Angle     :  0.605   8.587   7727  Z= 0.297
  Chirality :  0.044   0.141    950
  Planarity :  0.004   0.048    965
  Dihedral  :  4.048  18.178    775
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 22.02 %
    Favored  : 74.88 %
  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: -0.21 (0.33), residues: 737
  helix:  0.64 (0.29), residues: 367
  sheet: -0.70 (0.53), residues: 86
  loop : -0.88 (0.40), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1153 
 HIS   0.008   0.001   HIS A1312 
 PHE   0.012   0.001   PHE A 970 
 TYR   0.012   0.001   TYR A 713 
 ARG   0.005   0.001   ARG A1041 

*********************** 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
  123 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
REVERT: A  929 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7636 (mp)
REVERT: A  940 ILE cc_start: 0.7446 (tt) cc_final: 0.7179 (tt)
REVERT: A 1021 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8085 (mp)
REVERT: A 1164 ASP cc_start: 0.9293 (t0) cc_final: 0.8894 (p0)
REVERT: A 1359 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6689 (ttp)
  outliers start: 19
  outliers final: 13
  residues processed: 114
  average time/residue: 0.1365
  time to fit residues: 21.6356
Evaluate side-chains
  119 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
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  804 THR
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 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 1330 ILE
Chi-restraints excluded: chain A residue 1359 MET
Chi-restraints excluded: chain A residue 1380 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    0.0050
   chunk 66 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 20 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0770
   overall best weight:    0.5552

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

Flipped N/Q/H residues before XYZ refinement:
A 889 HIS
A1177 GLN
** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5689  Z= 0.168
  Angle     :  0.601   8.403   7727  Z= 0.294
  Chirality :  0.044   0.137    950
  Planarity :  0.004   0.048    965
  Dihedral  :  3.956  17.558    775
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.65 %
    Favored  : 73.90 %
  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: -0.17 (0.32), residues: 737
  helix:  0.71 (0.29), residues: 368
  sheet: -0.70 (0.53), residues: 86
  loop : -0.90 (0.40), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1153 
 HIS   0.008   0.001   HIS A1312 
 PHE   0.011   0.001   PHE A 970 
 TYR   0.012   0.001   TYR A 713 
 ARG   0.006   0.001   ARG A1155 

*********************** 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
  122 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
REVERT: A  929 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7662 (mp)
REVERT: A  940 ILE cc_start: 0.7416 (tt) cc_final: 0.7165 (tt)
REVERT: A 1021 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8120 (mp)
REVERT: A 1040 MET cc_start: 0.5885 (mtm) cc_final: 0.5476 (pmm)
REVERT: A 1164 ASP cc_start: 0.9283 (t0) cc_final: 0.8869 (p0)
REVERT: A 1177 GLN cc_start: 0.8185 (mt0) cc_final: 0.7868 (pt0)
REVERT: A 1191 MET cc_start: 0.8581 (mmm) cc_final: 0.8207 (mmm)
REVERT: A 1359 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6640 (ttp)
  outliers start: 15
  outliers final: 12
  residues processed: 115
  average time/residue: 0.1391
  time to fit residues: 22.2765
Evaluate side-chains
  121 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
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  804 THR
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 1359 MET
Chi-restraints excluded: chain A residue 1380 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 33 optimal weight:    0.3980
   chunk 48 optimal weight:    5.9990
   chunk 73 optimal weight:    0.1980
   chunk 67 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 45 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.2475

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= 0.183
  Angle     :  0.612   8.279   7727  Z= 0.300
  Chirality :  0.044   0.155    950
  Planarity :  0.004   0.048    965
  Dihedral  :  4.009  18.440    775
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 24.31 %
    Favored  : 72.92 %
  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: -0.16 (0.33), residues: 737
  helix:  0.70 (0.29), residues: 368
  sheet: -0.68 (0.53), residues: 86
  loop : -0.88 (0.40), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1153 
 HIS   0.008   0.001   HIS A1312 
 PHE   0.012   0.001   PHE A 970 
 TYR   0.012   0.001   TYR A 713 
 ARG   0.005   0.001   ARG A1155 

********************** 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
  121 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
REVERT: A  929 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7706 (mp)
REVERT: A  940 ILE cc_start: 0.7460 (tt) cc_final: 0.7203 (tt)
REVERT: A 1040 MET cc_start: 0.5918 (mtm) cc_final: 0.5466 (pmm)
REVERT: A 1090 TYR cc_start: 0.8029 (t80) cc_final: 0.7802 (t80)
REVERT: A 1177 GLN cc_start: 0.8153 (mt0) cc_final: 0.7740 (pt0)
REVERT: A 1191 MET cc_start: 0.8643 (mmm) cc_final: 0.8286 (mmm)
REVERT: A 1359 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6658 (ttp)
  outliers start: 17
  outliers final: 14
  residues processed: 112
  average time/residue: 0.1385
  time to fit residues: 21.6532
Evaluate side-chains
  119 residues out of total 613 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
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  804 THR
Chi-restraints excluded: chain A residue  929 ILE
Chi-restraints excluded: chain A residue  937 VAL
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 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 1330 ILE
Chi-restraints excluded: chain A residue 1359 MET
Chi-restraints excluded: chain A residue 1380 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 58 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 7 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A1277 GLN ** 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 = 0.4311 r_free = 0.4311 target = 0.154435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.117848 restraints weight = 9687.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3850 rms_B_bonded: 3.42
r_work: 0.3723 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5689  Z= 0.226
  Angle     :  0.634   8.656   7727  Z= 0.312
  Chirality :  0.045   0.142    950
  Planarity :  0.004   0.048    965
  Dihedral  :  4.149  19.749    775
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 24.31 %
    Favored  : 73.08 %
  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: -0.24 (0.33), residues: 737
  helix:  0.61 (0.29), residues: 369
  sheet: -0.75 (0.53), residues: 86
  loop : -0.88 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 712 
 HIS   0.008   0.001   HIS A1312 
 PHE   0.017   0.001   PHE A 970 
 TYR   0.012   0.001   TYR A 713 
 ARG   0.005   0.001   ARG A1041 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1567.10 seconds
wall clock time: 29 minutes 3.61 seconds (1743.61 seconds total)